Starting phenix.real_space_refine on Sat Oct 12 12:22:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v28_42901/10_2024/8v28_42901_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v28_42901/10_2024/8v28_42901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v28_42901/10_2024/8v28_42901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v28_42901/10_2024/8v28_42901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v28_42901/10_2024/8v28_42901_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v28_42901/10_2024/8v28_42901_neut.cif" } resolution = 3.36 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= 0.002 sd= 0.019 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 288 5.49 5 S 15 5.16 5 C 7046 2.51 5 N 2380 2.21 5 O 2930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 12659 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 764 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 7.35, per 1000 atoms: 0.58 Number of scatterers: 12659 At special positions: 0 Unit cell: (100.88, 122.22, 118.34, 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 15 16.00 P 288 15.00 O 2930 8.00 N 2380 7.00 C 7046 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: 2.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 67.0% alpha, 4.3% beta 139 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 5.93 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.829A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.772A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.653A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.171A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.562A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.631A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.518A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.657A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.645A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.564A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.717A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.520A 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 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.176A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.551A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.595A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.545A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.576A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 37 through 41 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A 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: 7.330A 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.738A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.385A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 12 through 16 421 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 4.62 Time building geometry restraints manager: 3.37 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: 2434 1.33 - 1.45: 4277 1.45 - 1.57: 6155 1.57 - 1.69: 576 1.69 - 1.81: 26 Bond restraints: 13468 Sorted by residual: bond pdb=" C1' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.460 1.384 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1' DG J -70 " pdb=" N9 DG J -70 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C1' DA I 72 " pdb=" N9 DA I 72 " ideal model delta sigma weight residual 1.460 1.390 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N TYR B 98 " pdb=" CA TYR B 98 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.21e-02 6.83e+03 5.20e+00 bond pdb=" N ASP H 65 " pdb=" CA ASP H 65 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.20e+00 ... (remaining 13463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19164 2.13 - 4.26: 239 4.26 - 6.39: 17 6.39 - 8.52: 1 8.52 - 10.65: 5 Bond angle restraints: 19426 Sorted by residual: angle pdb=" C3' DG J 71 " pdb=" O3' DG J 71 " pdb=" P DA J 72 " ideal model delta sigma weight residual 120.20 109.55 10.65 1.50e+00 4.44e-01 5.05e+01 angle pdb=" C3' DC J 70 " pdb=" O3' DC J 70 " pdb=" P DG J 71 " ideal model delta sigma weight residual 120.20 109.76 10.44 1.50e+00 4.44e-01 4.84e+01 angle pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sigma weight residual 120.20 110.58 9.62 1.50e+00 4.44e-01 4.12e+01 angle pdb=" CB ARG K 42 " pdb=" CG ARG K 42 " pdb=" CD ARG K 42 " ideal model delta sigma weight residual 111.30 120.88 -9.58 2.30e+00 1.89e-01 1.73e+01 angle pdb=" CA LYS C 118 " pdb=" CB LYS C 118 " pdb=" CG LYS C 118 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 ... (remaining 19421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 6009 35.66 - 71.32: 1362 71.32 - 106.98: 13 106.98 - 142.65: 4 142.65 - 178.31: 1 Dihedral angle restraints: 7389 sinusoidal: 4936 harmonic: 2453 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.31 -178.31 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 91.35 128.65 1 3.50e+01 8.16e-04 1.27e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 95.57 124.43 1 3.50e+01 8.16e-04 1.23e+01 ... (remaining 7386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2164 0.093 - 0.186: 48 0.186 - 0.279: 0 0.279 - 0.373: 0 0.373 - 0.466: 3 Chirality restraints: 2215 Sorted by residual: chirality pdb=" P DC J 70 " pdb=" OP1 DC J 70 " pdb=" OP2 DC J 70 " pdb=" O5' DC J 70 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" P DG J 71 " pdb=" OP1 DG J 71 " pdb=" OP2 DG J 71 " pdb=" O5' DG J 71 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" P DA J 72 " pdb=" OP1 DA J 72 " pdb=" OP2 DA J 72 " pdb=" O5' DA J 72 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 2212 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ASP F 24 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 24 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" CG ASP F 24 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP F 24 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP F 24 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.024 2.00e-02 2.50e+03 1.00e-02 3.01e+00 pdb=" N9 DG I 47 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2842 2.82 - 3.34: 10531 3.34 - 3.86: 22604 3.86 - 4.38: 26544 4.38 - 4.90: 38192 Nonbonded interactions: 100713 Sorted by model distance: nonbonded pdb=" O THR E 58 " pdb=" OG1 THR E 58 " model vdw 2.295 3.040 nonbonded pdb=" O GLN K 2 " pdb=" N GLU K 64 " model vdw 2.347 3.120 nonbonded pdb=" O ARG A 129 " pdb=" NH1 ARG A 129 " model vdw 2.361 3.120 nonbonded pdb=" N ASP F 85 " pdb=" OD1 ASP F 85 " model vdw 2.362 3.120 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.376 3.040 ... (remaining 100708 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' selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 26 through 121) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.110 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:2.520 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 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 : 0.004 0.076 13468 Z= 0.237 Angle : 0.582 10.654 19426 Z= 0.351 Chirality : 0.038 0.466 2215 Planarity : 0.004 0.037 1457 Dihedral : 27.274 178.308 5803 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.56 % Allowed : 19.15 % Favored : 80.28 % 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: 2.83 (0.30), residues: 827 helix: 3.33 (0.22), residues: 530 sheet: 1.37 (1.73), residues: 12 loop : -1.10 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE F 61 TYR 0.017 0.001 TYR H 80 ARG 0.008 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.062 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 114 average time/residue: 0.3694 time to fit residues: 55.0239 Evaluate side-chains 110 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13468 Z= 0.253 Angle : 0.547 7.287 19426 Z= 0.331 Chirality : 0.034 0.133 2215 Planarity : 0.004 0.035 1457 Dihedral : 29.358 178.217 4112 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.55 % Allowed : 19.44 % Favored : 79.01 % 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 (0.30), residues: 827 helix: 3.44 (0.22), residues: 531 sheet: 1.27 (1.31), residues: 20 loop : -1.02 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 106 PHE 0.010 0.001 PHE F 61 TYR 0.015 0.001 TYR B 98 ARG 0.004 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 0.985 Fit side-chains REVERT: A 83 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8354 (mtp180) REVERT: D 73 GLU cc_start: 0.9216 (tp30) cc_final: 0.8906 (tp30) REVERT: E 118 THR cc_start: 0.9538 (m) cc_final: 0.9322 (p) outliers start: 11 outliers final: 5 residues processed: 123 average time/residue: 0.3672 time to fit residues: 59.3225 Evaluate side-chains 113 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 106 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.066 13468 Z= 0.664 Angle : 0.746 7.576 19426 Z= 0.437 Chirality : 0.047 0.201 2215 Planarity : 0.006 0.060 1457 Dihedral : 29.870 179.856 4110 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.24 % Allowed : 20.28 % Favored : 76.48 % 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: 2.10 (0.29), residues: 827 helix: 2.71 (0.22), residues: 535 sheet: 0.82 (1.32), residues: 20 loop : -1.41 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 106 PHE 0.022 0.002 PHE D 67 TYR 0.019 0.002 TYR B 98 ARG 0.008 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.094 Fit side-chains REVERT: A 83 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8359 (mtp180) REVERT: D 73 GLU cc_start: 0.9273 (tp30) cc_final: 0.8912 (tp30) REVERT: E 118 THR cc_start: 0.9571 (m) cc_final: 0.9295 (p) REVERT: H 32 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7855 (mm-30) outliers start: 23 outliers final: 17 residues processed: 129 average time/residue: 0.3562 time to fit residues: 60.8864 Evaluate side-chains 123 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13468 Z= 0.196 Angle : 0.537 5.563 19426 Z= 0.326 Chirality : 0.034 0.128 2215 Planarity : 0.004 0.057 1457 Dihedral : 29.495 178.700 4110 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.69 % Allowed : 22.25 % Favored : 76.06 % 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: 2.90 (0.30), residues: 827 helix: 3.39 (0.22), residues: 532 sheet: 1.46 (1.33), residues: 19 loop : -1.20 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 106 PHE 0.011 0.001 PHE H 67 TYR 0.006 0.001 TYR D 37 ARG 0.006 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.886 Fit side-chains REVERT: A 59 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7935 (pm20) REVERT: A 83 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8720 (mtp85) REVERT: D 73 GLU cc_start: 0.9273 (tp30) cc_final: 0.8964 (tp30) outliers start: 12 outliers final: 7 residues processed: 123 average time/residue: 0.3558 time to fit residues: 57.8737 Evaluate side-chains 118 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 43 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 13468 Z= 0.432 Angle : 0.629 6.698 19426 Z= 0.375 Chirality : 0.039 0.147 2215 Planarity : 0.005 0.052 1457 Dihedral : 29.713 179.531 4110 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.24 % Allowed : 20.56 % Favored : 76.20 % 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: 2.45 (0.30), residues: 827 helix: 3.06 (0.22), residues: 531 sheet: 1.41 (1.35), residues: 19 loop : -1.42 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 106 PHE 0.015 0.002 PHE D 67 TYR 0.020 0.002 TYR H 80 ARG 0.009 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.968 Fit side-chains REVERT: A 59 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8119 (pm20) REVERT: A 83 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8394 (mtp180) REVERT: C 91 GLU cc_start: 0.8272 (tp30) cc_final: 0.7996 (tp30) REVERT: D 32 GLU cc_start: 0.8527 (mp0) cc_final: 0.8206 (mp0) REVERT: D 73 GLU cc_start: 0.9293 (tp30) cc_final: 0.8892 (tp30) REVERT: E 118 THR cc_start: 0.9575 (m) cc_final: 0.9337 (p) REVERT: H 32 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7663 (mm-30) outliers start: 23 outliers final: 16 residues processed: 128 average time/residue: 0.3546 time to fit residues: 60.1632 Evaluate side-chains 127 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 43 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.0370 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13468 Z= 0.184 Angle : 0.554 6.230 19426 Z= 0.335 Chirality : 0.035 0.131 2215 Planarity : 0.004 0.038 1457 Dihedral : 29.577 179.533 4110 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.25 % Allowed : 22.11 % Favored : 75.63 % 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: 2.67 (0.30), residues: 827 helix: 3.24 (0.22), residues: 531 sheet: 1.33 (1.32), residues: 19 loop : -1.35 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.011 0.001 PHE H 67 TYR 0.028 0.001 TYR H 80 ARG 0.009 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.072 Fit side-chains REVERT: A 59 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: A 83 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8274 (mtp180) REVERT: B 91 LYS cc_start: 0.9361 (tptm) cc_final: 0.9060 (tptm) REVERT: C 91 GLU cc_start: 0.8175 (tp30) cc_final: 0.7968 (tp30) REVERT: F 24 ASP cc_start: 0.8501 (p0) cc_final: 0.8281 (p0) REVERT: H 32 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7472 (mm-30) REVERT: H 65 ASP cc_start: 0.9076 (t0) cc_final: 0.8853 (t0) outliers start: 16 outliers final: 11 residues processed: 122 average time/residue: 0.3513 time to fit residues: 57.4452 Evaluate side-chains 123 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN G 104 GLN K 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13468 Z= 0.224 Angle : 0.537 5.502 19426 Z= 0.326 Chirality : 0.034 0.132 2215 Planarity : 0.004 0.044 1457 Dihedral : 29.559 179.206 4110 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.11 % Allowed : 22.39 % Favored : 75.49 % 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: 2.86 (0.30), residues: 827 helix: 3.42 (0.22), residues: 532 sheet: 1.50 (1.35), residues: 19 loop : -1.36 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 106 PHE 0.010 0.001 PHE F 61 TYR 0.020 0.001 TYR H 80 ARG 0.008 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.078 Fit side-chains REVERT: A 59 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: A 83 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8755 (mtp85) REVERT: C 91 GLU cc_start: 0.8215 (tp30) cc_final: 0.7956 (tp30) REVERT: F 24 ASP cc_start: 0.8525 (p0) cc_final: 0.8293 (p0) REVERT: H 32 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: H 65 ASP cc_start: 0.9081 (t0) cc_final: 0.8874 (t0) outliers start: 15 outliers final: 10 residues processed: 119 average time/residue: 0.3615 time to fit residues: 57.4012 Evaluate side-chains 119 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.0070 chunk 62 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13468 Z= 0.161 Angle : 0.523 6.019 19426 Z= 0.318 Chirality : 0.033 0.129 2215 Planarity : 0.004 0.037 1457 Dihedral : 29.529 179.230 4110 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.83 % Allowed : 22.39 % Favored : 75.77 % 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: 2.98 (0.30), residues: 827 helix: 3.49 (0.22), residues: 531 sheet: 1.42 (1.33), residues: 19 loop : -1.22 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 75 PHE 0.010 0.001 PHE H 67 TYR 0.015 0.001 TYR H 80 ARG 0.007 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 0.862 Fit side-chains REVERT: A 59 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: A 83 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8764 (mtp85) REVERT: C 91 GLU cc_start: 0.8177 (tp30) cc_final: 0.7945 (tp30) REVERT: F 24 ASP cc_start: 0.8577 (p0) cc_final: 0.8304 (p0) REVERT: H 65 ASP cc_start: 0.9066 (t0) cc_final: 0.8851 (t0) outliers start: 13 outliers final: 9 residues processed: 120 average time/residue: 0.3362 time to fit residues: 54.0814 Evaluate side-chains 121 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN K 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13468 Z= 0.387 Angle : 0.608 6.538 19426 Z= 0.363 Chirality : 0.038 0.143 2215 Planarity : 0.004 0.040 1457 Dihedral : 29.666 179.363 4110 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.25 % Allowed : 21.97 % Favored : 75.77 % 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: 2.58 (0.30), residues: 827 helix: 3.20 (0.22), residues: 532 sheet: 1.26 (1.32), residues: 19 loop : -1.46 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 106 PHE 0.012 0.002 PHE D 67 TYR 0.025 0.002 TYR H 80 ARG 0.010 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.087 Fit side-chains REVERT: A 59 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8085 (pm20) REVERT: A 83 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8372 (mtp180) REVERT: C 91 GLU cc_start: 0.8273 (tp30) cc_final: 0.8032 (tp30) REVERT: D 32 GLU cc_start: 0.8438 (mp0) cc_final: 0.8128 (mp0) REVERT: E 118 THR cc_start: 0.9575 (m) cc_final: 0.9331 (p) outliers start: 16 outliers final: 14 residues processed: 125 average time/residue: 0.3463 time to fit residues: 57.5665 Evaluate side-chains 125 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 0.0570 chunk 107 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 8 optimal weight: 0.0870 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.6276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13468 Z= 0.168 Angle : 0.525 6.035 19426 Z= 0.318 Chirality : 0.032 0.132 2215 Planarity : 0.004 0.047 1457 Dihedral : 29.419 178.685 4110 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.83 % Allowed : 22.54 % Favored : 75.63 % 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: 3.08 (0.30), residues: 827 helix: 3.59 (0.22), residues: 531 sheet: 1.45 (1.34), residues: 19 loop : -1.26 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 31 PHE 0.009 0.001 PHE H 67 TYR 0.011 0.001 TYR H 80 ARG 0.008 0.000 ARG D 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 0.907 Fit side-chains REVERT: A 59 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7843 (pm20) REVERT: A 83 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8775 (mtp85) REVERT: B 23 ARG cc_start: 0.7988 (mmm160) cc_final: 0.7736 (mmm160) REVERT: C 91 GLU cc_start: 0.8106 (tp30) cc_final: 0.7896 (tp30) REVERT: H 65 ASP cc_start: 0.9072 (t0) cc_final: 0.8859 (t0) outliers start: 13 outliers final: 10 residues processed: 121 average time/residue: 0.3396 time to fit residues: 54.4685 Evaluate side-chains 120 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 42 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 6.9990 chunk 26 optimal weight: 0.0870 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.062762 restraints weight = 29546.022| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.13 r_work: 0.2702 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13468 Z= 0.173 Angle : 0.519 6.333 19426 Z= 0.314 Chirality : 0.032 0.129 2215 Planarity : 0.004 0.045 1457 Dihedral : 29.467 178.938 4110 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.13 % Allowed : 23.66 % Favored : 75.21 % 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: 3.16 (0.30), residues: 827 helix: 3.66 (0.22), residues: 531 sheet: 1.47 (1.34), residues: 19 loop : -1.22 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 39 PHE 0.010 0.001 PHE H 67 TYR 0.013 0.001 TYR H 80 ARG 0.008 0.000 ARG D 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2220.95 seconds wall clock time: 41 minutes 19.26 seconds (2479.26 seconds total)