Starting phenix.real_space_refine on Wed Feb 4 17:30:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y46_72472/02_2026/9y46_72472.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y46_72472/02_2026/9y46_72472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y46_72472/02_2026/9y46_72472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y46_72472/02_2026/9y46_72472.map" model { file = "/net/cci-nas-00/data/ceres_data/9y46_72472/02_2026/9y46_72472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y46_72472/02_2026/9y46_72472.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 290 5.49 5 S 12 5.16 5 C 6654 2.51 5 N 2267 2.21 5 O 2810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12033 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Time building chain proxies: 2.27, per 1000 atoms: 0.19 Number of scatterers: 12033 At special positions: 0 Unit cell: (113.75, 119.21, 118.3, 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 12 16.00 P 290 15.00 O 2810 8.00 N 2267 7.00 C 6654 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: 0.95 Conformation dependent library (CDL) restraints added in 330.4 milliseconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 71.2% alpha, 3.1% beta 144 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.551A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.576A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.737A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.522A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.618A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.523A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.538A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.551A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.584A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.781A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.572A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.508A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.654A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.588A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.543A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.522A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.547A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.575A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.512A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.666A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.740A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.908A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.224A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.768A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.040A 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: 7.229A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 376 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.22 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: 1946 1.33 - 1.45: 4386 1.45 - 1.57: 5905 1.57 - 1.69: 578 1.69 - 1.81: 22 Bond restraints: 12837 Sorted by residual: bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" N ARG B 45 " pdb=" CA ARG B 45 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.24e-02 6.50e+03 7.97e-01 bond pdb=" CA ILE C 79 " pdb=" CB ILE C 79 " ideal model delta sigma weight residual 1.537 1.548 -0.011 1.29e-02 6.01e+03 7.52e-01 bond pdb=" O4' DC J 19 " pdb=" C1' DC J 19 " ideal model delta sigma weight residual 1.414 1.397 0.017 2.00e-02 2.50e+03 6.82e-01 bond pdb=" O4' DA J -22 " pdb=" C1' DA J -22 " ideal model delta sigma weight residual 1.414 1.398 0.016 2.00e-02 2.50e+03 6.55e-01 ... (remaining 12832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 17756 1.42 - 2.84: 774 2.84 - 4.26: 31 4.26 - 5.67: 11 5.67 - 7.09: 2 Bond angle restraints: 18574 Sorted by residual: angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 110.77 117.86 -7.09 1.93e+00 2.68e-01 1.35e+01 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 110.77 117.80 -7.03 1.93e+00 2.68e-01 1.33e+01 angle pdb=" CB GLU A 59 " pdb=" CG GLU A 59 " pdb=" CD GLU A 59 " ideal model delta sigma weight residual 112.60 117.43 -4.83 1.70e+00 3.46e-01 8.07e+00 angle pdb=" N LYS E 56 " pdb=" CA LYS E 56 " pdb=" C LYS E 56 " ideal model delta sigma weight residual 113.97 110.56 3.41 1.28e+00 6.10e-01 7.08e+00 angle pdb=" N GLY F 48 " pdb=" CA GLY F 48 " pdb=" C GLY F 48 " ideal model delta sigma weight residual 114.16 117.10 -2.94 1.21e+00 6.83e-01 5.90e+00 ... (remaining 18569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 5518 35.06 - 70.13: 1457 70.13 - 105.19: 3 105.19 - 140.26: 0 140.26 - 175.32: 1 Dihedral angle restraints: 6979 sinusoidal: 4758 harmonic: 2221 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 44.68 175.32 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ASP A 77 " pdb=" CB ASP A 77 " pdb=" CG ASP A 77 " pdb=" OD1 ASP A 77 " ideal model delta sinusoidal sigma weight residual -30.00 -89.15 59.15 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 6976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1210 0.027 - 0.055: 590 0.055 - 0.082: 227 0.082 - 0.110: 59 0.110 - 0.137: 26 Chirality restraints: 2112 Sorted by residual: chirality pdb=" C4' DG I -35 " pdb=" C5' DG I -35 " pdb=" O4' DG I -35 " pdb=" C3' DG I -35 " both_signs ideal model delta sigma weight residual False -2.53 -2.39 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE C 78 " pdb=" N ILE C 78 " pdb=" C ILE C 78 " pdb=" CB ILE C 78 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE G 78 " pdb=" N ILE G 78 " pdb=" C ILE G 78 " pdb=" CB ILE G 78 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 2109 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " -0.026 2.00e-02 2.50e+03 1.15e-02 3.64e+00 pdb=" N9 DA I 47 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " -0.025 2.00e-02 2.50e+03 1.05e-02 3.33e+00 pdb=" N9 DG I -35 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 17 " 0.023 2.00e-02 2.50e+03 1.05e-02 3.00e+00 pdb=" N9 DA I 17 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 17 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 17 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 17 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 17 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 17 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 17 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 17 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 17 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 17 " -0.002 2.00e-02 2.50e+03 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 5231 3.01 - 3.48: 9641 3.48 - 3.96: 22748 3.96 - 4.43: 26042 4.43 - 4.90: 34044 Nonbonded interactions: 97706 Sorted by model distance: nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.539 3.120 nonbonded pdb=" N GLU E 59 " pdb=" OE1 GLU E 59 " model vdw 2.567 3.120 nonbonded pdb=" N1 DG I -36 " pdb=" C4 DG I -36 " model vdw 2.591 2.672 nonbonded pdb=" N1 DG J -55 " pdb=" C4 DG J -55 " model vdw 2.591 2.672 nonbonded pdb=" N1 DG I -5 " pdb=" C4 DG I -5 " model vdw 2.593 2.672 ... (remaining 97701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 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 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.330 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 0.038 12837 Z= 0.205 Angle : 0.633 7.094 18574 Z= 0.394 Chirality : 0.039 0.137 2112 Planarity : 0.005 0.042 1345 Dihedral : 27.646 175.319 5547 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.25 % Allowed : 16.30 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.25), residues: 751 helix: -0.16 (0.19), residues: 524 sheet: None (None), residues: 0 loop : -1.58 (0.33), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 42 TYR 0.014 0.002 TYR G 57 PHE 0.019 0.002 PHE G 25 HIS 0.009 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00445 (12837) covalent geometry : angle 0.63294 (18574) hydrogen bonds : bond 0.22803 ( 744) hydrogen bonds : angle 4.35737 ( 1840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.206 Fit side-chains REVERT: A 133 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8030 (mt-10) REVERT: B 77 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8347 (mtpt) REVERT: C 13 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6538 (tmtm) REVERT: C 41 GLU cc_start: 0.8475 (tt0) cc_final: 0.7685 (mp0) REVERT: D 43 LYS cc_start: 0.8647 (mttt) cc_final: 0.8424 (mttp) REVERT: D 47 GLN cc_start: 0.8522 (mt0) cc_final: 0.8252 (mt0) REVERT: D 62 MET cc_start: 0.9245 (mmm) cc_final: 0.9015 (mmm) REVERT: D 82 HIS cc_start: 0.8258 (m170) cc_final: 0.7704 (t-90) REVERT: D 86 ARG cc_start: 0.8688 (mmt90) cc_final: 0.8426 (mmt90) REVERT: D 108 LYS cc_start: 0.8754 (mttm) cc_final: 0.8553 (mtpt) REVERT: F 52 GLU cc_start: 0.8503 (tp30) cc_final: 0.8217 (tp30) REVERT: F 84 MET cc_start: 0.8778 (tpt) cc_final: 0.8575 (mmt) REVERT: G 41 GLU cc_start: 0.8456 (tt0) cc_final: 0.7652 (mp0) REVERT: H 47 GLN cc_start: 0.8541 (mt0) cc_final: 0.8285 (mt0) REVERT: H 82 HIS cc_start: 0.8194 (m170) cc_final: 0.7661 (t-90) REVERT: H 86 ARG cc_start: 0.8653 (mmt90) cc_final: 0.8338 (mmt90) REVERT: H 108 LYS cc_start: 0.8717 (mttm) cc_final: 0.8506 (mttp) REVERT: H 116 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8840 (ttpp) outliers start: 8 outliers final: 2 residues processed: 143 average time/residue: 0.9400 time to fit residues: 140.4737 Evaluate side-chains 125 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116168 restraints weight = 11731.616| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 0.83 r_work: 0.3183 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12837 Z= 0.169 Angle : 0.555 5.024 18574 Z= 0.345 Chirality : 0.034 0.131 2112 Planarity : 0.004 0.039 1345 Dihedral : 29.390 169.593 4033 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.78 % Allowed : 15.05 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.30), residues: 751 helix: 2.24 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 42 TYR 0.009 0.001 TYR D 37 PHE 0.012 0.002 PHE G 25 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00336 (12837) covalent geometry : angle 0.55529 (18574) hydrogen bonds : bond 0.06459 ( 744) hydrogen bonds : angle 2.58143 ( 1840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.227 Fit side-chains REVERT: A 133 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7912 (mt-10) REVERT: C 41 GLU cc_start: 0.8219 (tt0) cc_final: 0.7643 (mp0) REVERT: C 95 LYS cc_start: 0.8860 (tttt) cc_final: 0.8472 (ttpt) REVERT: D 47 GLN cc_start: 0.8403 (mt0) cc_final: 0.8150 (mt0) REVERT: D 62 MET cc_start: 0.9033 (mmm) cc_final: 0.8754 (mmm) REVERT: D 71 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: E 133 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7812 (mt-10) REVERT: G 13 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6408 (tmtm) REVERT: G 41 GLU cc_start: 0.8202 (tt0) cc_final: 0.7701 (mp0) REVERT: H 47 GLN cc_start: 0.8397 (mt0) cc_final: 0.8157 (mt0) REVERT: H 71 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: H 86 ARG cc_start: 0.8541 (mmt90) cc_final: 0.8332 (mmt90) outliers start: 5 outliers final: 1 residues processed: 134 average time/residue: 0.8899 time to fit residues: 125.3095 Evaluate side-chains 124 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108054 restraints weight = 11677.756| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 0.81 r_work: 0.3066 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12837 Z= 0.287 Angle : 0.722 5.088 18574 Z= 0.432 Chirality : 0.045 0.147 2112 Planarity : 0.006 0.054 1345 Dihedral : 29.652 172.328 4023 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.45 % Allowed : 13.17 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.30), residues: 751 helix: 2.10 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.64 (0.33), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 39 TYR 0.014 0.002 TYR A 54 PHE 0.018 0.003 PHE G 25 HIS 0.012 0.002 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00617 (12837) covalent geometry : angle 0.72238 (18574) hydrogen bonds : bond 0.10150 ( 744) hydrogen bonds : angle 3.00021 ( 1840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.223 Fit side-chains REVERT: A 115 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8282 (mtpt) REVERT: C 13 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6808 (tmtm) REVERT: C 20 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8329 (ptp90) REVERT: C 41 GLU cc_start: 0.8339 (tt0) cc_final: 0.7792 (mp0) REVERT: D 47 GLN cc_start: 0.8505 (mt0) cc_final: 0.8269 (mt0) REVERT: D 62 MET cc_start: 0.9153 (mmm) cc_final: 0.8871 (mmm) REVERT: D 71 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: F 19 ARG cc_start: 0.1871 (OUTLIER) cc_final: 0.1295 (mmp-170) REVERT: G 13 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6479 (tmtm) REVERT: G 41 GLU cc_start: 0.8331 (tt0) cc_final: 0.7765 (mp0) REVERT: H 47 GLN cc_start: 0.8488 (mt0) cc_final: 0.8252 (mt0) REVERT: H 71 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: H 85 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8496 (mmtm) outliers start: 22 outliers final: 10 residues processed: 132 average time/residue: 0.8588 time to fit residues: 119.2079 Evaluate side-chains 130 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.131153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111150 restraints weight = 11647.726| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 0.81 r_work: 0.3111 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12837 Z= 0.195 Angle : 0.614 4.938 18574 Z= 0.380 Chirality : 0.038 0.132 2112 Planarity : 0.005 0.038 1345 Dihedral : 29.568 173.431 4023 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.19 % Allowed : 14.42 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.30), residues: 751 helix: 2.34 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.72 (0.34), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.010 0.001 TYR D 37 PHE 0.009 0.002 PHE F 61 HIS 0.007 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00386 (12837) covalent geometry : angle 0.61417 (18574) hydrogen bonds : bond 0.07934 ( 744) hydrogen bonds : angle 3.00732 ( 1840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.337 Fit side-chains REVERT: A 115 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7937 (mtpt) REVERT: C 13 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6784 (tmtm) REVERT: C 41 GLU cc_start: 0.8312 (tt0) cc_final: 0.7718 (mp0) REVERT: D 47 GLN cc_start: 0.8454 (mt0) cc_final: 0.8212 (mt0) REVERT: D 62 MET cc_start: 0.9073 (mmm) cc_final: 0.8828 (mmm) REVERT: D 71 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: D 85 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8423 (mmtm) REVERT: F 19 ARG cc_start: 0.1888 (OUTLIER) cc_final: 0.1326 (mmp-170) REVERT: G 13 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6441 (tmtm) REVERT: G 41 GLU cc_start: 0.8285 (tt0) cc_final: 0.7753 (mp0) REVERT: H 47 GLN cc_start: 0.8440 (mt0) cc_final: 0.8191 (mt0) REVERT: H 71 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: H 85 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8409 (mmtm) outliers start: 14 outliers final: 5 residues processed: 120 average time/residue: 1.0327 time to fit residues: 129.7854 Evaluate side-chains 124 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 85 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 0.0050 chunk 53 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109155 restraints weight = 11642.986| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 0.81 r_work: 0.3079 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12837 Z= 0.245 Angle : 0.668 4.994 18574 Z= 0.404 Chirality : 0.042 0.135 2112 Planarity : 0.005 0.047 1345 Dihedral : 29.595 172.719 4023 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.29 % Allowed : 12.54 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.30), residues: 751 helix: 2.29 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.63 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 77 TYR 0.014 0.002 TYR A 54 PHE 0.009 0.002 PHE G 25 HIS 0.009 0.002 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00518 (12837) covalent geometry : angle 0.66770 (18574) hydrogen bonds : bond 0.09047 ( 744) hydrogen bonds : angle 2.93401 ( 1840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.288 Fit side-chains REVERT: B 91 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8248 (ttpm) REVERT: C 20 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8379 (ptp90) REVERT: C 41 GLU cc_start: 0.8341 (tt0) cc_final: 0.7780 (mp0) REVERT: C 64 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: D 47 GLN cc_start: 0.8447 (mt0) cc_final: 0.8200 (mt0) REVERT: D 62 MET cc_start: 0.9105 (mmm) cc_final: 0.8847 (mmm) REVERT: D 71 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: D 85 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8413 (mmtm) REVERT: F 19 ARG cc_start: 0.1939 (OUTLIER) cc_final: 0.1338 (mmp-170) REVERT: G 13 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6401 (tmtm) REVERT: G 41 GLU cc_start: 0.8301 (tt0) cc_final: 0.7739 (mp0) REVERT: G 64 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: H 47 GLN cc_start: 0.8448 (mt0) cc_final: 0.8199 (mt0) REVERT: H 71 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7728 (mt-10) outliers start: 21 outliers final: 5 residues processed: 126 average time/residue: 0.9264 time to fit residues: 122.2145 Evaluate side-chains 126 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108637 restraints weight = 11667.892| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 0.81 r_work: 0.3072 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12837 Z= 0.264 Angle : 0.695 4.948 18574 Z= 0.418 Chirality : 0.043 0.135 2112 Planarity : 0.005 0.048 1345 Dihedral : 29.684 173.244 4023 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.29 % Allowed : 12.54 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.30), residues: 751 helix: 2.10 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 77 TYR 0.014 0.002 TYR A 54 PHE 0.011 0.002 PHE F 61 HIS 0.009 0.002 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00563 (12837) covalent geometry : angle 0.69514 (18574) hydrogen bonds : bond 0.09503 ( 744) hydrogen bonds : angle 2.96424 ( 1840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.337 Fit side-chains REVERT: B 91 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8255 (ttpm) REVERT: C 20 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8387 (ptp90) REVERT: C 41 GLU cc_start: 0.8347 (tt0) cc_final: 0.7788 (mp0) REVERT: C 64 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: D 47 GLN cc_start: 0.8436 (mt0) cc_final: 0.8194 (mt0) REVERT: D 62 MET cc_start: 0.9119 (mmm) cc_final: 0.8868 (mmm) REVERT: D 71 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: D 85 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8425 (mmtm) REVERT: E 133 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7803 (mt-10) REVERT: F 19 ARG cc_start: 0.2063 (OUTLIER) cc_final: 0.1314 (mmp-170) REVERT: G 13 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6330 (tmtm) REVERT: G 41 GLU cc_start: 0.8321 (tt0) cc_final: 0.7755 (mp0) REVERT: G 64 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: H 47 GLN cc_start: 0.8451 (mt0) cc_final: 0.8179 (mt0) REVERT: H 71 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: H 85 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8425 (mmtm) outliers start: 21 outliers final: 6 residues processed: 125 average time/residue: 0.8902 time to fit residues: 116.5602 Evaluate side-chains 128 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110536 restraints weight = 11635.520| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 0.81 r_work: 0.3101 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12837 Z= 0.187 Angle : 0.622 4.753 18574 Z= 0.384 Chirality : 0.038 0.131 2112 Planarity : 0.005 0.038 1345 Dihedral : 29.652 173.970 4023 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.45 % Allowed : 13.17 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.30), residues: 751 helix: 2.21 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.74 (0.35), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 39 TYR 0.009 0.001 TYR A 54 PHE 0.010 0.002 PHE F 61 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00364 (12837) covalent geometry : angle 0.62244 (18574) hydrogen bonds : bond 0.08156 ( 744) hydrogen bonds : angle 3.01871 ( 1840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.309 Fit side-chains REVERT: B 91 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8253 (ttpm) REVERT: C 20 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7800 (ptp90) REVERT: C 38 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8212 (m-40) REVERT: C 41 GLU cc_start: 0.8337 (tt0) cc_final: 0.7758 (mp0) REVERT: C 64 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: D 47 GLN cc_start: 0.8404 (mt0) cc_final: 0.8178 (mt0) REVERT: D 62 MET cc_start: 0.9068 (mmm) cc_final: 0.8821 (mmm) REVERT: D 71 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: D 85 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8489 (mmtm) REVERT: E 73 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: E 133 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7796 (mt-10) REVERT: F 19 ARG cc_start: 0.2023 (OUTLIER) cc_final: 0.1311 (mmp-170) REVERT: F 91 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8224 (ttpm) REVERT: G 13 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6270 (tmtm) REVERT: G 41 GLU cc_start: 0.8288 (tt0) cc_final: 0.7731 (mp0) REVERT: G 64 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: H 47 GLN cc_start: 0.8426 (mt0) cc_final: 0.8165 (mt0) REVERT: H 71 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: H 85 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8455 (mmtm) outliers start: 22 outliers final: 5 residues processed: 122 average time/residue: 0.9298 time to fit residues: 118.7922 Evaluate side-chains 131 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 0.0020 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 0.0060 chunk 90 optimal weight: 4.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111019 restraints weight = 11601.060| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 0.81 r_work: 0.3107 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12837 Z= 0.191 Angle : 0.613 4.939 18574 Z= 0.379 Chirality : 0.038 0.128 2112 Planarity : 0.004 0.034 1345 Dihedral : 29.610 173.936 4023 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.13 % Allowed : 13.48 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.30), residues: 751 helix: 2.32 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.71 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 134 TYR 0.009 0.001 TYR A 54 PHE 0.010 0.001 PHE F 61 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00375 (12837) covalent geometry : angle 0.61333 (18574) hydrogen bonds : bond 0.07990 ( 744) hydrogen bonds : angle 2.87135 ( 1840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.197 Fit side-chains REVERT: A 129 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7755 (tmt170) REVERT: B 79 LYS cc_start: 0.8888 (mttt) cc_final: 0.8679 (mppt) REVERT: B 91 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8237 (ttpm) REVERT: C 20 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7992 (ptp90) REVERT: C 38 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8164 (m-40) REVERT: C 41 GLU cc_start: 0.8327 (tt0) cc_final: 0.7732 (mp0) REVERT: C 64 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: D 47 GLN cc_start: 0.8390 (mt0) cc_final: 0.8163 (mt0) REVERT: D 62 MET cc_start: 0.9065 (mmm) cc_final: 0.8827 (mmm) REVERT: D 71 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: D 85 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8422 (mmtm) REVERT: E 73 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: E 133 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7752 (mt-10) REVERT: F 19 ARG cc_start: 0.2028 (OUTLIER) cc_final: 0.1302 (mmp-170) REVERT: G 13 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6260 (tmtm) REVERT: G 41 GLU cc_start: 0.8275 (tt0) cc_final: 0.7747 (mp0) REVERT: G 64 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: H 47 GLN cc_start: 0.8400 (mt0) cc_final: 0.8133 (mt0) REVERT: H 71 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: H 85 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8410 (mmtm) outliers start: 20 outliers final: 5 residues processed: 123 average time/residue: 0.9389 time to fit residues: 120.7528 Evaluate side-chains 131 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.131196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111243 restraints weight = 11603.453| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 0.81 r_work: 0.3113 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12837 Z= 0.202 Angle : 0.613 4.847 18574 Z= 0.376 Chirality : 0.038 0.129 2112 Planarity : 0.005 0.037 1345 Dihedral : 29.544 173.566 4023 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.13 % Allowed : 13.64 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.30), residues: 751 helix: 2.45 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.69 (0.35), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 39 TYR 0.010 0.001 TYR A 54 PHE 0.011 0.002 PHE F 61 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00411 (12837) covalent geometry : angle 0.61293 (18574) hydrogen bonds : bond 0.07812 ( 744) hydrogen bonds : angle 2.76540 ( 1840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.287 Fit side-chains REVERT: A 129 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7740 (tmt170) REVERT: B 79 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8655 (mppt) REVERT: B 91 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8223 (ttpm) REVERT: C 20 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7995 (ptp90) REVERT: C 38 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8199 (m-40) REVERT: C 41 GLU cc_start: 0.8323 (tt0) cc_final: 0.7746 (mp0) REVERT: C 64 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: D 47 GLN cc_start: 0.8389 (mt0) cc_final: 0.8160 (mt0) REVERT: D 62 MET cc_start: 0.9077 (mmm) cc_final: 0.8807 (mmm) REVERT: D 71 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: D 85 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8427 (mmtm) REVERT: E 73 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: E 133 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7791 (mt-10) REVERT: F 19 ARG cc_start: 0.2058 (OUTLIER) cc_final: 0.1358 (mmp-170) REVERT: F 91 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8223 (ttpm) REVERT: G 13 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6232 (tmtm) REVERT: G 41 GLU cc_start: 0.8259 (tt0) cc_final: 0.7712 (mp0) REVERT: G 64 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: H 47 GLN cc_start: 0.8375 (mt0) cc_final: 0.8127 (mt0) REVERT: H 71 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: H 85 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8409 (mmtm) outliers start: 20 outliers final: 4 residues processed: 121 average time/residue: 0.8996 time to fit residues: 113.9607 Evaluate side-chains 131 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107347 restraints weight = 11602.830| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 0.82 r_work: 0.3053 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 12837 Z= 0.319 Angle : 0.755 5.099 18574 Z= 0.449 Chirality : 0.047 0.164 2112 Planarity : 0.006 0.057 1345 Dihedral : 29.762 173.694 4023 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.98 % Allowed : 13.48 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.30), residues: 751 helix: 2.01 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.80 (0.35), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 77 TYR 0.018 0.003 TYR A 54 PHE 0.013 0.003 PHE H 70 HIS 0.011 0.002 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00697 (12837) covalent geometry : angle 0.75480 (18574) hydrogen bonds : bond 0.10569 ( 744) hydrogen bonds : angle 3.04852 ( 1840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.294 Fit side-chains REVERT: A 129 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7797 (tmt170) REVERT: B 91 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8276 (ttpm) REVERT: C 38 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8266 (m-40) REVERT: C 41 GLU cc_start: 0.8369 (tt0) cc_final: 0.7778 (mp0) REVERT: C 64 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: D 47 GLN cc_start: 0.8410 (mt0) cc_final: 0.8170 (mt0) REVERT: D 62 MET cc_start: 0.9161 (mmm) cc_final: 0.8914 (mmm) REVERT: D 71 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: D 85 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8432 (mmtm) REVERT: E 133 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7836 (mt-10) REVERT: F 19 ARG cc_start: 0.2123 (OUTLIER) cc_final: 0.1373 (mmp-170) REVERT: F 91 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8281 (ttpm) REVERT: G 13 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6355 (tmtm) REVERT: G 41 GLU cc_start: 0.8325 (tt0) cc_final: 0.7747 (mp0) REVERT: G 64 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: H 47 GLN cc_start: 0.8397 (mt0) cc_final: 0.8125 (mt0) REVERT: H 71 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7813 (mt-10) REVERT: H 85 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8431 (mmtm) outliers start: 19 outliers final: 5 residues processed: 125 average time/residue: 0.8918 time to fit residues: 116.8420 Evaluate side-chains 132 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.131285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111314 restraints weight = 11585.357| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 0.80 r_work: 0.3113 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12837 Z= 0.189 Angle : 0.612 4.942 18574 Z= 0.379 Chirality : 0.038 0.126 2112 Planarity : 0.004 0.047 1345 Dihedral : 29.644 175.058 4023 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.82 % Allowed : 14.11 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.30), residues: 751 helix: 2.25 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.75 (0.35), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 42 TYR 0.009 0.002 TYR D 37 PHE 0.009 0.001 PHE F 61 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00378 (12837) covalent geometry : angle 0.61247 (18574) hydrogen bonds : bond 0.07846 ( 744) hydrogen bonds : angle 2.92398 ( 1840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3763.82 seconds wall clock time: 64 minutes 30.50 seconds (3870.50 seconds total)