Starting phenix.real_space_refine on Fri Sep 11 22:02:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7i_33666/09_2026/7y7i_33666.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7i_33666/09_2026/7y7i_33666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y7i_33666/09_2026/7y7i_33666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7i_33666/09_2026/7y7i_33666.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y7i_33666/09_2026/7y7i_33666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7i_33666/09_2026/7y7i_33666.map" } resolution = 3.42 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= 0.001 sd= 0.010 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 286 5.49 5 S 14 5.16 5 C 6943 2.51 5 N 2341 2.21 5 O 2861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12445 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 845 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "B" 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: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 811 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2915 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2948 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 281 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "L" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 281 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Time building chain proxies: 2.84, per 1000 atoms: 0.23 Number of scatterers: 12445 At special positions: 0 Unit cell: (117.6, 111.72, 116.62, 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 14 16.00 P 286 15.00 O 2861 8.00 N 2341 7.00 C 6943 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: 0.93 Conformation dependent library (CDL) restraints added in 396.1 milliseconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 67.8% alpha, 3.6% beta 136 base pairs and 228 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 4.057A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 80 Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.684A pdb=" N LEU A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 3.629A pdb=" N LEU A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.901A pdb=" N GLY A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.684A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.058A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.694A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.607A pdb=" N ASN C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.987A pdb=" N LYS C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.707A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.558A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.553A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.691A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.978A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 80 removed outlier: 3.546A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.694A pdb=" N LEU E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 removed outlier: 3.794A pdb=" N LEU E 126 " --> pdb=" O TYR E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.615A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.812A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.504A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 removed outlier: 3.836A pdb=" N ALA G 22 " --> pdb=" O ARG G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.410A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 98 removed outlier: 4.103A pdb=" N LEU G 97 " --> pdb=" O GLU G 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.605A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.793A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'K' and resid 534 through 538 Processing helix chain 'L' and resid 534 through 538 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.594A pdb=" N ARG A 85 " --> 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 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.559A pdb=" N THR B 96 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.636A pdb=" N ARG C 43 " --> 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 78 through 79 removed outlier: 3.560A pdb=" N ILE C 79 " --> pdb=" O GLY D 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.818A pdb=" N ARG E 85 " --> 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 120 through 121 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.584A pdb=" N ARG G 43 " --> 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 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 541 through 543 Processing sheet with id=AB3, first strand: chain 'L' and resid 540 through 542 393 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 702 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 228 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2513 1.33 - 1.45: 4151 1.45 - 1.57: 6002 1.57 - 1.69: 570 1.69 - 1.81: 22 Bond restraints: 13258 Sorted by residual: bond pdb=" C1' DT I 103 " pdb=" N1 DT I 103 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.67e+01 bond pdb=" C3' DC J 242 " pdb=" C2' DC J 242 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.39e+01 bond pdb=" C3' DT I 103 " pdb=" C2' DT I 103 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DA I 134 " pdb=" C2' DA I 134 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DA I 105 " pdb=" C2' DA I 105 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 ... (remaining 13253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 17938 1.58 - 3.15: 1126 3.15 - 4.73: 61 4.73 - 6.30: 8 6.30 - 7.88: 2 Bond angle restraints: 19135 Sorted by residual: angle pdb=" O4' DG J 162 " pdb=" C4' DG J 162 " pdb=" C3' DG J 162 " ideal model delta sigma weight residual 106.00 101.85 4.15 6.00e-01 2.78e+00 4.78e+01 angle pdb=" O4' DG I 66 " pdb=" C4' DG I 66 " pdb=" C3' DG I 66 " ideal model delta sigma weight residual 106.00 102.19 3.81 6.00e-01 2.78e+00 4.03e+01 angle pdb=" O4' DA I 68 " pdb=" C4' DA I 68 " pdb=" C3' DA I 68 " ideal model delta sigma weight residual 106.00 102.28 3.72 6.00e-01 2.78e+00 3.83e+01 angle pdb=" O4' DT I 128 " pdb=" C4' DT I 128 " pdb=" C3' DT I 128 " ideal model delta sigma weight residual 106.00 102.47 3.53 6.00e-01 2.78e+00 3.47e+01 angle pdb=" O4' DA I 6 " pdb=" C4' DA I 6 " pdb=" C3' DA I 6 " ideal model delta sigma weight residual 106.00 102.94 3.06 6.00e-01 2.78e+00 2.60e+01 ... (remaining 19130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.68: 5122 25.68 - 51.37: 1590 51.37 - 77.05: 472 77.05 - 102.73: 26 102.73 - 128.41: 2 Dihedral angle restraints: 7212 sinusoidal: 4834 harmonic: 2378 Sorted by residual: dihedral pdb=" C4' DC J 178 " pdb=" C3' DC J 178 " pdb=" O3' DC J 178 " pdb=" P DT J 179 " ideal model delta sinusoidal sigma weight residual -140.00 -11.59 -128.41 1 3.50e+01 8.16e-04 1.27e+01 dihedral pdb=" C4' DC J 192 " pdb=" C3' DC J 192 " pdb=" O3' DC J 192 " pdb=" P DC J 193 " ideal model delta sinusoidal sigma weight residual -140.00 -13.98 -126.02 1 3.50e+01 8.16e-04 1.24e+01 dihedral pdb=" CA ARG E 80 " pdb=" C ARG E 80 " pdb=" N GLY E 81 " pdb=" CA GLY E 81 " ideal model delta harmonic sigma weight residual 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 7209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1185 0.028 - 0.055: 613 0.055 - 0.083: 243 0.083 - 0.111: 102 0.111 - 0.138: 22 Chirality restraints: 2165 Sorted by residual: chirality pdb=" P DT J 179 " pdb=" OP1 DT J 179 " pdb=" OP2 DT J 179 " pdb=" O5' DT J 179 " both_signs ideal model delta sigma weight residual True 2.34 -2.47 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" P DC J 193 " pdb=" OP1 DC J 193 " pdb=" OP2 DC J 193 " pdb=" O5' DC J 193 " both_signs ideal model delta sigma weight residual True 2.34 -2.47 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE G 112 " pdb=" N ILE G 112 " pdb=" C ILE G 112 " pdb=" CB ILE G 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 2162 not shown) Planarity restraints: 1429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 162 " -0.016 2.00e-02 2.50e+03 1.52e-02 6.92e+00 pdb=" N9 DG J 162 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG J 162 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG J 162 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG J 162 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG J 162 " -0.013 2.00e-02 2.50e+03 pdb=" O6 DG J 162 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DG J 162 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG J 162 " -0.034 2.00e-02 2.50e+03 pdb=" N2 DG J 162 " 0.026 2.00e-02 2.50e+03 pdb=" N3 DG J 162 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG J 162 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS K 530 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO K 531 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO K 531 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 531 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 63 " -0.006 2.00e-02 2.50e+03 1.30e-02 3.80e+00 pdb=" N1 DC I 63 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DC I 63 " -0.031 2.00e-02 2.50e+03 pdb=" O2 DC I 63 " 0.021 2.00e-02 2.50e+03 pdb=" N3 DC I 63 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 63 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 63 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC I 63 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC I 63 " 0.004 2.00e-02 2.50e+03 ... (remaining 1426 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1936 2.77 - 3.30: 11063 3.30 - 3.83: 23605 3.83 - 4.37: 26505 4.37 - 4.90: 40152 Nonbonded interactions: 103261 Sorted by model distance: nonbonded pdb=" OG1 THR L 523 " pdb=" OG SER L 525 " model vdw 2.234 3.040 nonbonded pdb=" NH2 ARG A 40 " pdb=" O2 DT J 227 " model vdw 2.242 3.120 nonbonded pdb=" O TYR C 40 " pdb=" OG SER D 78 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR C 40 " pdb=" OE1 GLU D 71 " model vdw 2.296 3.040 nonbonded pdb=" N2 DG I 127 " pdb=" N3 DC J 164 " model vdw 2.305 3.200 ... (remaining 103256 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' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 31 through 123) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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: 0.700 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.860 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 : 0.005 0.057 13258 Z= 0.493 Angle : 0.739 7.878 19135 Z= 0.687 Chirality : 0.041 0.138 2165 Planarity : 0.004 0.060 1429 Dihedral : 28.764 128.413 5684 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.15 % Allowed : 14.85 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.18 (0.30), residues: 804 helix: 2.59 (0.23), residues: 511 sheet: -2.85 (0.88), residues: 26 loop : -0.40 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.031 0.001 TYR B 88 PHE 0.006 0.001 PHE E 78 TRP 0.008 0.001 TRP K 536 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.49 (13258) covalent geometry : angle 0.73940 / 0.69 (19135) hydrogen bonds : bond 0.10507 / 7.10 ( 744) hydrogen bonds : angle 3.77518 / 2.74 ( 1854) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.343 Fit side-chains REVERT: B 91 LYS cc_start: 0.8317 (tttt) cc_final: 0.7879 (tmtt) REVERT: C 21 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7973 (mmm-85) REVERT: C 96 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7839 (mtmm) REVERT: D 99 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.8070 (mtm-85) REVERT: D 119 THR cc_start: 0.8233 (m) cc_final: 0.7866 (p) REVERT: E 42 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7364 (mtp180) REVERT: E 77 LEU cc_start: 0.8318 (tt) cc_final: 0.8055 (tp) REVERT: E 89 MET cc_start: 0.7559 (mmm) cc_final: 0.7159 (mmt) REVERT: F 29 ILE cc_start: 0.8516 (mp) cc_final: 0.8231 (mm) REVERT: F 79 LYS cc_start: 0.8403 (mttp) cc_final: 0.8168 (mmtp) REVERT: H 34 LYS cc_start: 0.7799 (tptt) cc_final: 0.6513 (mttt) REVERT: L 544 ASP cc_start: 0.7010 (p0) cc_final: 0.6722 (m-30) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.2039 time to fit residues: 40.4858 Evaluate side-chains 98 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 25 GLN H 84 ASN K 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.177969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.140647 restraints weight = 14982.198| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 0.87 r_work: 0.3126 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13258 Z= 0.217 Angle : 0.746 8.492 19135 Z= 0.420 Chirality : 0.052 0.300 2165 Planarity : 0.006 0.055 1429 Dihedral : 31.723 131.211 4056 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.33 % Allowed : 15.57 % Favored : 82.10 % 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: 1.84 (0.29), residues: 804 helix: 2.12 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -0.56 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 86 TYR 0.048 0.002 TYR B 88 PHE 0.015 0.002 PHE A 101 TRP 0.007 0.001 TRP K 536 HIS 0.008 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.22 (13258) covalent geometry : angle 0.74586 / 0.42 (19135) hydrogen bonds : bond 0.07352 / 4.91 ( 744) hydrogen bonds : angle 3.21796 / 2.32 ( 1854) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.259 Fit side-chains REVERT: A 48 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8551 (mt) REVERT: A 111 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8290 (mp) REVERT: B 91 LYS cc_start: 0.8365 (ttpt) cc_final: 0.7911 (tmtt) REVERT: C 65 GLU cc_start: 0.8621 (tt0) cc_final: 0.8365 (tt0) REVERT: D 99 ARG cc_start: 0.8819 (mmm-85) cc_final: 0.8422 (mtm-85) REVERT: D 119 THR cc_start: 0.8531 (m) cc_final: 0.8286 (p) REVERT: E 77 LEU cc_start: 0.8536 (tt) cc_final: 0.8291 (tp) REVERT: E 89 MET cc_start: 0.7789 (mmm) cc_final: 0.7243 (mmt) REVERT: E 108 ASP cc_start: 0.8216 (m-30) cc_final: 0.8007 (m-30) REVERT: F 79 LYS cc_start: 0.8505 (mttp) cc_final: 0.8297 (mmtp) REVERT: F 95 ARG cc_start: 0.8342 (mtt90) cc_final: 0.8115 (ptp90) REVERT: G 65 GLU cc_start: 0.8431 (tp30) cc_final: 0.7952 (tt0) REVERT: G 93 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7891 (mm-30) REVERT: H 34 LYS cc_start: 0.7566 (tptt) cc_final: 0.6603 (mttt) outliers start: 16 outliers final: 5 residues processed: 105 average time/residue: 0.1657 time to fit residues: 22.6306 Evaluate side-chains 89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 81 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 30.0000 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.179009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.142997 restraints weight = 15192.841| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 0.93 r_work: 0.3152 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13258 Z= 0.154 Angle : 0.628 8.301 19135 Z= 0.373 Chirality : 0.046 0.250 2165 Planarity : 0.004 0.053 1429 Dihedral : 31.594 131.929 4056 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.04 % Allowed : 15.43 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.32 (0.29), residues: 804 helix: 2.55 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.52 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 72 TYR 0.027 0.001 TYR B 88 PHE 0.008 0.001 PHE A 101 TRP 0.005 0.001 TRP K 536 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (13258) covalent geometry : angle 0.62760 / 0.37 (19135) hydrogen bonds : bond 0.05871 / 3.94 ( 744) hydrogen bonds : angle 3.01641 / 2.18 ( 1854) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.344 Fit side-chains REVERT: A 111 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8187 (mp) REVERT: B 91 LYS cc_start: 0.8372 (ttpt) cc_final: 0.7868 (tmtt) REVERT: C 65 GLU cc_start: 0.8642 (tt0) cc_final: 0.8353 (tt0) REVERT: D 119 THR cc_start: 0.8550 (m) cc_final: 0.8282 (p) REVERT: E 89 MET cc_start: 0.7866 (mmm) cc_final: 0.7463 (mmt) REVERT: E 108 ASP cc_start: 0.8184 (m-30) cc_final: 0.7855 (m-30) REVERT: E 133 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7098 (ptt180) REVERT: F 95 ARG cc_start: 0.8269 (mtt90) cc_final: 0.8038 (ptp90) REVERT: G 65 GLU cc_start: 0.8397 (tp30) cc_final: 0.7938 (tt0) REVERT: G 93 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7800 (mm-30) REVERT: G 102 THR cc_start: 0.9117 (t) cc_final: 0.8705 (p) REVERT: H 34 LYS cc_start: 0.7602 (tptt) cc_final: 0.6592 (mttt) REVERT: L 544 ASP cc_start: 0.7166 (p0) cc_final: 0.6218 (m-30) REVERT: L 549 VAL cc_start: 0.7254 (p) cc_final: 0.6973 (t) outliers start: 14 outliers final: 6 residues processed: 101 average time/residue: 0.1762 time to fit residues: 22.9578 Evaluate side-chains 90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 87 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 84 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.175395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.139195 restraints weight = 14997.330| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 0.93 r_work: 0.3105 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13258 Z= 0.191 Angle : 0.685 8.373 19135 Z= 0.393 Chirality : 0.049 0.277 2165 Planarity : 0.005 0.056 1429 Dihedral : 31.688 131.348 4056 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.89 % Allowed : 16.16 % Favored : 81.95 % 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: 2.07 (0.29), residues: 804 helix: 2.48 (0.22), residues: 521 sheet: -2.38 (1.27), residues: 20 loop : -0.61 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 35 TYR 0.024 0.002 TYR B 88 PHE 0.014 0.002 PHE A 101 TRP 0.005 0.001 TRP K 536 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (13258) covalent geometry : angle 0.68474 / 0.39 (19135) hydrogen bonds : bond 0.06816 / 4.56 ( 744) hydrogen bonds : angle 3.04837 / 2.21 ( 1854) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.414 Fit side-chains REVERT: A 48 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8570 (mt) REVERT: A 111 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8362 (mp) REVERT: B 91 LYS cc_start: 0.8411 (ttpt) cc_final: 0.7934 (tmtt) REVERT: C 65 GLU cc_start: 0.8652 (tt0) cc_final: 0.8349 (tt0) REVERT: D 119 THR cc_start: 0.8605 (m) cc_final: 0.8285 (p) REVERT: E 89 MET cc_start: 0.7971 (mmm) cc_final: 0.7461 (mmt) REVERT: E 108 ASP cc_start: 0.8209 (m-30) cc_final: 0.7891 (m-30) REVERT: E 133 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7229 (ptt180) REVERT: G 65 GLU cc_start: 0.8357 (tp30) cc_final: 0.8014 (tt0) REVERT: H 34 LYS cc_start: 0.7703 (tptt) cc_final: 0.6619 (mttt) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.1691 time to fit residues: 21.4181 Evaluate side-chains 94 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.177578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.140117 restraints weight = 15189.781| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 0.92 r_work: 0.3156 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13258 Z= 0.147 Angle : 0.619 8.537 19135 Z= 0.364 Chirality : 0.045 0.262 2165 Planarity : 0.004 0.052 1429 Dihedral : 31.566 131.809 4056 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.75 % Allowed : 16.59 % Favored : 81.66 % 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: 2.33 (0.30), residues: 804 helix: 2.67 (0.22), residues: 523 sheet: -2.03 (1.29), residues: 20 loop : -0.55 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 35 TYR 0.016 0.001 TYR B 88 PHE 0.008 0.001 PHE A 101 TRP 0.004 0.001 TRP K 536 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.15 (13258) covalent geometry : angle 0.61884 / 0.36 (19135) hydrogen bonds : bond 0.05759 / 3.88 ( 744) hydrogen bonds : angle 2.93472 / 2.13 ( 1854) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.358 Fit side-chains REVERT: A 111 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8301 (mp) REVERT: B 91 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7857 (tmtt) REVERT: C 65 GLU cc_start: 0.8621 (tt0) cc_final: 0.8333 (tt0) REVERT: D 119 THR cc_start: 0.8584 (m) cc_final: 0.8274 (p) REVERT: E 89 MET cc_start: 0.7942 (mmm) cc_final: 0.7440 (mmt) REVERT: E 92 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8171 (mm) REVERT: E 108 ASP cc_start: 0.8144 (m-30) cc_final: 0.7821 (m-30) REVERT: E 133 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7148 (ptt180) REVERT: G 65 GLU cc_start: 0.8434 (tp30) cc_final: 0.8117 (tp30) REVERT: G 93 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7824 (mm-30) REVERT: H 34 LYS cc_start: 0.7676 (tptt) cc_final: 0.6572 (mttt) outliers start: 12 outliers final: 9 residues processed: 95 average time/residue: 0.1717 time to fit residues: 21.2722 Evaluate side-chains 92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 63 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 97 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.177359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.140552 restraints weight = 15063.723| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 0.98 r_work: 0.3125 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13258 Z= 0.147 Angle : 0.610 8.544 19135 Z= 0.359 Chirality : 0.045 0.274 2165 Planarity : 0.004 0.051 1429 Dihedral : 31.532 131.722 4056 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.91 % Allowed : 16.30 % Favored : 80.79 % 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: 2.46 (0.30), residues: 804 helix: 2.75 (0.22), residues: 523 sheet: -1.98 (1.36), residues: 20 loop : -0.45 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 72 TYR 0.013 0.001 TYR B 88 PHE 0.009 0.001 PHE A 101 TRP 0.004 0.001 TRP K 536 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (13258) covalent geometry : angle 0.60974 / 0.36 (19135) hydrogen bonds : bond 0.05604 / 3.77 ( 744) hydrogen bonds : angle 2.85555 / 2.08 ( 1854) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.343 Fit side-chains REVERT: A 111 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8314 (mp) REVERT: B 91 LYS cc_start: 0.8391 (ttpt) cc_final: 0.7866 (tmtt) REVERT: C 65 GLU cc_start: 0.8653 (tt0) cc_final: 0.8310 (tt0) REVERT: C 113 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7396 (mt0) REVERT: D 119 THR cc_start: 0.8574 (m) cc_final: 0.8255 (p) REVERT: E 45 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8054 (m) REVERT: E 89 MET cc_start: 0.7926 (mmm) cc_final: 0.7429 (mmt) REVERT: E 108 ASP cc_start: 0.8108 (m-30) cc_final: 0.7788 (m-30) REVERT: E 133 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7230 (ptt180) REVERT: H 34 LYS cc_start: 0.7634 (tptt) cc_final: 0.6516 (mttt) outliers start: 20 outliers final: 12 residues processed: 97 average time/residue: 0.1651 time to fit residues: 21.0443 Evaluate side-chains 92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain K residue 534 SER Chi-restraints excluded: chain L residue 523 THR Chi-restraints excluded: chain L residue 533 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 30.0000 chunk 79 optimal weight: 30.0000 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.176900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.140376 restraints weight = 15032.645| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 0.99 r_work: 0.3114 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13258 Z= 0.155 Angle : 0.618 8.565 19135 Z= 0.362 Chirality : 0.045 0.273 2165 Planarity : 0.004 0.049 1429 Dihedral : 31.524 131.695 4056 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.35 % Allowed : 16.30 % Favored : 80.35 % 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: 2.41 (0.30), residues: 804 helix: 2.72 (0.22), residues: 523 sheet: -1.97 (1.40), residues: 20 loop : -0.49 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 72 TYR 0.011 0.001 TYR B 88 PHE 0.010 0.001 PHE A 101 TRP 0.004 0.001 TRP K 536 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (13258) covalent geometry : angle 0.61800 / 0.36 (19135) hydrogen bonds : bond 0.05723 / 3.86 ( 744) hydrogen bonds : angle 2.86450 / 2.09 ( 1854) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.351 Fit side-chains REVERT: A 111 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8315 (mp) REVERT: B 91 LYS cc_start: 0.8392 (ttpt) cc_final: 0.7871 (tmtt) REVERT: C 65 GLU cc_start: 0.8653 (tt0) cc_final: 0.8307 (tt0) REVERT: D 119 THR cc_start: 0.8583 (m) cc_final: 0.8240 (p) REVERT: E 45 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8079 (m) REVERT: E 89 MET cc_start: 0.7948 (mmm) cc_final: 0.7447 (mmt) REVERT: E 92 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8216 (mm) REVERT: E 108 ASP cc_start: 0.8111 (m-30) cc_final: 0.7789 (m-30) REVERT: E 133 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7222 (ptt180) REVERT: G 62 GLU cc_start: 0.8331 (tp30) cc_final: 0.8099 (mm-30) REVERT: H 34 LYS cc_start: 0.7621 (tptt) cc_final: 0.6530 (mttt) REVERT: K 521 ILE cc_start: 0.3162 (OUTLIER) cc_final: 0.2780 (mm) outliers start: 23 outliers final: 13 residues processed: 98 average time/residue: 0.1642 time to fit residues: 21.1428 Evaluate side-chains 94 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain K residue 521 ILE Chi-restraints excluded: chain K residue 534 SER Chi-restraints excluded: chain L residue 523 THR Chi-restraints excluded: chain L residue 533 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.175253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.137513 restraints weight = 14919.343| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 0.97 r_work: 0.3089 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13258 Z= 0.162 Angle : 0.634 8.462 19135 Z= 0.369 Chirality : 0.046 0.277 2165 Planarity : 0.005 0.050 1429 Dihedral : 31.521 131.558 4056 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.91 % Allowed : 17.32 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.35 (0.30), residues: 804 helix: 2.66 (0.22), residues: 522 sheet: -1.90 (1.30), residues: 20 loop : -0.50 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 72 TYR 0.010 0.001 TYR F 51 PHE 0.011 0.001 PHE A 101 TRP 0.004 0.001 TRP K 536 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (13258) covalent geometry : angle 0.63435 / 0.37 (19135) hydrogen bonds : bond 0.06046 / 4.06 ( 744) hydrogen bonds : angle 2.90255 / 2.12 ( 1854) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.339 Fit side-chains REVERT: A 111 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8344 (mp) REVERT: B 91 LYS cc_start: 0.8434 (ttpt) cc_final: 0.7897 (tmtt) REVERT: C 65 GLU cc_start: 0.8676 (tt0) cc_final: 0.8327 (tt0) REVERT: E 45 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8120 (m) REVERT: E 48 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8843 (mm) REVERT: E 89 MET cc_start: 0.8006 (mmm) cc_final: 0.7440 (mmt) REVERT: E 108 ASP cc_start: 0.8136 (m-30) cc_final: 0.7818 (m-30) REVERT: E 133 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7236 (ptt180) REVERT: H 34 LYS cc_start: 0.7584 (tptt) cc_final: 0.6481 (mttt) REVERT: K 521 ILE cc_start: 0.3507 (OUTLIER) cc_final: 0.3111 (mm) outliers start: 20 outliers final: 12 residues processed: 97 average time/residue: 0.1576 time to fit residues: 20.1324 Evaluate side-chains 91 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain K residue 521 ILE Chi-restraints excluded: chain K residue 534 SER Chi-restraints excluded: chain L residue 533 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 30.0000 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.178609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.141420 restraints weight = 15066.031| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 0.97 r_work: 0.3149 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13258 Z= 0.132 Angle : 0.590 8.517 19135 Z= 0.349 Chirality : 0.044 0.268 2165 Planarity : 0.004 0.051 1429 Dihedral : 31.386 132.754 4056 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.46 % Allowed : 18.63 % Favored : 79.91 % 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: 2.58 (0.30), residues: 804 helix: 2.85 (0.22), residues: 523 sheet: -1.81 (1.30), residues: 20 loop : -0.43 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 72 TYR 0.010 0.001 TYR B 88 PHE 0.007 0.001 PHE F 61 TRP 0.003 0.001 TRP K 536 HIS 0.002 0.000 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.13 (13258) covalent geometry : angle 0.59002 / 0.35 (19135) hydrogen bonds : bond 0.05145 / 3.47 ( 744) hydrogen bonds : angle 2.79578 / 2.05 ( 1854) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.371 Fit side-chains REVERT: A 111 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8189 (mp) REVERT: B 91 LYS cc_start: 0.8378 (ttpt) cc_final: 0.7867 (tmtt) REVERT: C 65 GLU cc_start: 0.8598 (tt0) cc_final: 0.8274 (tt0) REVERT: E 89 MET cc_start: 0.7922 (mmm) cc_final: 0.7339 (mmt) REVERT: E 92 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8048 (mm) REVERT: E 108 ASP cc_start: 0.8032 (m-30) cc_final: 0.7699 (m-30) REVERT: E 133 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7074 (ptt180) REVERT: H 34 LYS cc_start: 0.7593 (tptt) cc_final: 0.6500 (mttt) outliers start: 10 outliers final: 7 residues processed: 90 average time/residue: 0.1743 time to fit residues: 20.6066 Evaluate side-chains 88 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain L residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 30.0000 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 38 optimal weight: 0.3980 chunk 11 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 97 optimal weight: 30.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.179983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.141392 restraints weight = 15103.132| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 0.95 r_work: 0.3182 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13258 Z= 0.128 Angle : 0.576 8.490 19135 Z= 0.341 Chirality : 0.043 0.279 2165 Planarity : 0.004 0.051 1429 Dihedral : 31.349 132.963 4056 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.60 % Allowed : 18.92 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.65 (0.29), residues: 804 helix: 2.87 (0.22), residues: 523 sheet: -1.47 (1.37), residues: 20 loop : -0.37 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 72 TYR 0.008 0.001 TYR F 51 PHE 0.007 0.001 PHE F 61 TRP 0.004 0.001 TRP K 536 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.13 (13258) covalent geometry : angle 0.57563 / 0.34 (19135) hydrogen bonds : bond 0.04872 / 3.28 ( 744) hydrogen bonds : angle 2.72984 / 2.00 ( 1854) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.331 Fit side-chains REVERT: A 111 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8184 (mp) REVERT: B 91 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7854 (tmtt) REVERT: C 65 GLU cc_start: 0.8574 (tt0) cc_final: 0.8251 (tt0) REVERT: D 119 THR cc_start: 0.8670 (m) cc_final: 0.8270 (p) REVERT: E 89 MET cc_start: 0.7830 (mmm) cc_final: 0.7264 (mmt) REVERT: E 108 ASP cc_start: 0.7958 (m-30) cc_final: 0.7651 (m-30) REVERT: E 133 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7046 (ptt180) REVERT: G 62 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8106 (mm-30) REVERT: H 34 LYS cc_start: 0.7576 (tptt) cc_final: 0.6529 (mttt) outliers start: 11 outliers final: 6 residues processed: 86 average time/residue: 0.1854 time to fit residues: 20.6197 Evaluate side-chains 83 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain K residue 534 SER Chi-restraints excluded: chain L residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 95 optimal weight: 30.0000 chunk 89 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 30.0000 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.179364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.142546 restraints weight = 15048.751| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 0.98 r_work: 0.3161 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13258 Z= 0.134 Angle : 0.583 8.290 19135 Z= 0.343 Chirality : 0.043 0.284 2165 Planarity : 0.004 0.051 1429 Dihedral : 31.374 132.916 4056 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.46 % Allowed : 18.34 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.71 (0.30), residues: 804 helix: 2.95 (0.22), residues: 520 sheet: -1.49 (1.32), residues: 20 loop : -0.36 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 72 TYR 0.008 0.001 TYR B 88 PHE 0.008 0.001 PHE A 101 TRP 0.004 0.001 TRP K 536 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.13 (13258) covalent geometry : angle 0.58345 / 0.34 (19135) hydrogen bonds : bond 0.05010 / 3.37 ( 744) hydrogen bonds : angle 2.71416 / 1.98 ( 1854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2317.58 seconds wall clock time: 40 minutes 26.83 seconds (2426.83 seconds total)