Starting phenix.real_space_refine on Thu Jul 2 21:56:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x5a_33013/07_2026/7x5a_33013.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x5a_33013/07_2026/7x5a_33013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x5a_33013/07_2026/7x5a_33013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x5a_33013/07_2026/7x5a_33013.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x5a_33013/07_2026/7x5a_33013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x5a_33013/07_2026/7x5a_33013.map" } resolution = 3.01 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= 0.078 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 104 5.49 5 S 32 5.16 5 C 6510 2.51 5 N 1888 2.21 5 O 2152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10686 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 535 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 532 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "K" Number of atoms: 533 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 533 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "L" Number of atoms: 532 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 26, 532 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1083 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 129} Chain: "B" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "C" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "D" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 128} Chain: "E" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "F" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "G" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "H" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1066 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P A DT I 36 " occ=0.25 ... (18 atoms not shown) pdb=" C6 A DT I 36 " occ=0.25 residue: pdb=" P A DA I 42 " occ=0.25 ... (19 atoms not shown) pdb=" C4 A DA I 42 " occ=0.25 residue: pdb=" P A DA K 20 " occ=0.25 ... (19 atoms not shown) pdb=" C4 A DA K 20 " occ=0.25 residue: pdb=" P A DT K 26 " occ=0.25 ... (18 atoms not shown) pdb=" C6 A DT K 26 " occ=0.25 Time building chain proxies: 2.19, per 1000 atoms: 0.20 Number of scatterers: 10686 At special positions: 0 Unit cell: (98.77, 112.88, 121.18, 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 32 16.00 P 104 15.00 O 2152 8.00 N 1888 7.00 C 6510 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: 1.10 Conformation dependent library (CDL) restraints added in 342.6 milliseconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 2 sheets defined 47.6% alpha, 11.8% beta 36 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 106 through 113 removed outlier: 4.209A pdb=" N LEU A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'B' and resid 31 through 37 removed outlier: 3.570A pdb=" N ARG B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 106 through 113 removed outlier: 4.032A pdb=" N LEU C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 65 through 78 removed outlier: 3.605A pdb=" N LEU D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.607A pdb=" N LYS D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 132 removed outlier: 4.088A pdb=" N ASP D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 82 through 93 Processing helix chain 'E' and resid 94 through 105 Processing helix chain 'E' and resid 106 through 113 removed outlier: 3.868A pdb=" N LEU E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 132 removed outlier: 4.122A pdb=" N ASP E 130 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 36 Processing helix chain 'F' and resid 65 through 77 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 94 through 105 Processing helix chain 'F' and resid 107 through 113 removed outlier: 3.871A pdb=" N ILE F 113 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 128 removed outlier: 3.562A pdb=" N ALA F 121 " --> pdb=" O GLY F 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 37 removed outlier: 3.701A pdb=" N ARG G 37 " --> pdb=" O THR G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 94 through 105 Processing helix chain 'G' and resid 106 through 113 removed outlier: 4.124A pdb=" N LEU G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE G 113 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'H' and resid 31 through 36 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.501A pdb=" N LYS H 112 " --> pdb=" O SER H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 132 removed outlier: 3.871A pdb=" N ASP H 130 " --> pdb=" O VAL H 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 13 removed outlier: 6.766A pdb=" N ILE A 18 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS A 12 " --> pdb=" O HIS A 16 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N HIS A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 24 through 29 current: chain 'A' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 61 current: chain 'B' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 24 through 29 current: chain 'B' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 61 current: chain 'C' and resid 16 through 21 removed outlier: 3.507A pdb=" N VAL C 24 " --> pdb=" O VAL C 21 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 24 through 29 current: chain 'C' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 61 current: chain 'D' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 24 through 29 current: chain 'D' and resid 58 through 61 Processing sheet with id=AA2, first strand: chain 'E' and resid 2 through 13 removed outlier: 3.628A pdb=" N THR E 8 " --> pdb=" O ASP E 20 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE E 18 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS E 12 " --> pdb=" O HIS E 16 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N HIS E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 24 through 29 current: chain 'E' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 58 through 61 current: chain 'F' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 24 through 29 current: chain 'F' and resid 57 through 61 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 57 through 61 current: chain 'G' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 24 through 29 current: chain 'G' and resid 58 through 61 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 58 through 61 current: chain 'H' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 24 through 29 current: chain 'H' and resid 57 through 61 356 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2914 1.34 - 1.45: 2025 1.45 - 1.57: 5887 1.57 - 1.69: 204 1.69 - 1.81: 56 Bond restraints: 11086 Sorted by residual: bond pdb=" N1 DT K 22 " pdb=" C1'A DT K 22 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.28e+01 bond pdb=" C1' DT I 32 " pdb=" N1 DT I 32 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.39e+00 bond pdb=" C3'A DA I 21 " pdb=" C2'A DA I 21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.06e+00 bond pdb=" N1 DT J 22 " pdb=" C1'A DT J 22 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.35e+00 bond pdb=" C3'A DT L 45 " pdb=" C2'A DT L 45 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.23e+00 ... (remaining 11081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.84: 13819 0.84 - 1.68: 1105 1.68 - 2.52: 286 2.52 - 3.35: 197 3.35 - 4.19: 32 Bond angle restraints: 15439 Sorted by residual: angle pdb=" N3 DT K 29 " pdb=" C4 DT K 29 " pdb=" O4 DT K 29 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT J 21 " pdb=" C4 DT J 21 " pdb=" O4 DT J 21 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT J 19 " pdb=" C4 DT J 19 " pdb=" O4 DT J 19 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT L 24 " pdb=" C4 DT L 24 " pdb=" O4 DT L 24 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT K 22 " pdb=" C4 DT K 22 " pdb=" O4 DT K 22 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 15434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.37: 5939 31.37 - 62.74: 613 62.74 - 94.10: 18 94.10 - 125.47: 1 125.47 - 156.84: 2 Dihedral angle restraints: 6573 sinusoidal: 3484 harmonic: 3089 Sorted by residual: dihedral pdb=" C4'A DA I 20 " pdb=" C3'A DA I 20 " pdb=" O3'A DA I 20 " pdb=" P A DA I 21 " ideal model delta sinusoidal sigma weight residual 220.00 63.16 156.84 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4'A DT L 44 " pdb=" C3'A DT L 44 " pdb=" O3'A DT L 44 " pdb=" P A DT L 45 " ideal model delta sinusoidal sigma weight residual 220.00 65.27 154.73 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA LYS F 129 " pdb=" C LYS F 129 " pdb=" N ASP F 130 " pdb=" CA ASP F 130 " ideal model delta harmonic sigma weight residual -180.00 -162.89 -17.11 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 6570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1349 0.038 - 0.075: 232 0.075 - 0.113: 90 0.113 - 0.151: 114 0.151 - 0.188: 18 Chirality restraints: 1803 Sorted by residual: chirality pdb=" C3'A DA K 13 " pdb=" C4'A DA K 13 " pdb=" O3'A DA K 13 " pdb=" C2'A DA K 13 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" C3'A DA L 34 " pdb=" C4'A DA L 34 " pdb=" O3'A DA L 34 " pdb=" C2'A DA L 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" C3'A DA J 25 " pdb=" C4'A DA J 25 " pdb=" O3'A DA J 25 " pdb=" C2'A DA J 25 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 1800 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 38 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO D 39 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 39 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 39 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 113 " 0.021 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO F 114 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO F 114 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 114 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 118 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C LYS C 118 " -0.020 2.00e-02 2.50e+03 pdb=" O LYS C 118 " 0.008 2.00e-02 2.50e+03 pdb=" N LYS C 119 " 0.007 2.00e-02 2.50e+03 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 547 2.73 - 3.27: 9924 3.27 - 3.81: 18441 3.81 - 4.36: 22135 4.36 - 4.90: 36510 Nonbonded interactions: 87557 Sorted by model distance: nonbonded pdb=" O LYS H 118 " pdb=" OE1 GLU H 122 " model vdw 2.182 3.040 nonbonded pdb=" O VAL C 126 " pdb=" NZ LYS G 119 " model vdw 2.183 3.120 nonbonded pdb=" OP1A DA K 30 " pdb=" OG1 THR A 120 " model vdw 2.206 3.040 nonbonded pdb=" O ARG E 123 " pdb=" OE1 GLU E 127 " model vdw 2.241 3.040 nonbonded pdb=" O LYS H 118 " pdb=" N ALA H 121 " model vdw 2.248 3.120 ... (remaining 87552 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 1 through 135) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 1 through 135) selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'K' and (resid 12 through 22 or resid 24 through 30 or resid 32 through 3 \ 6)) selection = (chain 'L' and (resid 21 through 24 or resid 26 through 32 or resid 34 through 4 \ 5)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=0.92 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: 10.590 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.650 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 0.050 11086 Z= 0.323 Angle : 0.627 4.193 15439 Z= 0.508 Chirality : 0.049 0.188 1803 Planarity : 0.003 0.052 1598 Dihedral : 20.334 156.839 4583 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.22 (0.28), residues: 1067 helix: 1.12 (0.25), residues: 507 sheet: -1.52 (0.30), residues: 268 loop : 0.45 (0.42), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 100 TYR 0.007 0.001 TYR C 36 PHE 0.007 0.001 PHE E 132 TRP 0.001 0.000 TRP D 135 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.32 (11086) covalent geometry : angle 0.62713 / 0.51 (15439) hydrogen bonds : bond 0.13290 / 14.76 ( 428) hydrogen bonds : angle 5.89058 / 7.32 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: B 70 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8079 (mm-30) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1374 time to fit residues: 39.8530 Evaluate side-chains 174 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.179746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121631 restraints weight = 11353.845| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.11 r_work: 0.3277 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11086 Z= 0.204 Angle : 0.614 7.875 15439 Z= 0.338 Chirality : 0.043 0.270 1803 Planarity : 0.005 0.035 1598 Dihedral : 23.972 155.114 2423 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.18 % Allowed : 6.98 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.20 (0.27), residues: 1067 helix: 0.93 (0.24), residues: 499 sheet: -1.34 (0.29), residues: 278 loop : 0.67 (0.43), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 77 TYR 0.007 0.001 TYR A 26 PHE 0.011 0.002 PHE D 132 TRP 0.004 0.001 TRP D 135 HIS 0.009 0.002 HIS B 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (11086) covalent geometry : angle 0.61408 / 0.34 (15439) hydrogen bonds : bond 0.05430 / 6.25 ( 428) hydrogen bonds : angle 4.70044 / 6.04 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.367 Fit side-chains REVERT: B 68 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: C 112 LYS cc_start: 0.8063 (mptt) cc_final: 0.7768 (mptt) REVERT: C 122 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: D 106 ASP cc_start: 0.7889 (t0) cc_final: 0.7678 (t0) REVERT: E 109 THR cc_start: 0.7721 (m) cc_final: 0.7517 (p) REVERT: F 94 GLU cc_start: 0.7783 (mp0) cc_final: 0.7573 (mp0) REVERT: F 101 CYS cc_start: 0.6645 (m) cc_final: 0.6375 (m) outliers start: 11 outliers final: 5 residues processed: 183 average time/residue: 0.1560 time to fit residues: 36.3159 Evaluate side-chains 176 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain H residue 93 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.176126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117793 restraints weight = 11488.830| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.15 r_work: 0.3236 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11086 Z= 0.146 Angle : 0.544 6.625 15439 Z= 0.305 Chirality : 0.040 0.254 1803 Planarity : 0.004 0.035 1598 Dihedral : 24.117 156.172 2423 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.50 % Allowed : 7.52 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.26 (0.27), residues: 1067 helix: 1.02 (0.24), residues: 496 sheet: -1.36 (0.28), residues: 280 loop : 0.71 (0.43), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 123 TYR 0.010 0.001 TYR F 36 PHE 0.009 0.002 PHE F 63 TRP 0.003 0.000 TRP D 135 HIS 0.006 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (11086) covalent geometry : angle 0.54379 / 0.31 (15439) hydrogen bonds : bond 0.04924 / 5.68 ( 428) hydrogen bonds : angle 4.41597 / 5.70 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: B 68 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: C 17 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8208 (mt) REVERT: C 32 MET cc_start: 0.7939 (mmt) cc_final: 0.7671 (mmt) REVERT: C 112 LYS cc_start: 0.8030 (mptt) cc_final: 0.7766 (mmtm) REVERT: C 122 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: D 106 ASP cc_start: 0.7813 (t0) cc_final: 0.7500 (t0) REVERT: D 129 LYS cc_start: 0.7921 (tppt) cc_final: 0.7643 (tppt) REVERT: E 65 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8093 (mm-30) REVERT: E 100 ARG cc_start: 0.6941 (ttp80) cc_final: 0.6617 (ttp80) REVERT: E 109 THR cc_start: 0.7719 (m) cc_final: 0.7501 (p) REVERT: F 101 CYS cc_start: 0.6642 (m) cc_final: 0.6403 (m) REVERT: G 93 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7538 (pp) outliers start: 14 outliers final: 5 residues processed: 186 average time/residue: 0.1278 time to fit residues: 30.6453 Evaluate side-chains 176 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.0170 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 1.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.177947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.117777 restraints weight = 11620.540| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.16 r_work: 0.3175 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11086 Z= 0.181 Angle : 0.578 6.940 15439 Z= 0.314 Chirality : 0.041 0.256 1803 Planarity : 0.004 0.035 1598 Dihedral : 24.238 156.339 2423 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.36 % Allowed : 9.45 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.20 (0.27), residues: 1067 helix: 1.00 (0.24), residues: 496 sheet: -1.40 (0.28), residues: 280 loop : 0.65 (0.42), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 77 TYR 0.006 0.001 TYR F 36 PHE 0.011 0.002 PHE D 132 TRP 0.004 0.001 TRP D 135 HIS 0.008 0.002 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (11086) covalent geometry : angle 0.57784 / 0.31 (15439) hydrogen bonds : bond 0.04984 / 5.77 ( 428) hydrogen bonds : angle 4.34913 / 5.65 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.376 Fit side-chains REVERT: B 68 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: C 17 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8229 (mt) REVERT: C 112 LYS cc_start: 0.8122 (mptt) cc_final: 0.7740 (mmtm) REVERT: C 122 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: D 106 ASP cc_start: 0.7840 (t0) cc_final: 0.7482 (t0) REVERT: D 129 LYS cc_start: 0.7910 (tppt) cc_final: 0.7300 (tptt) REVERT: E 65 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8158 (mm-30) REVERT: E 100 ARG cc_start: 0.7032 (ttp80) cc_final: 0.6650 (ttp80) REVERT: E 118 LYS cc_start: 0.7969 (mptt) cc_final: 0.7663 (mtpp) REVERT: E 123 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7392 (mtp85) REVERT: F 101 CYS cc_start: 0.6698 (m) cc_final: 0.6470 (m) REVERT: G 93 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7533 (pp) outliers start: 22 outliers final: 12 residues processed: 186 average time/residue: 0.1400 time to fit residues: 33.4107 Evaluate side-chains 186 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 90 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN C 79 ASN ** G 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.179867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122463 restraints weight = 11517.904| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.28 r_work: 0.3140 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11086 Z= 0.124 Angle : 0.521 6.110 15439 Z= 0.292 Chirality : 0.039 0.260 1803 Planarity : 0.004 0.033 1598 Dihedral : 24.193 156.522 2423 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.83 % Allowed : 10.20 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.26 (0.27), residues: 1067 helix: 1.06 (0.24), residues: 496 sheet: -1.43 (0.28), residues: 280 loop : 0.73 (0.42), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 37 TYR 0.006 0.001 TYR F 36 PHE 0.009 0.002 PHE F 63 TRP 0.002 0.000 TRP D 135 HIS 0.004 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (11086) covalent geometry : angle 0.52106 / 0.29 (15439) hydrogen bonds : bond 0.04500 / 5.21 ( 428) hydrogen bonds : angle 4.23409 / 5.48 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.359 Fit side-chains REVERT: B 68 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: C 112 LYS cc_start: 0.8031 (mptt) cc_final: 0.7645 (mptt) REVERT: C 122 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: D 106 ASP cc_start: 0.7836 (t0) cc_final: 0.7495 (t0) REVERT: D 129 LYS cc_start: 0.7924 (tppt) cc_final: 0.7484 (tptt) REVERT: E 65 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8048 (mm-30) REVERT: E 100 ARG cc_start: 0.7132 (ttp80) cc_final: 0.6842 (ttp80) REVERT: F 101 CYS cc_start: 0.6798 (m) cc_final: 0.6541 (m) REVERT: G 93 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7558 (pp) outliers start: 17 outliers final: 9 residues processed: 183 average time/residue: 0.1466 time to fit residues: 34.2541 Evaluate side-chains 181 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 40.0000 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN G 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.180338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121869 restraints weight = 11616.207| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.31 r_work: 0.3128 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11086 Z= 0.139 Angle : 0.533 6.487 15439 Z= 0.294 Chirality : 0.040 0.257 1803 Planarity : 0.004 0.033 1598 Dihedral : 24.206 156.689 2423 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.83 % Allowed : 10.85 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.31 (0.27), residues: 1067 helix: 1.09 (0.24), residues: 496 sheet: -1.41 (0.28), residues: 280 loop : 0.76 (0.42), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 67 TYR 0.006 0.001 TYR F 36 PHE 0.008 0.002 PHE D 132 TRP 0.003 0.000 TRP D 135 HIS 0.005 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (11086) covalent geometry : angle 0.53299 / 0.29 (15439) hydrogen bonds : bond 0.04537 / 5.25 ( 428) hydrogen bonds : angle 4.16394 / 5.40 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.370 Fit side-chains REVERT: B 68 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: C 17 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8129 (mt) REVERT: C 112 LYS cc_start: 0.8012 (mptt) cc_final: 0.7590 (mmtm) REVERT: C 122 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: D 106 ASP cc_start: 0.7871 (t0) cc_final: 0.7504 (t0) REVERT: D 129 LYS cc_start: 0.7908 (tppt) cc_final: 0.7569 (tptt) REVERT: E 65 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8059 (mm-30) REVERT: E 100 ARG cc_start: 0.7154 (ttp80) cc_final: 0.6907 (ttp80) REVERT: E 118 LYS cc_start: 0.8014 (mptt) cc_final: 0.7718 (mtpp) REVERT: F 101 CYS cc_start: 0.6811 (m) cc_final: 0.6581 (m) REVERT: G 93 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7576 (pp) outliers start: 17 outliers final: 11 residues processed: 181 average time/residue: 0.1614 time to fit residues: 37.3892 Evaluate side-chains 185 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.180381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114863 restraints weight = 11483.800| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.16 r_work: 0.3170 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11086 Z= 0.151 Angle : 0.542 6.386 15439 Z= 0.297 Chirality : 0.040 0.256 1803 Planarity : 0.004 0.033 1598 Dihedral : 24.231 156.897 2423 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.26 % Allowed : 10.63 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.28 (0.27), residues: 1067 helix: 1.07 (0.24), residues: 496 sheet: -1.39 (0.28), residues: 280 loop : 0.73 (0.42), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 67 TYR 0.006 0.001 TYR F 36 PHE 0.009 0.002 PHE D 132 TRP 0.004 0.001 TRP D 135 HIS 0.006 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (11086) covalent geometry : angle 0.54166 / 0.30 (15439) hydrogen bonds : bond 0.04557 / 5.25 ( 428) hydrogen bonds : angle 4.18674 / 5.43 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.374 Fit side-chains REVERT: B 68 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: C 17 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8194 (mt) REVERT: C 101 CYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6676 (m) REVERT: C 112 LYS cc_start: 0.8049 (mptt) cc_final: 0.7614 (mmtm) REVERT: C 122 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: D 106 ASP cc_start: 0.7869 (t0) cc_final: 0.7461 (t0) REVERT: D 129 LYS cc_start: 0.7874 (tppt) cc_final: 0.7475 (tptt) REVERT: E 65 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8101 (mm-30) REVERT: E 100 ARG cc_start: 0.7084 (ttp80) cc_final: 0.6827 (ttp80) REVERT: F 96 ASP cc_start: 0.8141 (p0) cc_final: 0.7931 (p0) REVERT: F 97 GLU cc_start: 0.7546 (mp0) cc_final: 0.6988 (mp0) REVERT: F 101 CYS cc_start: 0.6643 (m) cc_final: 0.6411 (m) REVERT: G 93 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7521 (pp) outliers start: 21 outliers final: 13 residues processed: 187 average time/residue: 0.1512 time to fit residues: 36.2255 Evaluate side-chains 186 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 50 optimal weight: 0.0070 chunk 86 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.181361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116284 restraints weight = 11553.495| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.12 r_work: 0.3195 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 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 : 0.003 0.028 11086 Z= 0.126 Angle : 0.521 5.976 15439 Z= 0.289 Chirality : 0.039 0.258 1803 Planarity : 0.004 0.031 1598 Dihedral : 24.182 157.439 2423 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.04 % Allowed : 10.96 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.33 (0.27), residues: 1067 helix: 1.10 (0.24), residues: 498 sheet: -1.40 (0.28), residues: 280 loop : 0.77 (0.42), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 77 TYR 0.005 0.001 TYR F 36 PHE 0.007 0.002 PHE E 132 TRP 0.003 0.000 TRP D 135 HIS 0.004 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (11086) covalent geometry : angle 0.52058 / 0.29 (15439) hydrogen bonds : bond 0.04324 / 4.99 ( 428) hydrogen bonds : angle 4.14144 / 5.35 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.378 Fit side-chains REVERT: A 65 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8278 (mm-30) REVERT: B 68 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8321 (mt-10) REVERT: C 17 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8164 (mt) REVERT: C 101 CYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6704 (m) REVERT: C 112 LYS cc_start: 0.8075 (mptt) cc_final: 0.7782 (tptp) REVERT: C 122 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: D 106 ASP cc_start: 0.7857 (t0) cc_final: 0.7484 (t0) REVERT: D 129 LYS cc_start: 0.7868 (tppt) cc_final: 0.7488 (tptt) REVERT: E 65 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8111 (mm-30) REVERT: E 100 ARG cc_start: 0.7116 (ttp80) cc_final: 0.6886 (tmm160) REVERT: E 118 LYS cc_start: 0.8033 (mptt) cc_final: 0.7722 (mtpp) REVERT: E 123 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7345 (mtp85) REVERT: E 127 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6830 (mt-10) REVERT: F 101 CYS cc_start: 0.6717 (m) cc_final: 0.6494 (m) REVERT: G 93 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7498 (pp) outliers start: 19 outliers final: 12 residues processed: 185 average time/residue: 0.1495 time to fit residues: 35.3629 Evaluate side-chains 184 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 89 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.181233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120891 restraints weight = 11556.840| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.30 r_work: 0.3120 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11086 Z= 0.133 Angle : 0.529 6.116 15439 Z= 0.292 Chirality : 0.040 0.256 1803 Planarity : 0.004 0.034 1598 Dihedral : 24.172 157.766 2423 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.15 % Allowed : 10.74 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.33 (0.27), residues: 1067 helix: 1.11 (0.24), residues: 498 sheet: -1.40 (0.28), residues: 280 loop : 0.76 (0.42), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 67 TYR 0.005 0.001 TYR F 36 PHE 0.008 0.002 PHE E 132 TRP 0.003 0.000 TRP D 135 HIS 0.004 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (11086) covalent geometry : angle 0.52928 / 0.29 (15439) hydrogen bonds : bond 0.04350 / 5.02 ( 428) hydrogen bonds : angle 4.11855 / 5.33 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.375 Fit side-chains REVERT: B 68 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: C 17 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8128 (mt) REVERT: C 101 CYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6751 (m) REVERT: C 112 LYS cc_start: 0.8053 (mptt) cc_final: 0.7790 (tptp) REVERT: C 122 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: D 106 ASP cc_start: 0.7896 (t0) cc_final: 0.7567 (t0) REVERT: D 129 LYS cc_start: 0.7897 (tppt) cc_final: 0.7542 (tptt) REVERT: E 32 MET cc_start: 0.7805 (mmm) cc_final: 0.7364 (mmm) REVERT: E 65 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8068 (mm-30) REVERT: E 100 ARG cc_start: 0.7206 (ttp80) cc_final: 0.6974 (tmm160) REVERT: E 118 LYS cc_start: 0.8069 (mptt) cc_final: 0.7784 (mtpp) REVERT: E 123 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7383 (mtp85) REVERT: E 127 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6854 (mt-10) REVERT: F 101 CYS cc_start: 0.6865 (m) cc_final: 0.6613 (m) REVERT: G 93 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7577 (pp) outliers start: 20 outliers final: 12 residues processed: 180 average time/residue: 0.1552 time to fit residues: 35.7418 Evaluate side-chains 186 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 76 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.179952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121998 restraints weight = 11400.664| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.21 r_work: 0.3145 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11086 Z= 0.168 Angle : 0.560 6.580 15439 Z= 0.303 Chirality : 0.041 0.252 1803 Planarity : 0.004 0.033 1598 Dihedral : 24.215 157.909 2423 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.04 % Allowed : 10.85 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.25 (0.27), residues: 1067 helix: 1.01 (0.24), residues: 501 sheet: -1.38 (0.28), residues: 280 loop : 0.74 (0.43), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.006 0.001 TYR F 36 PHE 0.011 0.002 PHE D 132 TRP 0.005 0.001 TRP D 135 HIS 0.006 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (11086) covalent geometry : angle 0.56007 / 0.30 (15439) hydrogen bonds : bond 0.04609 / 5.30 ( 428) hydrogen bonds : angle 4.19740 / 5.45 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.394 Fit side-chains REVERT: C 17 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8152 (mt) REVERT: C 101 CYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6764 (m) REVERT: C 112 LYS cc_start: 0.8048 (mptt) cc_final: 0.7794 (tptp) REVERT: C 122 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: D 106 ASP cc_start: 0.7939 (t0) cc_final: 0.7634 (t0) REVERT: D 129 LYS cc_start: 0.7923 (tppt) cc_final: 0.7572 (tptt) REVERT: E 32 MET cc_start: 0.7787 (mmm) cc_final: 0.7330 (mmm) REVERT: E 100 ARG cc_start: 0.7242 (ttp80) cc_final: 0.6997 (ttp80) REVERT: E 118 LYS cc_start: 0.8078 (mptt) cc_final: 0.7815 (mtpp) REVERT: E 123 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7387 (mtp85) REVERT: E 127 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6896 (mt-10) REVERT: F 96 ASP cc_start: 0.8096 (p0) cc_final: 0.7792 (p0) REVERT: F 97 GLU cc_start: 0.7641 (mp0) cc_final: 0.6985 (mp0) REVERT: F 101 CYS cc_start: 0.6841 (m) cc_final: 0.6611 (m) REVERT: G 93 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7635 (pp) outliers start: 19 outliers final: 14 residues processed: 185 average time/residue: 0.1573 time to fit residues: 37.2570 Evaluate side-chains 184 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 CYS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 30.0000 chunk 66 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN H 16 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.180323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119027 restraints weight = 11434.847| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.22 r_work: 0.3127 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11086 Z= 0.179 Angle : 0.571 6.562 15439 Z= 0.307 Chirality : 0.041 0.252 1803 Planarity : 0.004 0.033 1598 Dihedral : 24.242 157.945 2423 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.04 % Allowed : 10.85 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.20 (0.27), residues: 1067 helix: 0.95 (0.24), residues: 500 sheet: -1.40 (0.28), residues: 280 loop : 0.74 (0.42), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 67 TYR 0.006 0.001 TYR F 36 PHE 0.010 0.002 PHE E 132 TRP 0.006 0.001 TRP D 135 HIS 0.006 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (11086) covalent geometry : angle 0.57112 / 0.31 (15439) hydrogen bonds : bond 0.04654 / 5.33 ( 428) hydrogen bonds : angle 4.25757 / 5.51 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3184.40 seconds wall clock time: 55 minutes 2.85 seconds (3302.85 seconds total)