Starting phenix.real_space_refine on Thu Sep 26 21:47:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p37_13178/09_2024/7p37_13178_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p37_13178/09_2024/7p37_13178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p37_13178/09_2024/7p37_13178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p37_13178/09_2024/7p37_13178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p37_13178/09_2024/7p37_13178_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p37_13178/09_2024/7p37_13178_neut.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.080 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: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 72 5.49 5 S 96 5.16 5 C 8652 2.51 5 N 2712 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14496 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "B" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24 SG CYS A 3 24.063 31.536 29.041 1.00 41.20 S ATOM 48 SG CYS A 6 21.180 29.864 27.166 1.00 45.02 S ATOM 254 SG CYS A 31 22.367 33.208 26.023 1.00 41.51 S ATOM 275 SG CYS A 34 20.540 32.972 29.312 1.00 44.03 S ATOM 6894 SG CYS B 3 74.054 42.619 65.365 1.00 11.76 S ATOM 6918 SG CYS B 6 72.100 45.890 65.731 1.00 12.15 S ATOM 7124 SG CYS B 31 75.196 45.364 67.758 1.00 13.45 S ATOM 7145 SG CYS B 34 72.067 43.335 68.534 1.00 13.85 S Restraints were copied for chains: C, E, G, I, K, D, F, H, J, L Time building chain proxies: 6.23, per 1000 atoms: 0.43 Number of scatterers: 14496 At special positions: 0 Unit cell: (129.31, 114.57, 89.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 96 16.00 P 72 15.00 O 2952 8.00 N 2712 7.00 C 8652 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: 3.81 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 203 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 31 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 6 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 34 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 3 " pdb=" ZN B 203 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 31 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 6 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 34 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 3 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 31 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 6 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 34 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 3 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 6 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 34 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 3 " pdb=" ZN E 203 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 31 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 6 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 34 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 3 " pdb=" ZN F 203 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 6 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 34 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 31 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 3 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 31 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 6 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 34 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 3 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 6 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 31 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 34 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 3 " pdb=" ZN I 203 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 31 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 6 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 34 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 3 " pdb=" ZN J 203 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 6 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 34 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 31 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 3 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 6 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 34 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 3 " pdb=" ZN L 203 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 6 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 3 " Number of angles added : 72 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 18 sheets defined 52.0% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 59 through 71 removed outlier: 3.719A pdb=" N VAL A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 95 removed outlier: 3.860A pdb=" N THR A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 removed outlier: 3.934A pdb=" N GLY A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 3.765A pdb=" N GLU A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 4.376A pdb=" N VAL A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.627A pdb=" N PHE A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.719A pdb=" N VAL E 63 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 95 removed outlier: 3.860A pdb=" N THR E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 removed outlier: 3.935A pdb=" N GLY E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Proline residue: E 112 - end of helix removed outlier: 3.764A pdb=" N GLU E 115 " --> pdb=" O GLY E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 removed outlier: 4.377A pdb=" N VAL E 127 " --> pdb=" O ARG E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 147 removed outlier: 3.627A pdb=" N PHE E 137 " --> pdb=" O SER E 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 71 removed outlier: 3.720A pdb=" N VAL I 63 " --> pdb=" O SER I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 95 removed outlier: 3.859A pdb=" N THR I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 117 removed outlier: 3.934A pdb=" N GLY I 111 " --> pdb=" O LEU I 107 " (cutoff:3.500A) Proline residue: I 112 - end of helix removed outlier: 3.765A pdb=" N GLU I 115 " --> pdb=" O GLY I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 129 removed outlier: 4.376A pdb=" N VAL I 127 " --> pdb=" O ARG I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 147 removed outlier: 3.627A pdb=" N PHE I 137 " --> pdb=" O SER I 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 71 removed outlier: 3.720A pdb=" N VAL C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 95 removed outlier: 3.860A pdb=" N THR C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 removed outlier: 3.934A pdb=" N GLY C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Proline residue: C 112 - end of helix removed outlier: 3.765A pdb=" N GLU C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 removed outlier: 4.376A pdb=" N VAL C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 147 removed outlier: 3.627A pdb=" N PHE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 71 removed outlier: 3.718A pdb=" N VAL G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 95 removed outlier: 3.860A pdb=" N THR G 95 " --> pdb=" O ALA G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 117 removed outlier: 3.934A pdb=" N GLY G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Proline residue: G 112 - end of helix removed outlier: 3.765A pdb=" N GLU G 115 " --> pdb=" O GLY G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 removed outlier: 4.377A pdb=" N VAL G 127 " --> pdb=" O ARG G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 147 removed outlier: 3.627A pdb=" N PHE G 137 " --> pdb=" O SER G 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 71 removed outlier: 3.720A pdb=" N VAL K 63 " --> pdb=" O SER K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 95 removed outlier: 3.860A pdb=" N THR K 95 " --> pdb=" O ALA K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 117 removed outlier: 3.934A pdb=" N GLY K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) Proline residue: K 112 - end of helix removed outlier: 3.765A pdb=" N GLU K 115 " --> pdb=" O GLY K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 129 removed outlier: 4.377A pdb=" N VAL K 127 " --> pdb=" O ARG K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 147 removed outlier: 3.628A pdb=" N PHE K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 removed outlier: 3.651A pdb=" N VAL B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 96 removed outlier: 3.752A pdb=" N GLY B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 109 through 117 removed outlier: 3.894A pdb=" N GLU B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 4.062A pdb=" N VAL B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 Processing helix chain 'F' and resid 59 through 71 removed outlier: 3.651A pdb=" N VAL F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 96 removed outlier: 3.751A pdb=" N GLY F 96 " --> pdb=" O VAL F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 108 Processing helix chain 'F' and resid 109 through 117 removed outlier: 3.894A pdb=" N GLU F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 129 removed outlier: 4.062A pdb=" N VAL F 127 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR F 128 " --> pdb=" O PHE F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 147 Processing helix chain 'J' and resid 59 through 71 removed outlier: 3.651A pdb=" N VAL J 63 " --> pdb=" O SER J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 96 removed outlier: 3.752A pdb=" N GLY J 96 " --> pdb=" O VAL J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 108 Processing helix chain 'J' and resid 109 through 117 removed outlier: 3.895A pdb=" N GLU J 115 " --> pdb=" O GLY J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 129 removed outlier: 4.062A pdb=" N VAL J 127 " --> pdb=" O ARG J 123 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR J 128 " --> pdb=" O PHE J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 147 Processing helix chain 'D' and resid 59 through 71 removed outlier: 3.650A pdb=" N VAL D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 96 removed outlier: 3.752A pdb=" N GLY D 96 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 108 Processing helix chain 'D' and resid 109 through 117 removed outlier: 3.895A pdb=" N GLU D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 removed outlier: 4.062A pdb=" N VAL D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 147 Processing helix chain 'H' and resid 59 through 71 removed outlier: 3.651A pdb=" N VAL H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 96 removed outlier: 3.752A pdb=" N GLY H 96 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 108 Processing helix chain 'H' and resid 109 through 117 removed outlier: 3.895A pdb=" N GLU H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 129 removed outlier: 4.062A pdb=" N VAL H 127 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR H 128 " --> pdb=" O PHE H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 147 Processing helix chain 'L' and resid 59 through 71 removed outlier: 3.650A pdb=" N VAL L 63 " --> pdb=" O SER L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 96 removed outlier: 3.751A pdb=" N GLY L 96 " --> pdb=" O VAL L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 108 Processing helix chain 'L' and resid 109 through 117 removed outlier: 3.895A pdb=" N GLU L 115 " --> pdb=" O GLY L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 129 removed outlier: 4.062A pdb=" N VAL L 127 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 6.422A pdb=" N ARG A 28 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER A 16 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG A 26 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLN D 30 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL D 13 " --> pdb=" O GLN D 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA3, first strand: chain 'E' and resid 12 through 18 removed outlier: 6.421A pdb=" N ARG E 28 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER E 16 " --> pdb=" O ARG E 26 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG E 26 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN H 30 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL H 13 " --> pdb=" O GLN H 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 55 through 57 Processing sheet with id=AA5, first strand: chain 'I' and resid 12 through 18 removed outlier: 6.421A pdb=" N ARG I 28 " --> pdb=" O VAL I 14 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER I 16 " --> pdb=" O ARG I 26 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG I 26 " --> pdb=" O SER I 16 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN L 30 " --> pdb=" O VAL L 13 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL L 13 " --> pdb=" O GLN L 30 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 55 through 57 Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 18 removed outlier: 6.421A pdb=" N ARG C 28 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER C 16 " --> pdb=" O ARG C 26 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG C 26 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 41 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN B 30 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL B 13 " --> pdb=" O GLN B 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 55 through 57 Processing sheet with id=AA9, first strand: chain 'G' and resid 12 through 18 removed outlier: 6.422A pdb=" N ARG G 28 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER G 16 " --> pdb=" O ARG G 26 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG G 26 " --> pdb=" O SER G 16 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN F 30 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL F 13 " --> pdb=" O GLN F 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 55 through 57 Processing sheet with id=AB2, first strand: chain 'K' and resid 12 through 18 removed outlier: 6.422A pdb=" N ARG K 28 " --> pdb=" O VAL K 14 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER K 16 " --> pdb=" O ARG K 26 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG K 26 " --> pdb=" O SER K 16 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN J 30 " --> pdb=" O VAL J 13 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL J 13 " --> pdb=" O GLN J 30 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 55 through 57 Processing sheet with id=AB4, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AB5, first strand: chain 'F' and resid 47 through 49 Processing sheet with id=AB6, first strand: chain 'J' and resid 47 through 49 Processing sheet with id=AB7, first strand: chain 'D' and resid 47 through 49 Processing sheet with id=AB8, first strand: chain 'H' and resid 47 through 49 Processing sheet with id=AB9, first strand: chain 'L' and resid 47 through 49 743 hydrogen bonds defined for protein. 2193 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.29 Time building geometry restraints manager: 4.39 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: 4948 1.34 - 1.46: 1802 1.46 - 1.57: 7740 1.57 - 1.69: 114 1.69 - 1.81: 120 Bond restraints: 14724 Sorted by residual: bond pdb=" O5' ATP H 201 " pdb=" PA ATP H 201 " ideal model delta sigma weight residual 1.579 1.615 -0.036 1.10e-02 8.26e+03 1.06e+01 bond pdb=" O5' ATP J 201 " pdb=" PA ATP J 201 " ideal model delta sigma weight residual 1.579 1.614 -0.035 1.10e-02 8.26e+03 1.03e+01 bond pdb=" O5' ATP D 201 " pdb=" PA ATP D 201 " ideal model delta sigma weight residual 1.579 1.614 -0.035 1.10e-02 8.26e+03 1.01e+01 bond pdb=" O5' ATP B 201 " pdb=" PA ATP B 201 " ideal model delta sigma weight residual 1.579 1.614 -0.035 1.10e-02 8.26e+03 1.00e+01 bond pdb=" O5' ATP F 201 " pdb=" PA ATP F 201 " ideal model delta sigma weight residual 1.579 1.614 -0.035 1.10e-02 8.26e+03 9.95e+00 ... (remaining 14719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 19597 2.57 - 5.14: 419 5.14 - 7.71: 36 7.71 - 10.29: 18 10.29 - 12.86: 6 Bond angle restraints: 20076 Sorted by residual: angle pdb=" PB ATP H 202 " pdb=" O3B ATP H 202 " pdb=" PG ATP H 202 " ideal model delta sigma weight residual 139.87 127.01 12.86 1.00e+00 1.00e+00 1.65e+02 angle pdb=" PB ATP F 202 " pdb=" O3B ATP F 202 " pdb=" PG ATP F 202 " ideal model delta sigma weight residual 139.87 127.02 12.85 1.00e+00 1.00e+00 1.65e+02 angle pdb=" PB ATP J 202 " pdb=" O3B ATP J 202 " pdb=" PG ATP J 202 " ideal model delta sigma weight residual 139.87 127.03 12.84 1.00e+00 1.00e+00 1.65e+02 angle pdb=" PB ATP L 202 " pdb=" O3B ATP L 202 " pdb=" PG ATP L 202 " ideal model delta sigma weight residual 139.87 127.04 12.83 1.00e+00 1.00e+00 1.65e+02 angle pdb=" PB ATP B 202 " pdb=" O3B ATP B 202 " pdb=" PG ATP B 202 " ideal model delta sigma weight residual 139.87 127.04 12.83 1.00e+00 1.00e+00 1.65e+02 ... (remaining 20071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 8430 17.45 - 34.90: 552 34.90 - 52.35: 336 52.35 - 69.81: 84 69.81 - 87.26: 42 Dihedral angle restraints: 9444 sinusoidal: 4332 harmonic: 5112 Sorted by residual: dihedral pdb=" C PHE L 137 " pdb=" N PHE L 137 " pdb=" CA PHE L 137 " pdb=" CB PHE L 137 " ideal model delta harmonic sigma weight residual -122.60 -114.26 -8.34 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" C PHE D 137 " pdb=" N PHE D 137 " pdb=" CA PHE D 137 " pdb=" CB PHE D 137 " ideal model delta harmonic sigma weight residual -122.60 -114.28 -8.32 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" C PHE B 137 " pdb=" N PHE B 137 " pdb=" CA PHE B 137 " pdb=" CB PHE B 137 " ideal model delta harmonic sigma weight residual -122.60 -114.31 -8.29 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 9441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1765 0.051 - 0.102: 371 0.102 - 0.154: 96 0.154 - 0.205: 28 0.205 - 0.256: 20 Chirality restraints: 2280 Sorted by residual: chirality pdb=" CA PHE D 137 " pdb=" N PHE D 137 " pdb=" C PHE D 137 " pdb=" CB PHE D 137 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA PHE L 137 " pdb=" N PHE L 137 " pdb=" C PHE L 137 " pdb=" CB PHE L 137 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PHE H 137 " pdb=" N PHE H 137 " pdb=" C PHE H 137 " pdb=" CB PHE H 137 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2277 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 141 " -0.019 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C ILE E 141 " 0.068 2.00e-02 2.50e+03 pdb=" O ILE E 141 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA E 142 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 141 " 0.019 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C ILE C 141 " -0.068 2.00e-02 2.50e+03 pdb=" O ILE C 141 " 0.026 2.00e-02 2.50e+03 pdb=" N ALA C 142 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 141 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C ILE A 141 " 0.068 2.00e-02 2.50e+03 pdb=" O ILE A 141 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA A 142 " -0.023 2.00e-02 2.50e+03 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3185 2.80 - 3.33: 13955 3.33 - 3.85: 23807 3.85 - 4.38: 29236 4.38 - 4.90: 48898 Nonbonded interactions: 119081 Sorted by model distance: nonbonded pdb=" O SER E 126 " pdb=" NH2 ARG F 123 " model vdw 2.280 3.120 nonbonded pdb=" OD2 ASP F 21 " pdb=" OG1 THR F 23 " model vdw 2.285 3.040 nonbonded pdb=" OD2 ASP J 21 " pdb=" OG1 THR J 23 " model vdw 2.285 3.040 nonbonded pdb=" OD2 ASP B 21 " pdb=" OG1 THR B 23 " model vdw 2.286 3.040 nonbonded pdb=" OD2 ASP H 21 " pdb=" OG1 THR H 23 " model vdw 2.286 3.040 ... (remaining 119076 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 34.460 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 0.038 14724 Z= 0.322 Angle : 0.848 12.857 20076 Z= 0.639 Chirality : 0.052 0.256 2280 Planarity : 0.004 0.040 2520 Dihedral : 16.905 87.257 6108 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.22), residues: 1740 helix: 1.95 (0.20), residues: 810 sheet: 0.76 (0.29), residues: 336 loop : 0.51 (0.28), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 2 PHE 0.018 0.002 PHE H 137 TYR 0.013 0.002 TYR E 128 ARG 0.003 0.000 ARG F 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.681 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 1.4791 time to fit residues: 488.7459 Evaluate side-chains 228 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.0870 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 0.0980 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN I 114 GLN B 114 GLN F 114 GLN J 114 GLN D 114 GLN H 114 GLN L 114 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14724 Z= 0.159 Angle : 0.467 4.060 20076 Z= 0.260 Chirality : 0.037 0.130 2280 Planarity : 0.004 0.025 2520 Dihedral : 16.988 87.692 2808 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.19 % Allowed : 12.43 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.22), residues: 1740 helix: 1.86 (0.19), residues: 858 sheet: 0.72 (0.27), residues: 396 loop : 0.38 (0.32), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 2 PHE 0.012 0.002 PHE J 137 TYR 0.017 0.003 TYR G 128 ARG 0.007 0.000 ARG A 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 231 time to evaluate : 1.675 Fit side-chains REVERT: I 7 ARG cc_start: 0.7117 (mpt180) cc_final: 0.6858 (mpt180) REVERT: C 99 GLU cc_start: 0.7317 (tt0) cc_final: 0.7089 (tt0) outliers start: 18 outliers final: 10 residues processed: 242 average time/residue: 1.6324 time to fit residues: 424.8837 Evaluate side-chains 202 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain L residue 45 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 0.0470 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 136 optimal weight: 0.6980 chunk 151 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN E 86 GLN E 114 GLN I 86 GLN I 114 GLN C 86 GLN G 86 GLN G 114 GLN K 86 GLN B 72 GLN H 72 GLN L 72 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14724 Z= 0.255 Angle : 0.519 4.386 20076 Z= 0.285 Chirality : 0.039 0.144 2280 Planarity : 0.004 0.027 2520 Dihedral : 16.400 87.997 2808 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.84 % Allowed : 13.69 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1740 helix: 1.62 (0.19), residues: 852 sheet: 0.40 (0.26), residues: 396 loop : 0.34 (0.32), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 2 PHE 0.015 0.002 PHE D 38 TYR 0.021 0.004 TYR G 128 ARG 0.009 0.001 ARG G 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 189 time to evaluate : 1.680 Fit side-chains REVERT: I 7 ARG cc_start: 0.7179 (mpt180) cc_final: 0.6902 (mpt180) REVERT: F 7 ARG cc_start: 0.6842 (mtp85) cc_final: 0.6564 (mmp-170) REVERT: H 72 GLN cc_start: 0.5538 (OUTLIER) cc_final: 0.4781 (mt0) REVERT: L 72 GLN cc_start: 0.5521 (OUTLIER) cc_final: 0.4796 (mt0) outliers start: 43 outliers final: 23 residues processed: 211 average time/residue: 1.5856 time to fit residues: 361.6181 Evaluate side-chains 208 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 72 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN I 114 GLN G 114 GLN ** K 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 14724 Z= 0.447 Angle : 0.635 6.754 20076 Z= 0.346 Chirality : 0.044 0.168 2280 Planarity : 0.006 0.047 2520 Dihedral : 17.521 89.894 2808 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.44 % Allowed : 14.15 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1740 helix: 1.12 (0.18), residues: 846 sheet: 0.17 (0.28), residues: 336 loop : 0.31 (0.30), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS J 2 PHE 0.020 0.003 PHE B 38 TYR 0.028 0.005 TYR G 128 ARG 0.007 0.001 ARG E 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 200 time to evaluate : 1.671 Fit side-chains REVERT: A 110 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8374 (mp) REVERT: I 7 ARG cc_start: 0.7310 (mpt180) cc_final: 0.7015 (mpt180) REVERT: C 110 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8343 (mp) REVERT: F 7 ARG cc_start: 0.6856 (mtp85) cc_final: 0.6589 (mmp-170) REVERT: F 72 GLN cc_start: 0.5716 (OUTLIER) cc_final: 0.4952 (mt0) outliers start: 52 outliers final: 31 residues processed: 221 average time/residue: 1.6540 time to fit residues: 393.8274 Evaluate side-chains 224 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 190 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 0.0170 chunk 145 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 1.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN I 114 GLN G 114 GLN J 65 ASN H 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14724 Z= 0.219 Angle : 0.502 4.067 20076 Z= 0.278 Chirality : 0.038 0.134 2280 Planarity : 0.004 0.039 2520 Dihedral : 16.509 89.832 2808 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.11 % Allowed : 15.54 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1740 helix: 1.46 (0.18), residues: 852 sheet: 0.23 (0.26), residues: 396 loop : 0.33 (0.33), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 2 PHE 0.014 0.002 PHE F 124 TYR 0.019 0.004 TYR G 128 ARG 0.005 0.000 ARG K 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 1.743 Fit side-chains REVERT: A 110 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8401 (mp) REVERT: I 7 ARG cc_start: 0.7263 (mpt180) cc_final: 0.6962 (mpt180) REVERT: C 110 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8420 (mp) REVERT: H 45 SER cc_start: 0.7810 (OUTLIER) cc_final: 0.7592 (m) outliers start: 47 outliers final: 32 residues processed: 202 average time/residue: 1.5042 time to fit residues: 328.3146 Evaluate side-chains 210 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.0770 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN I 114 GLN G 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 14724 Z= 0.395 Angle : 0.602 5.929 20076 Z= 0.328 Chirality : 0.042 0.155 2280 Planarity : 0.005 0.050 2520 Dihedral : 17.211 89.946 2808 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.44 % Allowed : 17.39 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.21), residues: 1740 helix: 1.12 (0.18), residues: 852 sheet: 0.22 (0.28), residues: 336 loop : 0.41 (0.31), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS H 2 PHE 0.018 0.003 PHE F 124 TYR 0.026 0.005 TYR G 128 ARG 0.007 0.001 ARG E 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 1.719 Fit side-chains REVERT: A 17 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6894 (ttm170) REVERT: I 7 ARG cc_start: 0.7319 (mpt180) cc_final: 0.7028 (mpt180) REVERT: C 110 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8370 (mp) REVERT: J 17 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6532 (ptt-90) outliers start: 52 outliers final: 31 residues processed: 212 average time/residue: 1.5996 time to fit residues: 365.6365 Evaluate side-chains 221 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain J residue 17 ARG Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN I 114 GLN G 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14724 Z= 0.223 Angle : 0.510 6.265 20076 Z= 0.281 Chirality : 0.038 0.174 2280 Planarity : 0.004 0.043 2520 Dihedral : 16.324 89.823 2808 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.98 % Allowed : 18.78 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.22), residues: 1740 helix: 1.41 (0.18), residues: 852 sheet: 0.21 (0.26), residues: 396 loop : 0.37 (0.34), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 2 PHE 0.013 0.002 PHE J 124 TYR 0.019 0.004 TYR G 128 ARG 0.007 0.000 ARG E 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 183 time to evaluate : 1.603 Fit side-chains REVERT: F 7 ARG cc_start: 0.6874 (mtp85) cc_final: 0.6631 (mmp-170) REVERT: J 17 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6447 (ptt-90) outliers start: 45 outliers final: 32 residues processed: 204 average time/residue: 1.6538 time to fit residues: 367.4321 Evaluate side-chains 210 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain J residue 17 ARG Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN I 114 GLN G 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14724 Z= 0.275 Angle : 0.545 8.976 20076 Z= 0.297 Chirality : 0.040 0.254 2280 Planarity : 0.005 0.045 2520 Dihedral : 16.365 89.189 2808 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.65 % Allowed : 18.98 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.22), residues: 1740 helix: 1.39 (0.18), residues: 852 sheet: 0.16 (0.26), residues: 396 loop : 0.37 (0.34), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 2 PHE 0.014 0.002 PHE F 124 TYR 0.022 0.004 TYR G 128 ARG 0.008 0.001 ARG E 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 176 time to evaluate : 1.818 Fit side-chains REVERT: A 110 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8343 (mp) REVERT: F 7 ARG cc_start: 0.6899 (mtp85) cc_final: 0.6661 (mmp-170) REVERT: J 17 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6454 (ptt-90) outliers start: 40 outliers final: 32 residues processed: 197 average time/residue: 1.6663 time to fit residues: 353.2190 Evaluate side-chains 208 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 174 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain J residue 17 ARG Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN I 114 GLN G 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14724 Z= 0.152 Angle : 0.475 7.586 20076 Z= 0.262 Chirality : 0.037 0.201 2280 Planarity : 0.004 0.032 2520 Dihedral : 15.197 89.996 2808 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.79 % Allowed : 19.71 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.22), residues: 1740 helix: 1.70 (0.19), residues: 852 sheet: 0.42 (0.26), residues: 396 loop : 0.37 (0.33), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 2 PHE 0.010 0.001 PHE H 124 TYR 0.016 0.003 TYR E 128 ARG 0.007 0.000 ARG E 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 1.704 Fit side-chains REVERT: F 7 ARG cc_start: 0.6863 (mtp85) cc_final: 0.6615 (mmp-170) outliers start: 27 outliers final: 17 residues processed: 203 average time/residue: 1.5993 time to fit residues: 349.9312 Evaluate side-chains 193 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 154 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 105 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 114 GLN G 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14724 Z= 0.154 Angle : 0.488 7.301 20076 Z= 0.266 Chirality : 0.037 0.193 2280 Planarity : 0.004 0.051 2520 Dihedral : 14.780 89.829 2808 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.46 % Allowed : 20.77 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.22), residues: 1740 helix: 1.79 (0.19), residues: 852 sheet: 0.55 (0.26), residues: 396 loop : 0.36 (0.33), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 2 PHE 0.011 0.001 PHE G 124 TYR 0.018 0.003 TYR E 128 ARG 0.007 0.000 ARG I 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 185 time to evaluate : 1.713 Fit side-chains REVERT: E 1 MET cc_start: 0.7977 (ttt) cc_final: 0.7402 (ttt) REVERT: E 21 ASP cc_start: 0.7647 (p0) cc_final: 0.7245 (p0) REVERT: K 21 ASP cc_start: 0.7653 (p0) cc_final: 0.7256 (p0) REVERT: F 7 ARG cc_start: 0.6874 (mtp85) cc_final: 0.6619 (mmp-170) outliers start: 22 outliers final: 17 residues processed: 200 average time/residue: 1.5870 time to fit residues: 342.2088 Evaluate side-chains 199 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain L residue 45 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 19 optimal weight: 0.0020 chunk 37 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 114 GLN G 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.190946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.161319 restraints weight = 13946.756| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.54 r_work: 0.3751 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14724 Z= 0.146 Angle : 0.476 7.177 20076 Z= 0.261 Chirality : 0.037 0.176 2280 Planarity : 0.004 0.037 2520 Dihedral : 14.305 89.775 2808 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.39 % Allowed : 21.16 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.22), residues: 1740 helix: 1.91 (0.19), residues: 852 sheet: 0.74 (0.27), residues: 396 loop : 0.33 (0.32), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS L 2 PHE 0.012 0.001 PHE E 124 TYR 0.017 0.002 TYR G 128 ARG 0.008 0.000 ARG G 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6024.85 seconds wall clock time: 107 minutes 39.49 seconds (6459.49 seconds total)