Starting phenix.real_space_refine on Fri Feb 16 05:42:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p37_13178/02_2024/7p37_13178_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p37_13178/02_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_13178/02_2024/7p37_13178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p37_13178/02_2024/7p37_13178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p37_13178/02_2024/7p37_13178_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p37_13178/02_2024/7p37_13178_neut_updated.pdb" } 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 Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14496 Number of models: 1 Model: "" Number of chains: 24 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: "E" 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: "I" 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: "C" 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: "G" 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: "K" 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: "F" 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: "J" 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: "D" 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: "H" 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: "L" 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: "E" 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: "I" 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: "C" 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: "G" 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: "K" 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} Chain: "F" 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: "J" 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: "D" 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: "H" 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: "L" 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 1169 SG CYS E 3 105.958 33.851 29.058 1.00 41.20 S ATOM 1193 SG CYS E 6 108.856 32.200 27.188 1.00 45.02 S ATOM 1399 SG CYS E 31 105.372 31.546 26.037 1.00 41.51 S ATOM 1420 SG CYS E 34 106.487 30.083 29.327 1.00 44.03 S ATOM 2314 SG CYS I 3 62.979 103.538 29.082 1.00 41.20 S ATOM 2338 SG CYS I 6 62.966 106.872 27.210 1.00 45.02 S ATOM 2544 SG CYS I 31 65.273 104.177 26.063 1.00 41.51 S ATOM 2565 SG CYS I 34 65.980 105.876 29.354 1.00 44.03 S ATOM 3459 SG CYS C 3 104.568 31.439 59.369 1.00 41.20 S ATOM 3483 SG CYS C 6 107.450 29.761 61.241 1.00 45.02 S ATOM 3689 SG CYS C 31 106.273 33.108 62.384 1.00 41.51 S ATOM 3710 SG CYS C 34 108.095 32.865 59.092 1.00 44.03 S ATOM 4604 SG CYS G 3 65.627 103.526 59.350 1.00 41.20 S ATOM 4628 SG CYS G 6 65.634 106.862 61.220 1.00 45.02 S ATOM 4834 SG CYS G 31 63.332 104.164 62.368 1.00 41.51 S ATOM 4855 SG CYS G 34 62.622 105.859 59.076 1.00 44.03 S ATOM 5749 SG CYS K 3 22.709 33.799 59.363 1.00 41.20 S ATOM 5773 SG CYS K 6 19.814 32.142 61.231 1.00 45.02 S ATOM 5979 SG CYS K 31 23.300 31.492 62.381 1.00 41.51 S ATOM 6000 SG CYS K 34 22.187 30.031 59.089 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 ATOM 8039 SG CYS F 3 71.271 71.487 65.321 1.00 11.76 S ATOM 8063 SG CYS F 6 69.425 68.154 65.684 1.00 12.15 S ATOM 8269 SG CYS F 31 68.325 71.093 67.715 1.00 13.45 S ATOM 8290 SG CYS F 34 71.652 69.406 68.488 1.00 13.85 S ATOM 9184 SG CYS J 3 47.633 54.690 65.354 1.00 11.76 S ATOM 9208 SG CYS J 6 51.443 54.754 65.721 1.00 12.15 S ATOM 9414 SG CYS J 31 49.444 52.332 67.747 1.00 13.45 S ATOM 9435 SG CYS J 34 49.244 56.056 68.523 1.00 13.85 S ATOM 10329 SG CYS D 3 54.682 42.651 23.104 1.00 11.76 S ATOM 10353 SG CYS D 6 56.649 45.914 22.740 1.00 12.15 S ATOM 10559 SG CYS D 31 53.555 45.398 20.707 1.00 13.45 S ATOM 10580 SG CYS D 34 56.678 43.357 19.939 1.00 13.85 S ATOM 11474 SG CYS H 3 80.960 54.720 23.114 1.00 11.76 S ATOM 11498 SG CYS H 6 77.150 54.780 22.754 1.00 12.15 S ATOM 11704 SG CYS H 31 79.148 52.361 20.723 1.00 13.45 S ATOM 11725 SG CYS H 34 79.343 56.086 19.949 1.00 13.85 S ATOM 12619 SG CYS L 3 57.366 71.463 23.138 1.00 11.76 S ATOM 12643 SG CYS L 6 59.210 68.129 22.778 1.00 12.15 S ATOM 12849 SG CYS L 31 60.315 71.067 20.748 1.00 13.45 S ATOM 12870 SG CYS L 34 56.989 69.382 19.971 1.00 13.85 S Time building chain proxies: 8.29, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 6.18 Conformation dependent library (CDL) restraints added in 2.7 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... running ksdssp... Secondary structure from input PDB file: 60 helices and 24 sheets defined 45.9% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 78 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 116 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 118 through 128 removed outlier: 4.376A pdb=" N VAL A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 146 Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 78 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 116 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 118 through 128 removed outlier: 4.377A pdb=" N VAL E 127 " --> pdb=" O ARG E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 146 Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 78 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 116 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 118 through 128 removed outlier: 4.376A pdb=" N VAL I 127 " --> pdb=" O ARG I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 146 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 78 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 116 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 118 through 128 removed outlier: 4.376A pdb=" N VAL C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 146 Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 78 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 116 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 118 through 128 removed outlier: 4.377A pdb=" N VAL G 127 " --> pdb=" O ARG G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 146 Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 78 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 116 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 118 through 128 removed outlier: 4.377A pdb=" N VAL K 127 " --> pdb=" O ARG K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 146 Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.647A pdb=" N ILE B 109 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix removed outlier: 3.894A pdb=" N GLU B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 128 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 134 through 146 Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 78 through 95 Processing helix chain 'F' and resid 102 through 116 removed outlier: 3.647A pdb=" N ILE F 109 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU F 110 " --> pdb=" O GLY F 106 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Proline residue: F 112 - end of helix removed outlier: 3.894A pdb=" N GLU F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 128 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 134 through 146 Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 78 through 95 Processing helix chain 'J' and resid 102 through 116 removed outlier: 3.647A pdb=" N ILE J 109 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU J 110 " --> pdb=" O GLY J 106 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY J 111 " --> pdb=" O LEU J 107 " (cutoff:3.500A) Proline residue: J 112 - end of helix removed outlier: 3.895A pdb=" N GLU J 115 " --> pdb=" O GLY J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 128 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 134 through 146 Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 78 through 95 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.647A pdb=" N ILE D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Proline residue: D 112 - end of helix removed outlier: 3.895A pdb=" N GLU D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 128 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 134 through 146 Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 78 through 95 Processing helix chain 'H' and resid 102 through 116 removed outlier: 3.647A pdb=" N ILE H 109 " --> pdb=" O VAL H 105 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY H 111 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Proline residue: H 112 - end of helix removed outlier: 3.895A pdb=" N GLU H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 128 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 134 through 146 Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 78 through 95 Processing helix chain 'L' and resid 102 through 116 removed outlier: 3.646A pdb=" N ILE L 109 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU L 110 " --> pdb=" O GLY L 106 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY L 111 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Proline residue: L 112 - end of helix removed outlier: 3.895A pdb=" N GLU L 115 " --> pdb=" O GLY L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 128 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 134 through 146 Processing sheet with id= A, first strand: chain 'A' and resid 37 through 42 removed outlier: 6.355A pdb=" N GLN A 30 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL A 13 " --> pdb=" O GLN A 30 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 55 through 57 Processing sheet with id= C, first strand: chain 'E' and resid 37 through 42 removed outlier: 6.356A pdb=" N GLN E 30 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL E 13 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 55 through 57 Processing sheet with id= E, first strand: chain 'I' and resid 37 through 42 removed outlier: 6.355A pdb=" N GLN I 30 " --> pdb=" O VAL I 13 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL I 13 " --> pdb=" O GLN I 30 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 55 through 57 Processing sheet with id= G, first strand: chain 'C' and resid 37 through 42 removed outlier: 6.355A pdb=" N GLN C 30 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL C 13 " --> pdb=" O GLN C 30 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 55 through 57 Processing sheet with id= I, first strand: chain 'G' and resid 37 through 42 removed outlier: 6.356A pdb=" N GLN G 30 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL G 13 " --> pdb=" O GLN G 30 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 55 through 57 Processing sheet with id= K, first strand: chain 'K' and resid 37 through 42 removed outlier: 6.356A pdb=" N GLN K 30 " --> pdb=" O VAL K 13 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL K 13 " --> pdb=" O GLN K 30 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 55 through 57 Processing sheet with id= M, first strand: chain 'B' and resid 37 through 43 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= N, first strand: chain 'B' and resid 47 through 49 Processing sheet with id= O, first strand: chain 'F' and resid 37 through 43 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= P, first strand: chain 'F' and resid 47 through 49 Processing sheet with id= Q, first strand: chain 'J' and resid 37 through 43 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= R, first strand: chain 'J' and resid 47 through 49 Processing sheet with id= S, first strand: chain 'D' and resid 37 through 43 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= T, first strand: chain 'D' and resid 47 through 49 Processing sheet with id= U, first strand: chain 'H' and resid 37 through 43 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= V, first strand: chain 'H' and resid 47 through 49 Processing sheet with id= W, first strand: chain 'L' and resid 37 through 43 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= X, first strand: chain 'L' and resid 47 through 49 630 hydrogen bonds defined for protein. 1872 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: 4.39 Time building geometry restraints manager: 6.69 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: 98.94 - 106.64: 648 106.64 - 114.34: 8734 114.34 - 122.03: 7769 122.03 - 129.73: 2823 129.73 - 137.43: 102 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: 3197 2.80 - 3.33: 14045 3.33 - 3.85: 23919 3.85 - 4.38: 29419 4.38 - 4.90: 48953 Nonbonded interactions: 119533 Sorted by model distance: nonbonded pdb=" O SER E 126 " pdb=" NH2 ARG F 123 " model vdw 2.280 2.520 nonbonded pdb=" OD2 ASP F 21 " pdb=" OG1 THR F 23 " model vdw 2.285 2.440 nonbonded pdb=" OD2 ASP J 21 " pdb=" OG1 THR J 23 " model vdw 2.285 2.440 nonbonded pdb=" OD2 ASP B 21 " pdb=" OG1 THR B 23 " model vdw 2.286 2.440 nonbonded pdb=" OD2 ASP H 21 " pdb=" OG1 THR H 23 " model vdw 2.286 2.440 ... (remaining 119528 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.740 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: 6.580 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 44.540 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.130 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.170 ------------------------------------------------------------------------------- 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 : 1.626 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 1.4300 time to fit residues: 473.0506 Evaluate side-chains 228 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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: 3.9990 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 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: 0.4980 chunk 152 optimal weight: 0.8980 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 K 86 GLN B 72 GLN F 114 GLN J 114 GLN H 114 GLN L 114 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14724 Z= 0.290 Angle : 0.527 5.378 20076 Z= 0.290 Chirality : 0.040 0.150 2280 Planarity : 0.005 0.029 2520 Dihedral : 16.931 86.768 2808 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.45 % Allowed : 11.31 % Favored : 86.24 % 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: 1.14 (0.21), residues: 1740 helix: 1.39 (0.19), residues: 846 sheet: 0.39 (0.26), residues: 396 loop : 0.17 (0.31), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 2 PHE 0.016 0.002 PHE J 137 TYR 0.022 0.004 TYR G 128 ARG 0.005 0.001 ARG I 36 *********************** 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 240 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 1.761 Fit side-chains REVERT: E 7 ARG cc_start: 0.7267 (mpt180) cc_final: 0.7056 (mpt180) REVERT: I 7 ARG cc_start: 0.7134 (mpt180) cc_final: 0.6786 (mpt180) REVERT: F 7 ARG cc_start: 0.6849 (mtp85) cc_final: 0.6536 (mmp-170) REVERT: H 17 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6859 (ptt-90) outliers start: 37 outliers final: 28 residues processed: 226 average time/residue: 1.5612 time to fit residues: 380.4883 Evaluate side-chains 208 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain K residue 114 GLN Chi-restraints excluded: chain B residue 11 SER 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 11 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain D residue 11 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 11 SER 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 11 SER Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.7464 moved from start: 0.2284 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= 0.155 Angle : 0.443 4.100 20076 Z= 0.246 Chirality : 0.037 0.132 2280 Planarity : 0.004 0.034 2520 Dihedral : 15.638 88.974 2808 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.45 % Allowed : 13.43 % Favored : 84.13 % 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 (0.22), residues: 1740 helix: 1.60 (0.19), residues: 846 sheet: 0.48 (0.26), residues: 396 loop : 0.32 (0.31), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 2 PHE 0.010 0.001 PHE L 38 TYR 0.016 0.003 TYR G 128 ARG 0.008 0.000 ARG A 12 *********************** 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 217 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 1.603 Fit side-chains REVERT: A 110 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8443 (mp) REVERT: I 7 ARG cc_start: 0.7109 (mpt180) cc_final: 0.6750 (mpt180) REVERT: I 21 ASP cc_start: 0.7452 (p0) cc_final: 0.7232 (p0) REVERT: C 110 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8440 (mp) REVERT: F 7 ARG cc_start: 0.6805 (mtp85) cc_final: 0.6491 (mmp-170) outliers start: 37 outliers final: 18 residues processed: 203 average time/residue: 1.4028 time to fit residues: 309.9536 Evaluate side-chains 190 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain I residue 49 VAL 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 B residue 11 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 45 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.0870 chunk 114 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN ** I 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 GLN G 114 GLN ** K 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN D 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 14724 Z= 0.468 Angle : 0.636 6.993 20076 Z= 0.345 Chirality : 0.044 0.171 2280 Planarity : 0.006 0.046 2520 Dihedral : 17.131 89.771 2808 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.77 % Allowed : 13.43 % Favored : 82.80 % 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: 0.70 (0.21), residues: 1740 helix: 0.91 (0.18), residues: 834 sheet: -0.08 (0.25), residues: 396 loop : 0.49 (0.33), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS J 2 PHE 0.019 0.003 PHE F 124 TYR 0.026 0.005 TYR G 128 ARG 0.008 0.001 ARG C 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 231 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 174 time to evaluate : 1.761 Fit side-chains REVERT: A 7 ARG cc_start: 0.7185 (mpt180) cc_final: 0.6977 (mpt180) REVERT: I 7 ARG cc_start: 0.7201 (mpt180) cc_final: 0.6865 (mpt180) REVERT: I 21 ASP cc_start: 0.7539 (p0) cc_final: 0.7326 (p0) REVERT: F 7 ARG cc_start: 0.6879 (mtp85) cc_final: 0.6602 (mmp-170) REVERT: H 17 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6916 (ptt-90) outliers start: 57 outliers final: 42 residues processed: 211 average time/residue: 1.5753 time to fit residues: 358.8857 Evaluate side-chains 213 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 170 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 49 VAL 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 49 VAL Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain B residue 11 SER 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 11 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain D residue 11 SER 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 11 SER 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 H residue 101 THR Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 54 VAL 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: 0.8980 chunk 92 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.7513 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14724 Z= 0.168 Angle : 0.459 5.517 20076 Z= 0.255 Chirality : 0.037 0.169 2280 Planarity : 0.004 0.035 2520 Dihedral : 15.523 87.707 2808 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.38 % Allowed : 15.74 % Favored : 81.88 % 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: 1.15 (0.22), residues: 1740 helix: 1.36 (0.19), residues: 846 sheet: 0.13 (0.25), residues: 408 loop : 0.52 (0.33), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 2 PHE 0.011 0.001 PHE H 124 TYR 0.017 0.003 TYR G 128 ARG 0.004 0.000 ARG K 36 *********************** 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 215 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 1.739 Fit side-chains REVERT: A 12 ARG cc_start: 0.7450 (pmt-80) cc_final: 0.7226 (pmt170) REVERT: F 7 ARG cc_start: 0.6861 (mtp85) cc_final: 0.6554 (mmp-170) outliers start: 36 outliers final: 24 residues processed: 198 average time/residue: 1.5596 time to fit residues: 334.1525 Evaluate side-chains 197 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG 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 49 VAL 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 J residue 61 THR Chi-restraints excluded: chain J residue 101 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 45 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 101 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: 0.7980 chunk 146 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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: 0.7597 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14724 Z= 0.362 Angle : 0.572 8.028 20076 Z= 0.310 Chirality : 0.041 0.218 2280 Planarity : 0.005 0.049 2520 Dihedral : 16.299 89.897 2808 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.91 % Allowed : 15.61 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1740 helix: 1.03 (0.18), residues: 846 sheet: 0.02 (0.26), residues: 396 loop : 0.40 (0.33), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS H 2 PHE 0.017 0.003 PHE L 124 TYR 0.023 0.004 TYR G 128 ARG 0.004 0.001 ARG L 51 *********************** 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 218 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 174 time to evaluate : 1.642 Fit side-chains REVERT: I 7 ARG cc_start: 0.7210 (mpt180) cc_final: 0.6868 (mpt180) REVERT: G 21 ASP cc_start: 0.7670 (p0) cc_final: 0.7379 (p0) REVERT: F 7 ARG cc_start: 0.6906 (mtp85) cc_final: 0.6613 (mmp-170) REVERT: H 17 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6864 (ptt-90) outliers start: 44 outliers final: 32 residues processed: 200 average time/residue: 1.6258 time to fit residues: 350.1524 Evaluate side-chains 207 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain C residue 49 VAL 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 11 SER 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 11 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain D residue 11 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 11 SER 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 H residue 101 THR Chi-restraints excluded: chain L residue 11 SER 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: 5.9990 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 161 optimal weight: 0.4980 chunk 101 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.7539 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14724 Z= 0.207 Angle : 0.497 11.121 20076 Z= 0.270 Chirality : 0.038 0.278 2280 Planarity : 0.004 0.043 2520 Dihedral : 15.468 88.211 2808 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.78 % Allowed : 16.93 % Favored : 80.29 % 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: 1.09 (0.22), residues: 1740 helix: 1.28 (0.19), residues: 846 sheet: 0.08 (0.25), residues: 408 loop : 0.59 (0.33), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 2 PHE 0.012 0.002 PHE H 124 TYR 0.018 0.003 TYR G 128 ARG 0.004 0.000 ARG C 36 *********************** 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 214 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 1.695 Fit side-chains REVERT: I 12 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7272 (ppt90) REVERT: G 12 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7271 (ppt90) REVERT: G 21 ASP cc_start: 0.7538 (p0) cc_final: 0.7260 (p0) REVERT: J 17 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6556 (ptt-90) outliers start: 42 outliers final: 33 residues processed: 196 average time/residue: 1.5172 time to fit residues: 322.0290 Evaluate side-chains 202 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain B residue 11 SER 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 11 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain J residue 17 ARG Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 101 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 11 SER Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain L residue 11 SER 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: 7.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.7544 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14724 Z= 0.220 Angle : 0.500 9.362 20076 Z= 0.272 Chirality : 0.038 0.236 2280 Planarity : 0.004 0.043 2520 Dihedral : 15.207 88.719 2808 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.84 % Allowed : 17.53 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.22), residues: 1740 helix: 1.39 (0.19), residues: 840 sheet: 0.14 (0.26), residues: 408 loop : 0.52 (0.33), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 2 PHE 0.012 0.002 PHE H 124 TYR 0.019 0.004 TYR G 128 ARG 0.005 0.000 ARG F 7 *********************** 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 210 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 1.706 Fit side-chains REVERT: F 7 ARG cc_start: 0.6860 (mtp85) cc_final: 0.6612 (mmp-170) REVERT: J 45 SER cc_start: 0.7709 (OUTLIER) cc_final: 0.7458 (m) outliers start: 43 outliers final: 38 residues processed: 198 average time/residue: 1.5090 time to fit residues: 323.4548 Evaluate side-chains 203 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 164 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 40 THR 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 40 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain B residue 11 SER 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 11 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 101 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 11 SER Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain L residue 11 SER 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: 3.9990 chunk 141 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 0.0870 chunk 118 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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: 0.7543 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14724 Z= 0.222 Angle : 0.504 8.969 20076 Z= 0.275 Chirality : 0.038 0.213 2280 Planarity : 0.004 0.043 2520 Dihedral : 15.154 89.346 2808 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.84 % Allowed : 17.59 % Favored : 79.56 % 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: 1.40 (0.19), residues: 840 sheet: 0.15 (0.26), residues: 408 loop : 0.50 (0.33), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 2 PHE 0.012 0.002 PHE B 38 TYR 0.019 0.004 TYR G 128 ARG 0.009 0.000 ARG I 129 *********************** 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 211 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 168 time to evaluate : 1.569 Fit side-chains REVERT: F 7 ARG cc_start: 0.6883 (mtp85) cc_final: 0.6617 (mmp-170) outliers start: 43 outliers final: 40 residues processed: 199 average time/residue: 1.4667 time to fit residues: 316.5137 Evaluate side-chains 205 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 40 THR 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 40 THR 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 49 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain B residue 11 SER 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 11 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain D residue 11 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 11 SER Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L 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: 2.9990 chunk 75 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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: 0.3056 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= 0.188 Angle : 0.486 8.149 20076 Z= 0.266 Chirality : 0.037 0.196 2280 Planarity : 0.004 0.040 2520 Dihedral : 14.843 89.130 2808 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.51 % Allowed : 18.19 % Favored : 79.30 % 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: 1.28 (0.22), residues: 1740 helix: 1.50 (0.19), residues: 840 sheet: 0.20 (0.26), residues: 408 loop : 0.53 (0.33), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 2 PHE 0.011 0.001 PHE H 124 TYR 0.017 0.003 TYR G 128 ARG 0.004 0.000 ARG F 7 ********************** 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 208 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 170 time to evaluate : 1.518 Fit side-chains REVERT: F 7 ARG cc_start: 0.6870 (mtp85) cc_final: 0.6623 (mmp-170) REVERT: J 45 SER cc_start: 0.7698 (OUTLIER) cc_final: 0.7448 (m) outliers start: 38 outliers final: 31 residues processed: 193 average time/residue: 1.5009 time to fit residues: 316.5586 Evaluate side-chains 197 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 40 THR 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 40 THR 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 J residue 61 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain D residue 11 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 11 SER Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 19 optimal weight: 0.0060 chunk 37 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 137 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 114 GLN H 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.188364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.158249 restraints weight = 13984.210| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.56 r_work: 0.3724 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3042 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= 0.135 Angle : 0.449 7.505 20076 Z= 0.247 Chirality : 0.036 0.147 2280 Planarity : 0.003 0.030 2520 Dihedral : 14.104 89.580 2808 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.46 % Allowed : 19.38 % 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: 1.46 (0.22), residues: 1740 helix: 1.66 (0.19), residues: 852 sheet: 0.38 (0.26), residues: 408 loop : 0.44 (0.33), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 2 PHE 0.008 0.001 PHE H 124 TYR 0.014 0.002 TYR G 128 ARG 0.005 0.000 ARG K 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5752.33 seconds wall clock time: 102 minutes 58.89 seconds (6178.89 seconds total)