Starting phenix.real_space_refine on Sat Feb 17 18:16:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/02_2024/6ytv_10924.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/02_2024/6ytv_10924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/02_2024/6ytv_10924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/02_2024/6ytv_10924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/02_2024/6ytv_10924.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/02_2024/6ytv_10924.pdb" } resolution = 4.39 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= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 12760 2.51 5 N 3250 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 73": "NH1" <-> "NH2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B ARG 282": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C ARG 282": "NH1" <-> "NH2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D ARG 282": "NH1" <-> "NH2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E ARG 282": "NH1" <-> "NH2" Residue "F ARG 73": "NH1" <-> "NH2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F ARG 144": "NH1" <-> "NH2" Residue "F ARG 197": "NH1" <-> "NH2" Residue "F GLU 256": "OE1" <-> "OE2" Residue "F ARG 282": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G ARG 144": "NH1" <-> "NH2" Residue "G ARG 197": "NH1" <-> "NH2" Residue "G GLU 256": "OE1" <-> "OE2" Residue "G ARG 282": "NH1" <-> "NH2" Residue "H ARG 73": "NH1" <-> "NH2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H ARG 144": "NH1" <-> "NH2" Residue "H ARG 197": "NH1" <-> "NH2" Residue "H GLU 256": "OE1" <-> "OE2" Residue "H ARG 282": "NH1" <-> "NH2" Residue "I ARG 73": "NH1" <-> "NH2" Residue "I GLU 125": "OE1" <-> "OE2" Residue "I ARG 144": "NH1" <-> "NH2" Residue "I ARG 197": "NH1" <-> "NH2" Residue "I GLU 256": "OE1" <-> "OE2" Residue "I ARG 282": "NH1" <-> "NH2" Residue "J ARG 73": "NH1" <-> "NH2" Residue "J GLU 125": "OE1" <-> "OE2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "J ARG 197": "NH1" <-> "NH2" Residue "J GLU 256": "OE1" <-> "OE2" Residue "J ARG 282": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19560 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "B" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "C" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "E" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "F" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "G" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "H" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "I" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "J" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Time building chain proxies: 10.41, per 1000 atoms: 0.53 Number of scatterers: 19560 At special positions: 0 Unit cell: (140.7, 138.02, 104.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 3420 8.00 N 3250 7.00 C 12760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 146 " distance=2.04 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 146 " distance=2.04 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 146 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 155 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 146 " distance=2.04 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 155 " distance=2.04 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 146 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 155 " distance=2.04 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 146 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 155 " distance=2.04 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 146 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 155 " distance=2.04 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 146 " distance=2.04 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 155 " distance=2.04 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 146 " distance=2.04 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 126 " distance=2.03 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 155 " distance=2.04 Simple disulfide: pdb=" SG CYS J 139 " - pdb=" SG CYS J 146 " distance=2.04 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: 7.62 Conformation dependent library (CDL) restraints added in 3.4 seconds 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 20 through 37 Processing helix chain 'A' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR A 51 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.781A pdb=" N SER A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 160 through 199 removed outlier: 4.490A pdb=" N LYS A 168 " --> pdb=" O GLN A 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 Processing helix chain 'B' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR B 51 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 3.782A pdb=" N SER B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 79 removed outlier: 4.205A pdb=" N TRP B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'B' and resid 160 through 199 removed outlier: 4.490A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 186 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 37 Processing helix chain 'C' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR C 51 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 55 " --> pdb=" O TYR C 51 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.782A pdb=" N SER C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 79 removed outlier: 4.205A pdb=" N TRP C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.734A pdb=" N ALA C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 153 No H-bonds generated for 'chain 'C' and resid 151 through 153' Processing helix chain 'C' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 274 through 279 removed outlier: 3.594A pdb=" N LYS C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 37 Processing helix chain 'D' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR D 51 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 3.781A pdb=" N SER D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP D 75 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 121 removed outlier: 5.548A pdb=" N ALA D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 153 No H-bonds generated for 'chain 'D' and resid 151 through 153' Processing helix chain 'D' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 243 removed outlier: 3.880A pdb=" N PHE D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS D 278 " --> pdb=" O SER D 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 37 Processing helix chain 'E' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR E 51 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Proline residue: E 59 - end of helix removed outlier: 3.781A pdb=" N SER E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 removed outlier: 5.548A pdb=" N ALA E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 131 through 139 removed outlier: 3.732A pdb=" N ALA E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 153 No H-bonds generated for 'chain 'E' and resid 151 through 153' Processing helix chain 'E' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS E 168 " --> pdb=" O GLN E 164 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP E 169 " --> pdb=" O ASP E 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 186 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE E 209 " --> pdb=" O LEU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 260 Processing helix chain 'E' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS E 278 " --> pdb=" O SER E 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 37 Processing helix chain 'F' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR F 51 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Proline residue: F 59 - end of helix removed outlier: 3.781A pdb=" N SER F 71 " --> pdb=" O GLY F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 79 removed outlier: 4.205A pdb=" N TRP F 75 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU F 77 " --> pdb=" O ARG F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA F 135 " --> pdb=" O SER F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 150 removed outlier: 4.127A pdb=" N GLU F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 153 No H-bonds generated for 'chain 'F' and resid 151 through 153' Processing helix chain 'F' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS F 168 " --> pdb=" O GLN F 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 186 " --> pdb=" O ILE F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE F 209 " --> pdb=" O LEU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 260 Processing helix chain 'F' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS F 278 " --> pdb=" O SER F 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 37 Processing helix chain 'G' and resid 47 through 71 removed outlier: 3.834A pdb=" N TYR G 51 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Proline residue: G 59 - end of helix removed outlier: 3.781A pdb=" N SER G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA G 109 " --> pdb=" O ALA G 105 " (cutoff:3.500A) Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 121 through 127 Processing helix chain 'G' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA G 135 " --> pdb=" O SER G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 153 No H-bonds generated for 'chain 'G' and resid 151 through 153' Processing helix chain 'G' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS G 168 " --> pdb=" O GLN G 164 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP G 169 " --> pdb=" O ASP G 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE G 186 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE G 209 " --> pdb=" O LEU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 260 Processing helix chain 'G' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS G 278 " --> pdb=" O SER G 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 37 Processing helix chain 'H' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR H 51 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Proline residue: H 59 - end of helix removed outlier: 3.781A pdb=" N SER H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU H 77 " --> pdb=" O ARG H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 153 No H-bonds generated for 'chain 'H' and resid 151 through 153' Processing helix chain 'H' and resid 160 through 199 removed outlier: 4.490A pdb=" N LYS H 168 " --> pdb=" O GLN H 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP H 169 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE H 186 " --> pdb=" O ILE H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 243 removed outlier: 3.880A pdb=" N PHE H 209 " --> pdb=" O LEU H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 260 Processing helix chain 'H' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS H 278 " --> pdb=" O SER H 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 37 Processing helix chain 'I' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR I 51 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE I 55 " --> pdb=" O TYR I 51 " (cutoff:3.500A) Proline residue: I 59 - end of helix removed outlier: 3.781A pdb=" N SER I 71 " --> pdb=" O GLY I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU I 77 " --> pdb=" O ARG I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 131 through 139 removed outlier: 3.734A pdb=" N ALA I 135 " --> pdb=" O SER I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 153 No H-bonds generated for 'chain 'I' and resid 151 through 153' Processing helix chain 'I' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS I 168 " --> pdb=" O GLN I 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP I 169 " --> pdb=" O ASP I 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE I 186 " --> pdb=" O ILE I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 243 removed outlier: 3.880A pdb=" N PHE I 209 " --> pdb=" O LEU I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 260 Processing helix chain 'I' and resid 274 through 279 removed outlier: 3.594A pdb=" N LYS I 278 " --> pdb=" O SER I 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 37 Processing helix chain 'J' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR J 51 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) Proline residue: J 59 - end of helix removed outlier: 3.781A pdb=" N SER J 71 " --> pdb=" O GLY J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 79 removed outlier: 4.205A pdb=" N TRP J 75 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU J 77 " --> pdb=" O ARG J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 121 through 127 Processing helix chain 'J' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA J 135 " --> pdb=" O SER J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 153 No H-bonds generated for 'chain 'J' and resid 151 through 153' Processing helix chain 'J' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS J 168 " --> pdb=" O GLN J 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP J 169 " --> pdb=" O ASP J 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE J 186 " --> pdb=" O ILE J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE J 209 " --> pdb=" O LEU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 260 Processing helix chain 'J' and resid 274 through 279 removed outlier: 3.594A pdb=" N LYS J 278 " --> pdb=" O SER J 274 " (cutoff:3.500A) 1311 hydrogen bonds defined for protein. 3933 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: 5.08 Time building geometry restraints manager: 8.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6040 1.34 - 1.46: 4782 1.46 - 1.58: 9038 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 20010 Sorted by residual: bond pdb=" C LEU I 150 " pdb=" N PRO I 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.06e-01 bond pdb=" C LEU B 150 " pdb=" N PRO B 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.98e-01 bond pdb=" C LEU J 150 " pdb=" N PRO J 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.90e-01 bond pdb=" C LEU H 150 " pdb=" N PRO H 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.89e-01 bond pdb=" C LEU E 150 " pdb=" N PRO E 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.79e-01 ... (remaining 20005 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.40: 666 107.40 - 114.07: 11494 114.07 - 120.74: 9025 120.74 - 127.41: 5795 127.41 - 134.08: 220 Bond angle restraints: 27200 Sorted by residual: angle pdb=" CA LEU A 190 " pdb=" CB LEU A 190 " pdb=" CG LEU A 190 " ideal model delta sigma weight residual 116.30 106.69 9.61 3.50e+00 8.16e-02 7.54e+00 angle pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " pdb=" CG LEU B 190 " ideal model delta sigma weight residual 116.30 106.69 9.61 3.50e+00 8.16e-02 7.54e+00 angle pdb=" CA LEU J 190 " pdb=" CB LEU J 190 " pdb=" CG LEU J 190 " ideal model delta sigma weight residual 116.30 106.70 9.60 3.50e+00 8.16e-02 7.52e+00 angle pdb=" CA LEU D 190 " pdb=" CB LEU D 190 " pdb=" CG LEU D 190 " ideal model delta sigma weight residual 116.30 106.71 9.59 3.50e+00 8.16e-02 7.51e+00 angle pdb=" CA LEU G 190 " pdb=" CB LEU G 190 " pdb=" CG LEU G 190 " ideal model delta sigma weight residual 116.30 106.71 9.59 3.50e+00 8.16e-02 7.51e+00 ... (remaining 27195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 10562 17.73 - 35.46: 1128 35.46 - 53.19: 200 53.19 - 70.93: 20 70.93 - 88.66: 20 Dihedral angle restraints: 11930 sinusoidal: 4570 harmonic: 7360 Sorted by residual: dihedral pdb=" CB CYS E 43 " pdb=" SG CYS E 43 " pdb=" SG CYS E 155 " pdb=" CB CYS E 155 " ideal model delta sinusoidal sigma weight residual -86.00 -20.20 -65.80 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS J 43 " pdb=" SG CYS J 43 " pdb=" SG CYS J 155 " pdb=" CB CYS J 155 " ideal model delta sinusoidal sigma weight residual -86.00 -20.21 -65.79 1 1.00e+01 1.00e-02 5.66e+01 dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 155 " pdb=" CB CYS C 155 " ideal model delta sinusoidal sigma weight residual -86.00 -20.22 -65.78 1 1.00e+01 1.00e-02 5.66e+01 ... (remaining 11927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2561 0.051 - 0.102: 557 0.102 - 0.153: 42 0.153 - 0.203: 0 0.203 - 0.254: 10 Chirality restraints: 3170 Sorted by residual: chirality pdb=" CG LEU C 190 " pdb=" CB LEU C 190 " pdb=" CD1 LEU C 190 " pdb=" CD2 LEU C 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU E 190 " pdb=" CB LEU E 190 " pdb=" CD1 LEU E 190 " pdb=" CD2 LEU E 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU G 190 " pdb=" CB LEU G 190 " pdb=" CD1 LEU G 190 " pdb=" CD2 LEU G 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 3167 not shown) Planarity restraints: 3350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 173 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C GLN F 173 " 0.033 2.00e-02 2.50e+03 pdb=" O GLN F 173 " -0.012 2.00e-02 2.50e+03 pdb=" N SER F 174 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 173 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.59e+00 pdb=" C GLN H 173 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN H 173 " 0.012 2.00e-02 2.50e+03 pdb=" N SER H 174 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 173 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C GLN A 173 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN A 173 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 174 " 0.011 2.00e-02 2.50e+03 ... (remaining 3347 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1407 2.73 - 3.27: 22326 3.27 - 3.81: 31951 3.81 - 4.36: 34735 4.36 - 4.90: 57513 Nonbonded interactions: 147932 Sorted by model distance: nonbonded pdb=" O PRO C 42 " pdb=" ND2 ASN C 48 " model vdw 2.183 2.520 nonbonded pdb=" O PRO I 42 " pdb=" ND2 ASN I 48 " model vdw 2.184 2.520 nonbonded pdb=" O PRO D 42 " pdb=" ND2 ASN D 48 " model vdw 2.184 2.520 nonbonded pdb=" O PRO G 42 " pdb=" ND2 ASN G 48 " model vdw 2.184 2.520 nonbonded pdb=" O PRO H 42 " pdb=" ND2 ASN H 48 " model vdw 2.184 2.520 ... (remaining 147927 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.900 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 48.780 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20010 Z= 0.275 Angle : 0.779 9.611 27200 Z= 0.413 Chirality : 0.043 0.254 3170 Planarity : 0.005 0.031 3350 Dihedral : 14.562 88.658 7080 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.05 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % 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: -2.08 (0.16), residues: 2480 helix: -0.63 (0.11), residues: 1880 sheet: None (None), residues: 0 loop : -3.55 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP J 113 HIS 0.004 0.002 HIS H 277 PHE 0.018 0.002 PHE I 266 TYR 0.014 0.002 TYR A 68 ARG 0.002 0.001 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 785 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7016 (ttt-90) cc_final: 0.6343 (tpt170) REVERT: A 111 LEU cc_start: 0.8362 (mt) cc_final: 0.8116 (mt) REVERT: A 197 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7566 (mtt90) REVERT: A 215 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8336 (tp30) REVERT: A 231 GLU cc_start: 0.8624 (pp20) cc_final: 0.8249 (pp20) REVERT: A 234 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7543 (ttpt) REVERT: A 235 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8335 (tm-30) REVERT: A 236 ASN cc_start: 0.8036 (m110) cc_final: 0.7560 (m110) REVERT: A 256 GLU cc_start: 0.8374 (tt0) cc_final: 0.8047 (tt0) REVERT: B 32 ARG cc_start: 0.6573 (ttt-90) cc_final: 0.6160 (tpt170) REVERT: B 73 ARG cc_start: 0.7934 (ttp-110) cc_final: 0.7691 (tpp-160) REVERT: B 197 ARG cc_start: 0.7858 (mtt-85) cc_final: 0.7532 (mtt90) REVERT: B 215 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8322 (tm-30) REVERT: B 231 GLU cc_start: 0.8658 (pp20) cc_final: 0.8230 (pp20) REVERT: B 234 LYS cc_start: 0.8450 (ttmt) cc_final: 0.7705 (ttpt) REVERT: B 235 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7975 (tm-30) REVERT: B 236 ASN cc_start: 0.8286 (m110) cc_final: 0.7640 (m-40) REVERT: C 51 TYR cc_start: 0.8813 (t80) cc_final: 0.8539 (t80) REVERT: C 55 PHE cc_start: 0.8550 (m-80) cc_final: 0.7842 (m-80) REVERT: C 73 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.7629 (tpp-160) REVERT: C 94 ARG cc_start: 0.4800 (ttm110) cc_final: 0.4539 (ptt180) REVERT: C 231 GLU cc_start: 0.8697 (pp20) cc_final: 0.8386 (pp20) REVERT: C 234 LYS cc_start: 0.8378 (ttmt) cc_final: 0.7833 (ttpt) REVERT: C 235 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8085 (tm-30) REVERT: C 236 ASN cc_start: 0.8328 (m110) cc_final: 0.7944 (m110) REVERT: D 32 ARG cc_start: 0.6392 (ttt-90) cc_final: 0.6087 (tpt170) REVERT: D 125 GLU cc_start: 0.7591 (tp30) cc_final: 0.7144 (tp30) REVERT: D 189 LEU cc_start: 0.8624 (tt) cc_final: 0.8197 (tp) REVERT: D 198 CYS cc_start: 0.9041 (t) cc_final: 0.8758 (t) REVERT: D 208 LYS cc_start: 0.8312 (mtpp) cc_final: 0.8073 (mtmt) REVERT: D 231 GLU cc_start: 0.8559 (pp20) cc_final: 0.8350 (pp20) REVERT: D 234 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7753 (ttpt) REVERT: D 236 ASN cc_start: 0.8286 (m110) cc_final: 0.7951 (m-40) REVERT: D 279 TYR cc_start: 0.7605 (t80) cc_final: 0.7331 (t80) REVERT: D 282 ARG cc_start: 0.7555 (mtm-85) cc_final: 0.6932 (mmm160) REVERT: E 32 ARG cc_start: 0.7334 (ttt-90) cc_final: 0.6948 (tpp-160) REVERT: E 73 ARG cc_start: 0.7934 (ttp-110) cc_final: 0.7522 (tpp-160) REVERT: E 94 ARG cc_start: 0.5258 (ttm110) cc_final: 0.4883 (ptt180) REVERT: E 231 GLU cc_start: 0.8513 (pp20) cc_final: 0.7896 (pp20) REVERT: E 234 LYS cc_start: 0.8372 (ttmt) cc_final: 0.7751 (tttt) REVERT: E 235 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8237 (tm-30) REVERT: E 236 ASN cc_start: 0.7996 (m110) cc_final: 0.7607 (m110) REVERT: E 282 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6765 (mmm160) REVERT: F 32 ARG cc_start: 0.6948 (ttt-90) cc_final: 0.6391 (tpt170) REVERT: F 94 ARG cc_start: 0.5099 (ttm110) cc_final: 0.4839 (ptt180) REVERT: F 166 LEU cc_start: 0.8220 (tt) cc_final: 0.7482 (mt) REVERT: F 197 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7726 (mtt90) REVERT: F 231 GLU cc_start: 0.8756 (pp20) cc_final: 0.8288 (pp20) REVERT: F 234 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7513 (tttt) REVERT: F 235 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8283 (tm-30) REVERT: F 236 ASN cc_start: 0.8175 (m110) cc_final: 0.7706 (m110) REVERT: F 256 GLU cc_start: 0.8321 (tt0) cc_final: 0.8041 (tt0) REVERT: G 32 ARG cc_start: 0.6885 (ttt-90) cc_final: 0.6518 (tpt170) REVERT: G 73 ARG cc_start: 0.7627 (ttp-110) cc_final: 0.7422 (tpp-160) REVERT: G 134 PHE cc_start: 0.8455 (t80) cc_final: 0.8061 (t80) REVERT: G 236 ASN cc_start: 0.8046 (m110) cc_final: 0.7442 (m-40) REVERT: H 73 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7608 (tpp-160) REVERT: H 94 ARG cc_start: 0.4815 (ttm110) cc_final: 0.4529 (ptt180) REVERT: H 215 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8304 (tm-30) REVERT: H 220 ILE cc_start: 0.8378 (mm) cc_final: 0.8018 (mm) REVERT: H 234 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7689 (tttt) REVERT: H 236 ASN cc_start: 0.7913 (m110) cc_final: 0.7546 (m-40) REVERT: H 258 GLN cc_start: 0.7808 (tt0) cc_final: 0.7575 (tm-30) REVERT: I 32 ARG cc_start: 0.6662 (ttt-90) cc_final: 0.6306 (tpt170) REVERT: I 208 LYS cc_start: 0.8333 (mtpp) cc_final: 0.8128 (mtpt) REVERT: I 231 GLU cc_start: 0.8436 (pp20) cc_final: 0.7975 (pp20) REVERT: I 234 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7700 (ttpt) REVERT: I 236 ASN cc_start: 0.8332 (m110) cc_final: 0.8036 (m-40) REVERT: I 282 ARG cc_start: 0.7345 (mtm-85) cc_final: 0.6789 (mmm160) REVERT: J 32 ARG cc_start: 0.7135 (ttt-90) cc_final: 0.6894 (ttt90) REVERT: J 73 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7379 (tpp-160) REVERT: J 94 ARG cc_start: 0.5394 (ttm110) cc_final: 0.4810 (ptt180) REVERT: J 205 LEU cc_start: 0.9264 (tp) cc_final: 0.9044 (tp) REVERT: J 217 GLU cc_start: 0.7728 (tt0) cc_final: 0.7474 (tt0) REVERT: J 231 GLU cc_start: 0.8510 (pp20) cc_final: 0.7979 (pp20) REVERT: J 234 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7550 (tttt) REVERT: J 235 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7945 (tm-30) REVERT: J 236 ASN cc_start: 0.8040 (m110) cc_final: 0.7543 (m110) REVERT: J 282 ARG cc_start: 0.7321 (mtm-85) cc_final: 0.6852 (mmm160) outliers start: 0 outliers final: 0 residues processed: 785 average time/residue: 0.3291 time to fit residues: 381.0556 Evaluate side-chains 637 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 637 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 206 GLN A 216 GLN A 245 HIS A 277 HIS B 175 GLN B 206 GLN B 216 GLN B 245 HIS B 277 HIS ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 216 GLN C 245 HIS C 277 HIS D 175 GLN D 206 GLN D 216 GLN D 277 HIS E 206 GLN E 216 GLN E 258 GLN E 277 HIS F 175 GLN F 206 GLN F 216 GLN F 277 HIS ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN G 216 GLN G 277 HIS H 175 GLN H 206 GLN H 216 GLN H 277 HIS I 175 GLN I 206 GLN I 216 GLN I 258 GLN I 277 HIS J 175 GLN J 206 GLN J 216 GLN J 258 GLN J 277 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20010 Z= 0.271 Angle : 0.738 7.906 27200 Z= 0.372 Chirality : 0.041 0.202 3170 Planarity : 0.005 0.046 3350 Dihedral : 5.387 24.254 2690 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.29 % Favored : 93.31 % Rotamer: Outliers : 0.10 % Allowed : 8.46 % Favored : 91.44 % 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: -0.93 (0.17), residues: 2480 helix: 0.31 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -3.62 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 113 HIS 0.005 0.002 HIS D 245 PHE 0.016 0.002 PHE E 266 TYR 0.024 0.002 TYR A 51 ARG 0.004 0.001 ARG F 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 700 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7109 (ttt-90) cc_final: 0.6908 (ttt90) REVERT: A 134 PHE cc_start: 0.8481 (t80) cc_final: 0.8083 (t80) REVERT: A 215 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8256 (tp30) REVERT: A 234 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7564 (ttpt) REVERT: A 235 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8252 (tm-30) REVERT: A 236 ASN cc_start: 0.7933 (m110) cc_final: 0.7681 (m-40) REVERT: A 267 ASN cc_start: 0.8191 (t0) cc_final: 0.7736 (t0) REVERT: B 32 ARG cc_start: 0.6570 (ttt-90) cc_final: 0.6199 (tpt170) REVERT: B 73 ARG cc_start: 0.7908 (ttp-110) cc_final: 0.7644 (tpp-160) REVERT: B 125 GLU cc_start: 0.7795 (tp30) cc_final: 0.7388 (tp30) REVERT: B 205 LEU cc_start: 0.9068 (tp) cc_final: 0.8865 (tp) REVERT: B 215 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8114 (tp30) REVERT: B 224 LYS cc_start: 0.8335 (ttmt) cc_final: 0.8074 (ttpt) REVERT: B 231 GLU cc_start: 0.8557 (pp20) cc_final: 0.8233 (pp20) REVERT: B 234 LYS cc_start: 0.8355 (ttmt) cc_final: 0.7757 (tttm) REVERT: B 235 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8052 (tm-30) REVERT: B 236 ASN cc_start: 0.8031 (m110) cc_final: 0.7705 (m-40) REVERT: C 73 ARG cc_start: 0.8045 (ttp-110) cc_final: 0.7705 (tpp-160) REVERT: C 94 ARG cc_start: 0.5394 (ttm110) cc_final: 0.4892 (ptt180) REVERT: C 125 GLU cc_start: 0.7742 (tp30) cc_final: 0.7513 (tp30) REVERT: C 134 PHE cc_start: 0.8456 (t80) cc_final: 0.8235 (t80) REVERT: C 205 LEU cc_start: 0.9137 (tp) cc_final: 0.8900 (tp) REVERT: C 231 GLU cc_start: 0.8712 (pp20) cc_final: 0.8482 (pp20) REVERT: C 234 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7823 (ttpt) REVERT: C 235 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8226 (tm-30) REVERT: C 236 ASN cc_start: 0.8097 (m110) cc_final: 0.7808 (m-40) REVERT: C 267 ASN cc_start: 0.8304 (t0) cc_final: 0.7833 (t0) REVERT: D 32 ARG cc_start: 0.6441 (ttt-90) cc_final: 0.6178 (tpt170) REVERT: D 51 TYR cc_start: 0.9163 (t80) cc_final: 0.8960 (t80) REVERT: D 125 GLU cc_start: 0.7839 (tp30) cc_final: 0.7609 (tp30) REVERT: D 189 LEU cc_start: 0.8675 (tt) cc_final: 0.8272 (tp) REVERT: D 208 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7914 (mtpt) REVERT: D 231 GLU cc_start: 0.8563 (pp20) cc_final: 0.8328 (pp20) REVERT: D 234 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7797 (ttpt) REVERT: D 267 ASN cc_start: 0.8470 (t0) cc_final: 0.7971 (t0) REVERT: E 32 ARG cc_start: 0.7319 (ttt-90) cc_final: 0.6748 (tpp-160) REVERT: E 73 ARG cc_start: 0.8056 (ttp-110) cc_final: 0.7602 (tpp-160) REVERT: E 94 ARG cc_start: 0.5317 (ttm110) cc_final: 0.4845 (ptt180) REVERT: E 197 ARG cc_start: 0.8593 (mtt90) cc_final: 0.7917 (mtt90) REVERT: E 234 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7665 (tttt) REVERT: E 235 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8193 (tm-30) REVERT: E 236 ASN cc_start: 0.7866 (m110) cc_final: 0.7587 (m110) REVERT: F 32 ARG cc_start: 0.7180 (ttt-90) cc_final: 0.6927 (ttt90) REVERT: F 94 ARG cc_start: 0.5293 (ttm110) cc_final: 0.4938 (ptt180) REVERT: F 125 GLU cc_start: 0.7608 (tp30) cc_final: 0.7339 (tp30) REVERT: F 166 LEU cc_start: 0.8121 (tt) cc_final: 0.7412 (mt) REVERT: F 234 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7590 (ttpt) REVERT: F 235 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8256 (tm-30) REVERT: F 236 ASN cc_start: 0.7914 (m110) cc_final: 0.7610 (m110) REVERT: F 256 GLU cc_start: 0.8213 (tt0) cc_final: 0.7864 (tt0) REVERT: F 258 GLN cc_start: 0.8054 (tt0) cc_final: 0.7737 (tm-30) REVERT: F 267 ASN cc_start: 0.8196 (t0) cc_final: 0.7767 (t0) REVERT: F 278 LYS cc_start: 0.7963 (tttt) cc_final: 0.7443 (ttpt) REVERT: G 32 ARG cc_start: 0.6723 (ttt-90) cc_final: 0.6267 (tpt170) REVERT: G 125 GLU cc_start: 0.7661 (tp30) cc_final: 0.7380 (tp30) REVERT: G 134 PHE cc_start: 0.8330 (t80) cc_final: 0.8061 (t80) REVERT: G 144 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8149 (ttp80) REVERT: G 205 LEU cc_start: 0.8995 (tp) cc_final: 0.8687 (tp) REVERT: G 220 ILE cc_start: 0.8664 (tt) cc_final: 0.8349 (tt) REVERT: G 234 LYS cc_start: 0.8354 (ttmt) cc_final: 0.7653 (ttpt) REVERT: G 236 ASN cc_start: 0.7742 (m110) cc_final: 0.7510 (m-40) REVERT: G 275 MET cc_start: 0.7964 (mmp) cc_final: 0.7718 (mmm) REVERT: G 278 LYS cc_start: 0.8459 (tttt) cc_final: 0.7934 (ttpt) REVERT: H 32 ARG cc_start: 0.6651 (ttt-90) cc_final: 0.5940 (tpt170) REVERT: H 73 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7618 (tpp-160) REVERT: H 94 ARG cc_start: 0.5328 (ttm110) cc_final: 0.4600 (ptt180) REVERT: H 111 LEU cc_start: 0.8475 (mt) cc_final: 0.8264 (mt) REVERT: H 125 GLU cc_start: 0.7633 (tp30) cc_final: 0.7354 (tp30) REVERT: H 234 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7682 (ttpt) REVERT: H 258 GLN cc_start: 0.7822 (tt0) cc_final: 0.7552 (tm-30) REVERT: H 267 ASN cc_start: 0.8342 (t0) cc_final: 0.7906 (t0) REVERT: I 32 ARG cc_start: 0.7005 (ttt-90) cc_final: 0.6469 (tpt170) REVERT: I 125 GLU cc_start: 0.7895 (tp30) cc_final: 0.7694 (tp30) REVERT: I 208 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8123 (mtpt) REVERT: I 224 LYS cc_start: 0.8495 (ttpt) cc_final: 0.7950 (ttpt) REVERT: I 234 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7756 (ttpt) REVERT: I 256 GLU cc_start: 0.8314 (tt0) cc_final: 0.8113 (tt0) REVERT: I 267 ASN cc_start: 0.8678 (t0) cc_final: 0.8078 (t0) REVERT: I 279 TYR cc_start: 0.7975 (t80) cc_final: 0.7677 (t80) REVERT: J 32 ARG cc_start: 0.7215 (ttt-90) cc_final: 0.6866 (ttt90) REVERT: J 73 ARG cc_start: 0.7973 (ttp-110) cc_final: 0.7449 (tpp-160) REVERT: J 94 ARG cc_start: 0.5096 (ttm110) cc_final: 0.4771 (ptt180) REVERT: J 231 GLU cc_start: 0.8462 (pp20) cc_final: 0.8013 (pp20) REVERT: J 234 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7665 (tttt) REVERT: J 235 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8311 (tm-30) REVERT: J 267 ASN cc_start: 0.8500 (t0) cc_final: 0.8095 (t0) outliers start: 2 outliers final: 0 residues processed: 702 average time/residue: 0.3023 time to fit residues: 320.9835 Evaluate side-chains 603 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 603 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 126 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 227 optimal weight: 0.0270 chunk 245 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 206 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN F 206 GLN G 175 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 GLN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20010 Z= 0.211 Angle : 0.703 9.810 27200 Z= 0.348 Chirality : 0.040 0.246 3170 Planarity : 0.005 0.045 3350 Dihedral : 5.087 24.573 2690 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.06 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % 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: -0.51 (0.17), residues: 2480 helix: 0.64 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.66 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 113 HIS 0.003 0.001 HIS I 245 PHE 0.017 0.002 PHE E 241 TYR 0.026 0.002 TYR A 51 ARG 0.004 0.000 ARG I 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 750 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7147 (ttt-90) cc_final: 0.6849 (ttt90) REVERT: A 125 GLU cc_start: 0.7647 (tp30) cc_final: 0.7432 (tp30) REVERT: A 134 PHE cc_start: 0.8449 (t80) cc_final: 0.8208 (t80) REVERT: A 166 LEU cc_start: 0.8213 (tt) cc_final: 0.7433 (mt) REVERT: A 215 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8108 (tp30) REVERT: A 234 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7465 (ttpt) REVERT: A 235 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8253 (tm-30) REVERT: A 236 ASN cc_start: 0.7987 (m110) cc_final: 0.7736 (m110) REVERT: A 258 GLN cc_start: 0.8103 (tt0) cc_final: 0.7825 (tm-30) REVERT: B 32 ARG cc_start: 0.6521 (ttt-90) cc_final: 0.6122 (tpt170) REVERT: B 73 ARG cc_start: 0.7932 (ttp-110) cc_final: 0.7669 (tpp-160) REVERT: B 125 GLU cc_start: 0.7724 (tp30) cc_final: 0.7376 (tp30) REVERT: B 134 PHE cc_start: 0.8424 (t80) cc_final: 0.8205 (t80) REVERT: B 215 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 234 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7692 (tttm) REVERT: B 235 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8086 (tm-30) REVERT: B 236 ASN cc_start: 0.8022 (m110) cc_final: 0.7727 (m110) REVERT: C 63 LEU cc_start: 0.8890 (tp) cc_final: 0.8685 (tp) REVERT: C 73 ARG cc_start: 0.7914 (ttp-110) cc_final: 0.7701 (tpp-160) REVERT: C 94 ARG cc_start: 0.5278 (ttm110) cc_final: 0.4703 (ptt180) REVERT: C 125 GLU cc_start: 0.7425 (tp30) cc_final: 0.7145 (tp30) REVERT: C 166 LEU cc_start: 0.8270 (tt) cc_final: 0.7664 (mt) REVERT: C 205 LEU cc_start: 0.9136 (tp) cc_final: 0.8778 (tp) REVERT: C 220 ILE cc_start: 0.8488 (tt) cc_final: 0.8098 (tt) REVERT: C 234 LYS cc_start: 0.8486 (ttmt) cc_final: 0.7813 (ttpt) REVERT: C 235 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8234 (tm-30) REVERT: C 236 ASN cc_start: 0.8053 (m110) cc_final: 0.7796 (m-40) REVERT: D 32 ARG cc_start: 0.6553 (ttt-90) cc_final: 0.6271 (tpt170) REVERT: D 68 TYR cc_start: 0.7263 (t80) cc_final: 0.6965 (t80) REVERT: D 177 LEU cc_start: 0.9242 (tp) cc_final: 0.8966 (tp) REVERT: D 189 LEU cc_start: 0.8664 (tt) cc_final: 0.8215 (tp) REVERT: D 208 LYS cc_start: 0.8295 (mtpp) cc_final: 0.7949 (mtmt) REVERT: D 231 GLU cc_start: 0.8382 (pp20) cc_final: 0.8116 (pp20) REVERT: D 234 LYS cc_start: 0.8249 (ttmt) cc_final: 0.7755 (ttpt) REVERT: D 267 ASN cc_start: 0.8523 (t0) cc_final: 0.7944 (t0) REVERT: E 32 ARG cc_start: 0.7425 (ttt-90) cc_final: 0.6778 (tpp-160) REVERT: E 73 ARG cc_start: 0.8019 (ttp-110) cc_final: 0.7576 (tpp-160) REVERT: E 94 ARG cc_start: 0.5189 (ttm110) cc_final: 0.4825 (ptt180) REVERT: E 125 GLU cc_start: 0.7641 (tp30) cc_final: 0.7338 (tp30) REVERT: E 166 LEU cc_start: 0.8360 (tt) cc_final: 0.7606 (mt) REVERT: E 231 GLU cc_start: 0.8263 (pp20) cc_final: 0.7873 (pp20) REVERT: E 234 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7648 (tttt) REVERT: E 235 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8175 (tm-30) REVERT: E 236 ASN cc_start: 0.7832 (m110) cc_final: 0.7578 (m110) REVERT: E 258 GLN cc_start: 0.7934 (tt0) cc_final: 0.7421 (tm-30) REVERT: F 94 ARG cc_start: 0.5167 (ttm110) cc_final: 0.4807 (ptt180) REVERT: F 125 GLU cc_start: 0.7611 (tp30) cc_final: 0.7291 (tp30) REVERT: F 166 LEU cc_start: 0.8095 (tt) cc_final: 0.7452 (mt) REVERT: F 234 LYS cc_start: 0.8276 (ttmt) cc_final: 0.7607 (ttpt) REVERT: F 235 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8284 (tm-30) REVERT: F 258 GLN cc_start: 0.8196 (tt0) cc_final: 0.7862 (tm-30) REVERT: F 278 LYS cc_start: 0.7949 (tttt) cc_final: 0.7636 (ttmt) REVERT: G 32 ARG cc_start: 0.6403 (ttt-90) cc_final: 0.6082 (tpt170) REVERT: G 48 ASN cc_start: 0.7292 (t0) cc_final: 0.6951 (t0) REVERT: G 73 ARG cc_start: 0.5286 (tpp-160) cc_final: 0.4377 (tpt170) REVERT: G 125 GLU cc_start: 0.7582 (tp30) cc_final: 0.7134 (tp30) REVERT: G 144 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8297 (ttp80) REVERT: G 220 ILE cc_start: 0.8586 (tt) cc_final: 0.8325 (tt) REVERT: G 234 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7637 (tttm) REVERT: G 236 ASN cc_start: 0.7885 (m110) cc_final: 0.7520 (m-40) REVERT: G 274 SER cc_start: 0.7978 (p) cc_final: 0.7424 (p) REVERT: H 32 ARG cc_start: 0.6563 (ttt-90) cc_final: 0.5814 (tpt170) REVERT: H 51 TYR cc_start: 0.8542 (t80) cc_final: 0.7856 (t80) REVERT: H 55 PHE cc_start: 0.9170 (m-80) cc_final: 0.8578 (m-80) REVERT: H 73 ARG cc_start: 0.7921 (ttp-110) cc_final: 0.7657 (tpp-160) REVERT: H 94 ARG cc_start: 0.5093 (ttm110) cc_final: 0.4527 (ptt180) REVERT: H 125 GLU cc_start: 0.7719 (tp30) cc_final: 0.7248 (tp30) REVERT: H 144 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8249 (tmm-80) REVERT: H 166 LEU cc_start: 0.8615 (tt) cc_final: 0.7967 (mt) REVERT: H 173 GLN cc_start: 0.8813 (mt0) cc_final: 0.8277 (mp10) REVERT: H 210 TRP cc_start: 0.8865 (t60) cc_final: 0.8599 (t60) REVERT: H 234 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7601 (ttpt) REVERT: H 267 ASN cc_start: 0.8290 (t0) cc_final: 0.7776 (t0) REVERT: I 32 ARG cc_start: 0.6926 (ttt-90) cc_final: 0.6326 (tpt170) REVERT: I 173 GLN cc_start: 0.8917 (mt0) cc_final: 0.7965 (mp10) REVERT: I 208 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8065 (mtpt) REVERT: I 224 LYS cc_start: 0.8499 (ttpt) cc_final: 0.8221 (ttpt) REVERT: I 231 GLU cc_start: 0.8541 (pp20) cc_final: 0.8215 (pp20) REVERT: I 234 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7712 (ttpt) REVERT: J 32 ARG cc_start: 0.7089 (ttt-90) cc_final: 0.6805 (ttt90) REVERT: J 39 PHE cc_start: 0.8430 (t80) cc_final: 0.7785 (t80) REVERT: J 41 CYS cc_start: 0.5571 (t) cc_final: 0.5364 (t) REVERT: J 73 ARG cc_start: 0.7937 (ttp-110) cc_final: 0.7442 (tpp-160) REVERT: J 94 ARG cc_start: 0.5253 (ttm110) cc_final: 0.4818 (ptt180) REVERT: J 125 GLU cc_start: 0.7480 (tp30) cc_final: 0.7197 (tp30) REVERT: J 217 GLU cc_start: 0.8499 (tt0) cc_final: 0.8142 (tt0) REVERT: J 231 GLU cc_start: 0.8403 (pp20) cc_final: 0.8194 (tm-30) REVERT: J 234 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7602 (tttt) REVERT: J 235 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8231 (tm-30) REVERT: J 236 ASN cc_start: 0.7824 (m110) cc_final: 0.7554 (m110) REVERT: J 274 SER cc_start: 0.8243 (p) cc_final: 0.7204 (p) outliers start: 0 outliers final: 0 residues processed: 750 average time/residue: 0.3021 time to fit residues: 343.6925 Evaluate side-chains 622 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 622 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 224 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 241 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN D 175 GLN ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20010 Z= 0.266 Angle : 0.742 8.835 27200 Z= 0.370 Chirality : 0.041 0.204 3170 Planarity : 0.005 0.045 3350 Dihedral : 5.137 23.877 2690 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.62 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: -0.37 (0.17), residues: 2480 helix: 0.83 (0.12), residues: 1840 sheet: None (None), residues: 0 loop : -3.52 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 113 HIS 0.005 0.001 HIS C 245 PHE 0.017 0.002 PHE J 266 TYR 0.029 0.002 TYR J 51 ARG 0.006 0.001 ARG I 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 727 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7271 (ttt-90) cc_final: 0.6860 (ttt90) REVERT: A 63 LEU cc_start: 0.8865 (tp) cc_final: 0.8637 (tp) REVERT: A 125 GLU cc_start: 0.7451 (tp30) cc_final: 0.7238 (tp30) REVERT: A 166 LEU cc_start: 0.8178 (tt) cc_final: 0.7421 (mt) REVERT: A 215 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8092 (tp30) REVERT: A 234 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7491 (ttpt) REVERT: A 235 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8219 (tm-30) REVERT: A 236 ASN cc_start: 0.7936 (m110) cc_final: 0.7637 (m110) REVERT: A 258 GLN cc_start: 0.8212 (tt0) cc_final: 0.7886 (tm-30) REVERT: A 267 ASN cc_start: 0.8111 (t0) cc_final: 0.7708 (t0) REVERT: A 274 SER cc_start: 0.8164 (p) cc_final: 0.7628 (p) REVERT: B 32 ARG cc_start: 0.6567 (ttt-90) cc_final: 0.6111 (tpt170) REVERT: B 73 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.7647 (tpp-160) REVERT: B 125 GLU cc_start: 0.7752 (tp30) cc_final: 0.7468 (tp30) REVERT: B 205 LEU cc_start: 0.9006 (tp) cc_final: 0.8599 (tp) REVERT: B 215 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8150 (tm-30) REVERT: B 231 GLU cc_start: 0.8386 (pp20) cc_final: 0.8067 (pp20) REVERT: B 234 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7707 (tttm) REVERT: B 236 ASN cc_start: 0.7868 (m110) cc_final: 0.7520 (m110) REVERT: B 278 LYS cc_start: 0.8472 (tttt) cc_final: 0.8097 (ttpt) REVERT: C 73 ARG cc_start: 0.7858 (ttp-110) cc_final: 0.7624 (tpp-160) REVERT: C 94 ARG cc_start: 0.5219 (ttm110) cc_final: 0.4611 (ptt180) REVERT: C 125 GLU cc_start: 0.7695 (tp30) cc_final: 0.7473 (tp30) REVERT: C 177 LEU cc_start: 0.9059 (tp) cc_final: 0.8759 (tp) REVERT: C 205 LEU cc_start: 0.9113 (tp) cc_final: 0.8759 (tp) REVERT: C 220 ILE cc_start: 0.8433 (tt) cc_final: 0.7996 (tt) REVERT: C 234 LYS cc_start: 0.8453 (ttmt) cc_final: 0.7822 (ttpt) REVERT: C 236 ASN cc_start: 0.8064 (m110) cc_final: 0.7863 (m110) REVERT: C 267 ASN cc_start: 0.8301 (t0) cc_final: 0.7771 (t0) REVERT: D 32 ARG cc_start: 0.6548 (ttt-90) cc_final: 0.6274 (tpt170) REVERT: D 68 TYR cc_start: 0.7262 (t80) cc_final: 0.6977 (t80) REVERT: D 177 LEU cc_start: 0.9259 (tp) cc_final: 0.9001 (tp) REVERT: D 205 LEU cc_start: 0.9293 (tp) cc_final: 0.9027 (tp) REVERT: D 208 LYS cc_start: 0.8354 (mtpp) cc_final: 0.7968 (mtmt) REVERT: D 231 GLU cc_start: 0.8523 (pp20) cc_final: 0.8047 (pp20) REVERT: D 234 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7706 (tttt) REVERT: D 267 ASN cc_start: 0.8428 (t0) cc_final: 0.7798 (t0) REVERT: E 32 ARG cc_start: 0.7335 (ttt-90) cc_final: 0.6716 (tpp-160) REVERT: E 73 ARG cc_start: 0.7981 (ttp-110) cc_final: 0.7536 (tpp-160) REVERT: E 94 ARG cc_start: 0.4914 (ttm110) cc_final: 0.4611 (ptt180) REVERT: E 205 LEU cc_start: 0.9045 (tp) cc_final: 0.8789 (tp) REVERT: E 217 GLU cc_start: 0.8396 (tt0) cc_final: 0.7910 (tt0) REVERT: E 231 GLU cc_start: 0.8426 (pp20) cc_final: 0.7924 (pp20) REVERT: E 234 LYS cc_start: 0.8388 (ttmt) cc_final: 0.7693 (tttt) REVERT: E 235 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8156 (tm-30) REVERT: E 236 ASN cc_start: 0.7662 (m110) cc_final: 0.7415 (m110) REVERT: F 63 LEU cc_start: 0.8870 (tp) cc_final: 0.8664 (tp) REVERT: F 125 GLU cc_start: 0.7666 (tp30) cc_final: 0.7451 (tp30) REVERT: F 166 LEU cc_start: 0.8147 (tt) cc_final: 0.7483 (mt) REVERT: F 234 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7519 (ttpt) REVERT: F 258 GLN cc_start: 0.8208 (tt0) cc_final: 0.7878 (tm-30) REVERT: F 274 SER cc_start: 0.8278 (p) cc_final: 0.7940 (p) REVERT: G 32 ARG cc_start: 0.6710 (ttt-90) cc_final: 0.6216 (tpt170) REVERT: G 125 GLU cc_start: 0.7542 (tp30) cc_final: 0.7026 (tp30) REVERT: G 134 PHE cc_start: 0.8488 (t80) cc_final: 0.7860 (t80) REVERT: G 205 LEU cc_start: 0.8975 (tp) cc_final: 0.8605 (tp) REVERT: G 220 ILE cc_start: 0.8582 (tt) cc_final: 0.8344 (tt) REVERT: G 224 LYS cc_start: 0.8459 (ttmt) cc_final: 0.7916 (ttpt) REVERT: G 231 GLU cc_start: 0.8387 (pp20) cc_final: 0.8152 (tm-30) REVERT: G 234 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7686 (ttpt) REVERT: H 32 ARG cc_start: 0.6729 (ttt-90) cc_final: 0.5915 (tpt170) REVERT: H 73 ARG cc_start: 0.7971 (ttp-110) cc_final: 0.7667 (tpp-160) REVERT: H 94 ARG cc_start: 0.5119 (ttm110) cc_final: 0.4545 (ptt180) REVERT: H 111 LEU cc_start: 0.8556 (mt) cc_final: 0.8305 (mt) REVERT: H 125 GLU cc_start: 0.7726 (tp30) cc_final: 0.7305 (tp30) REVERT: H 144 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8322 (tmm-80) REVERT: H 166 LEU cc_start: 0.8395 (tt) cc_final: 0.7606 (mt) REVERT: H 234 LYS cc_start: 0.8475 (ttmt) cc_final: 0.7753 (ttpt) REVERT: H 267 ASN cc_start: 0.8403 (t0) cc_final: 0.7872 (t0) REVERT: I 32 ARG cc_start: 0.6994 (ttt-90) cc_final: 0.6465 (tpt170) REVERT: I 56 LEU cc_start: 0.8988 (tp) cc_final: 0.8782 (tp) REVERT: I 63 LEU cc_start: 0.8902 (tp) cc_final: 0.8701 (tp) REVERT: I 125 GLU cc_start: 0.7821 (tp30) cc_final: 0.7589 (tp30) REVERT: I 166 LEU cc_start: 0.8269 (tt) cc_final: 0.7660 (mt) REVERT: I 173 GLN cc_start: 0.8819 (mt0) cc_final: 0.7961 (mt0) REVERT: I 208 LYS cc_start: 0.8403 (mtpp) cc_final: 0.8082 (mtpt) REVERT: I 217 GLU cc_start: 0.8491 (tt0) cc_final: 0.8140 (tt0) REVERT: I 224 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8111 (ttpt) REVERT: I 231 GLU cc_start: 0.8524 (pp20) cc_final: 0.7987 (pp20) REVERT: I 234 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7555 (tttt) REVERT: I 267 ASN cc_start: 0.8527 (t0) cc_final: 0.7892 (t0) REVERT: I 274 SER cc_start: 0.8451 (p) cc_final: 0.7398 (p) REVERT: J 32 ARG cc_start: 0.7254 (ttt-90) cc_final: 0.6707 (ttt90) REVERT: J 39 PHE cc_start: 0.8362 (t80) cc_final: 0.8102 (t80) REVERT: J 63 LEU cc_start: 0.8991 (tp) cc_final: 0.8780 (tp) REVERT: J 73 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7479 (tpp-160) REVERT: J 94 ARG cc_start: 0.5053 (ttm110) cc_final: 0.4712 (ptt180) REVERT: J 210 TRP cc_start: 0.8764 (t60) cc_final: 0.8536 (t60) REVERT: J 217 GLU cc_start: 0.8613 (tt0) cc_final: 0.8071 (tt0) REVERT: J 234 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7676 (tttt) REVERT: J 235 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8247 (tm-30) REVERT: J 274 SER cc_start: 0.8286 (p) cc_final: 0.7147 (p) REVERT: J 278 LYS cc_start: 0.8381 (tttt) cc_final: 0.7998 (ttmt) outliers start: 0 outliers final: 0 residues processed: 727 average time/residue: 0.2971 time to fit residues: 327.6589 Evaluate side-chains 621 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 621 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 201 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 179 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 206 optimal weight: 20.0000 chunk 167 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 0.0870 chunk 216 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN D 236 ASN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 GLN I 236 ASN ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20010 Z= 0.197 Angle : 0.689 8.346 27200 Z= 0.338 Chirality : 0.039 0.188 3170 Planarity : 0.004 0.044 3350 Dihedral : 4.921 22.316 2690 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.18 % Favored : 92.46 % Rotamer: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % 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: -0.23 (0.17), residues: 2480 helix: 0.89 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.75 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 113 HIS 0.005 0.001 HIS C 277 PHE 0.015 0.001 PHE I 55 TYR 0.029 0.002 TYR A 279 ARG 0.007 0.000 ARG G 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 742 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7048 (ttt-90) cc_final: 0.6600 (ttt90) REVERT: A 48 ASN cc_start: 0.8342 (t0) cc_final: 0.8128 (t0) REVERT: A 111 LEU cc_start: 0.8422 (mt) cc_final: 0.8119 (mt) REVERT: A 125 GLU cc_start: 0.7495 (tp30) cc_final: 0.7231 (tp30) REVERT: A 166 LEU cc_start: 0.8280 (tt) cc_final: 0.7556 (mt) REVERT: A 215 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7955 (tp30) REVERT: A 234 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7470 (ttpt) REVERT: A 235 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8277 (tm-30) REVERT: A 236 ASN cc_start: 0.7971 (m110) cc_final: 0.7752 (m110) REVERT: A 258 GLN cc_start: 0.8224 (tt0) cc_final: 0.7983 (tm-30) REVERT: A 267 ASN cc_start: 0.8248 (t0) cc_final: 0.7834 (t0) REVERT: A 274 SER cc_start: 0.8385 (p) cc_final: 0.7485 (p) REVERT: B 32 ARG cc_start: 0.6548 (ttt-90) cc_final: 0.6084 (tpt170) REVERT: B 73 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7648 (tpp-160) REVERT: B 125 GLU cc_start: 0.7510 (tp30) cc_final: 0.7201 (tp30) REVERT: B 205 LEU cc_start: 0.8960 (tp) cc_final: 0.8731 (tp) REVERT: B 215 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8042 (tm-30) REVERT: B 234 LYS cc_start: 0.8341 (ttmt) cc_final: 0.7686 (tttm) REVERT: B 278 LYS cc_start: 0.8402 (tttt) cc_final: 0.7899 (ttpt) REVERT: C 73 ARG cc_start: 0.7868 (ttp-110) cc_final: 0.7631 (tpp-160) REVERT: C 94 ARG cc_start: 0.5196 (ttm110) cc_final: 0.4613 (ptt180) REVERT: C 125 GLU cc_start: 0.7575 (tp30) cc_final: 0.7318 (tp30) REVERT: C 210 TRP cc_start: 0.8753 (t60) cc_final: 0.8514 (t60) REVERT: C 220 ILE cc_start: 0.8433 (tt) cc_final: 0.8009 (tt) REVERT: C 234 LYS cc_start: 0.8458 (ttmt) cc_final: 0.7847 (ttpt) REVERT: C 258 GLN cc_start: 0.8245 (tt0) cc_final: 0.7778 (tm-30) REVERT: D 32 ARG cc_start: 0.6529 (ttt-90) cc_final: 0.6325 (tpt170) REVERT: D 51 TYR cc_start: 0.8546 (t80) cc_final: 0.8255 (t80) REVERT: D 68 TYR cc_start: 0.7340 (t80) cc_final: 0.7113 (t80) REVERT: D 125 GLU cc_start: 0.7940 (tp30) cc_final: 0.7656 (tp30) REVERT: D 173 GLN cc_start: 0.8824 (mt0) cc_final: 0.7737 (mp10) REVERT: D 177 LEU cc_start: 0.9216 (tp) cc_final: 0.8968 (tp) REVERT: D 192 PHE cc_start: 0.8660 (t80) cc_final: 0.8454 (t80) REVERT: D 208 LYS cc_start: 0.8338 (mtpp) cc_final: 0.7920 (mtmt) REVERT: D 231 GLU cc_start: 0.8437 (pp20) cc_final: 0.8235 (tm-30) REVERT: D 234 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7799 (tttt) REVERT: D 236 ASN cc_start: 0.8204 (m110) cc_final: 0.7983 (m-40) REVERT: D 267 ASN cc_start: 0.8455 (t0) cc_final: 0.7784 (t0) REVERT: E 32 ARG cc_start: 0.7348 (ttt-90) cc_final: 0.6725 (tpp-160) REVERT: E 73 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7557 (tpp-160) REVERT: E 94 ARG cc_start: 0.5138 (ttm110) cc_final: 0.4682 (ptt180) REVERT: E 173 GLN cc_start: 0.8689 (mt0) cc_final: 0.7943 (mp10) REVERT: E 205 LEU cc_start: 0.9012 (tp) cc_final: 0.8584 (tp) REVERT: E 217 GLU cc_start: 0.8461 (tt0) cc_final: 0.8125 (tt0) REVERT: E 234 LYS cc_start: 0.8387 (ttmt) cc_final: 0.7736 (tttt) REVERT: E 235 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8108 (tm-30) REVERT: E 236 ASN cc_start: 0.7434 (m110) cc_final: 0.7009 (m110) REVERT: E 279 TYR cc_start: 0.7599 (t80) cc_final: 0.7176 (t80) REVERT: F 111 LEU cc_start: 0.8449 (mt) cc_final: 0.8122 (mt) REVERT: F 125 GLU cc_start: 0.7666 (tp30) cc_final: 0.7306 (tp30) REVERT: F 166 LEU cc_start: 0.8024 (tt) cc_final: 0.7349 (mt) REVERT: F 234 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7393 (ttpt) REVERT: F 235 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8270 (tm-30) REVERT: F 258 GLN cc_start: 0.8215 (tt0) cc_final: 0.7970 (tm-30) REVERT: F 274 SER cc_start: 0.8341 (p) cc_final: 0.7687 (p) REVERT: G 32 ARG cc_start: 0.6749 (ttt-90) cc_final: 0.6170 (tpt170) REVERT: G 125 GLU cc_start: 0.7473 (tp30) cc_final: 0.6986 (tp30) REVERT: G 134 PHE cc_start: 0.8447 (t80) cc_final: 0.8122 (t80) REVERT: G 173 GLN cc_start: 0.8869 (mt0) cc_final: 0.8019 (mp10) REVERT: G 220 ILE cc_start: 0.8594 (tt) cc_final: 0.8380 (tt) REVERT: G 224 LYS cc_start: 0.8452 (ttmt) cc_final: 0.7885 (ttpt) REVERT: G 231 GLU cc_start: 0.8253 (pp20) cc_final: 0.8001 (tm-30) REVERT: G 274 SER cc_start: 0.7919 (p) cc_final: 0.7192 (p) REVERT: H 32 ARG cc_start: 0.6700 (ttt-90) cc_final: 0.5988 (tpt170) REVERT: H 63 LEU cc_start: 0.8946 (tp) cc_final: 0.8741 (tp) REVERT: H 73 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7703 (tpp-160) REVERT: H 94 ARG cc_start: 0.5107 (ttm110) cc_final: 0.4505 (ptt180) REVERT: H 125 GLU cc_start: 0.7636 (tp30) cc_final: 0.7248 (tp30) REVERT: H 144 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8202 (tmm-80) REVERT: H 166 LEU cc_start: 0.8356 (tt) cc_final: 0.7571 (mt) REVERT: H 220 ILE cc_start: 0.8621 (tt) cc_final: 0.8288 (tt) REVERT: H 224 LYS cc_start: 0.8355 (ttpt) cc_final: 0.7904 (ttpt) REVERT: H 231 GLU cc_start: 0.8204 (pp20) cc_final: 0.7992 (tm-30) REVERT: H 234 LYS cc_start: 0.8387 (ttmt) cc_final: 0.7603 (ttpt) REVERT: H 267 ASN cc_start: 0.8180 (t0) cc_final: 0.7708 (t0) REVERT: I 32 ARG cc_start: 0.6943 (ttt-90) cc_final: 0.6465 (tpt170) REVERT: I 63 LEU cc_start: 0.8957 (tp) cc_final: 0.8748 (tp) REVERT: I 125 GLU cc_start: 0.7752 (tp30) cc_final: 0.7538 (tp30) REVERT: I 173 GLN cc_start: 0.8877 (mt0) cc_final: 0.7998 (mt0) REVERT: I 208 LYS cc_start: 0.8363 (mtpp) cc_final: 0.8012 (mtpt) REVERT: I 217 GLU cc_start: 0.8549 (tt0) cc_final: 0.8177 (tt0) REVERT: I 224 LYS cc_start: 0.8624 (ttmt) cc_final: 0.8277 (ttpt) REVERT: I 234 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7579 (tttt) REVERT: J 32 ARG cc_start: 0.7256 (ttt-90) cc_final: 0.6702 (ttt90) REVERT: J 63 LEU cc_start: 0.8987 (tp) cc_final: 0.8747 (tp) REVERT: J 73 ARG cc_start: 0.8038 (ttp-110) cc_final: 0.7594 (tpp-160) REVERT: J 94 ARG cc_start: 0.4913 (ttm110) cc_final: 0.4612 (ptt180) REVERT: J 173 GLN cc_start: 0.8703 (mt0) cc_final: 0.7856 (mp10) REVERT: J 210 TRP cc_start: 0.8856 (t60) cc_final: 0.8516 (t60) REVERT: J 217 GLU cc_start: 0.8609 (tt0) cc_final: 0.8115 (tt0) REVERT: J 234 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7636 (tttt) REVERT: J 235 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7917 (tm-30) REVERT: J 236 ASN cc_start: 0.7222 (m110) cc_final: 0.6463 (m110) outliers start: 1 outliers final: 1 residues processed: 743 average time/residue: 0.2957 time to fit residues: 335.7852 Evaluate side-chains 633 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 632 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 81 optimal weight: 6.9990 chunk 217 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 111 optimal weight: 0.0060 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN E 175 GLN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN J 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20010 Z= 0.203 Angle : 0.686 8.199 27200 Z= 0.336 Chirality : 0.039 0.225 3170 Planarity : 0.004 0.042 3350 Dihedral : 4.805 22.692 2690 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.46 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: -0.07 (0.17), residues: 2480 helix: 1.05 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -3.78 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 113 HIS 0.003 0.001 HIS C 245 PHE 0.019 0.001 PHE D 64 TYR 0.031 0.002 TYR F 279 ARG 0.007 0.001 ARG J 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 746 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7116 (ttt-90) cc_final: 0.6705 (ttt90) REVERT: A 48 ASN cc_start: 0.8358 (t0) cc_final: 0.7937 (t0) REVERT: A 125 GLU cc_start: 0.7511 (tp30) cc_final: 0.7254 (tp30) REVERT: A 166 LEU cc_start: 0.8202 (tt) cc_final: 0.7468 (mt) REVERT: A 215 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7952 (tp30) REVERT: A 217 GLU cc_start: 0.8718 (tt0) cc_final: 0.8314 (tt0) REVERT: A 219 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7147 (tm-30) REVERT: A 220 ILE cc_start: 0.8923 (tt) cc_final: 0.8653 (tt) REVERT: A 234 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7474 (ttpt) REVERT: A 235 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8289 (tm-30) REVERT: A 236 ASN cc_start: 0.7475 (m110) cc_final: 0.7140 (m110) REVERT: A 258 GLN cc_start: 0.8233 (tt0) cc_final: 0.7995 (tm-30) REVERT: A 274 SER cc_start: 0.8095 (p) cc_final: 0.7196 (p) REVERT: A 279 TYR cc_start: 0.7307 (t80) cc_final: 0.7100 (t80) REVERT: B 32 ARG cc_start: 0.6606 (ttt-90) cc_final: 0.6263 (tpt170) REVERT: B 73 ARG cc_start: 0.7945 (ttp-110) cc_final: 0.7628 (tpp-160) REVERT: B 125 GLU cc_start: 0.7515 (tp30) cc_final: 0.7225 (tp30) REVERT: B 205 LEU cc_start: 0.8958 (tp) cc_final: 0.8579 (tp) REVERT: B 215 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8025 (tm-30) REVERT: B 234 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7685 (tttm) REVERT: B 278 LYS cc_start: 0.8345 (tttt) cc_final: 0.7745 (ttmt) REVERT: C 94 ARG cc_start: 0.5192 (ttm110) cc_final: 0.4603 (ptt180) REVERT: C 125 GLU cc_start: 0.7478 (tp30) cc_final: 0.7200 (tp30) REVERT: C 166 LEU cc_start: 0.8222 (tt) cc_final: 0.7543 (mt) REVERT: C 220 ILE cc_start: 0.8417 (tt) cc_final: 0.7956 (tt) REVERT: C 234 LYS cc_start: 0.8569 (ttmt) cc_final: 0.7879 (ttpt) REVERT: C 258 GLN cc_start: 0.8258 (tt0) cc_final: 0.7886 (tm-30) REVERT: D 32 ARG cc_start: 0.6588 (ttt-90) cc_final: 0.6343 (tpt170) REVERT: D 68 TYR cc_start: 0.7344 (t80) cc_final: 0.7104 (t80) REVERT: D 118 LEU cc_start: 0.8716 (tp) cc_final: 0.8499 (tp) REVERT: D 125 GLU cc_start: 0.7830 (tp30) cc_final: 0.7449 (tp30) REVERT: D 173 GLN cc_start: 0.8954 (mt0) cc_final: 0.7843 (mp10) REVERT: D 208 LYS cc_start: 0.8334 (mtpp) cc_final: 0.7947 (mtmt) REVERT: D 234 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7636 (tttt) REVERT: D 267 ASN cc_start: 0.8393 (t0) cc_final: 0.7723 (t0) REVERT: E 32 ARG cc_start: 0.7328 (ttt-90) cc_final: 0.6692 (tpp-160) REVERT: E 73 ARG cc_start: 0.7988 (ttp-110) cc_final: 0.7588 (tpp-160) REVERT: E 94 ARG cc_start: 0.5124 (ttm110) cc_final: 0.4710 (ptt180) REVERT: E 144 ARG cc_start: 0.8497 (tmm-80) cc_final: 0.8152 (ptm-80) REVERT: E 173 GLN cc_start: 0.8729 (mt0) cc_final: 0.7936 (mp10) REVERT: E 205 LEU cc_start: 0.9047 (tp) cc_final: 0.8747 (tp) REVERT: E 217 GLU cc_start: 0.8501 (tt0) cc_final: 0.7927 (tt0) REVERT: E 234 LYS cc_start: 0.8415 (ttmt) cc_final: 0.7721 (tttt) REVERT: E 235 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8104 (tm-30) REVERT: E 236 ASN cc_start: 0.7494 (m110) cc_final: 0.7104 (m110) REVERT: E 278 LYS cc_start: 0.8125 (tttt) cc_final: 0.7906 (ttmt) REVERT: E 279 TYR cc_start: 0.7544 (t80) cc_final: 0.7051 (t80) REVERT: F 111 LEU cc_start: 0.8427 (mt) cc_final: 0.8104 (mt) REVERT: F 125 GLU cc_start: 0.7557 (tp30) cc_final: 0.7183 (tp30) REVERT: F 166 LEU cc_start: 0.8077 (tt) cc_final: 0.7434 (mt) REVERT: F 219 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7374 (tm-30) REVERT: F 234 LYS cc_start: 0.8221 (ttmt) cc_final: 0.7424 (ttpt) REVERT: F 235 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8304 (tm-30) REVERT: F 258 GLN cc_start: 0.8226 (tt0) cc_final: 0.8012 (tm-30) REVERT: F 274 SER cc_start: 0.8242 (p) cc_final: 0.7449 (p) REVERT: G 32 ARG cc_start: 0.6835 (ttt-90) cc_final: 0.6309 (tpt170) REVERT: G 125 GLU cc_start: 0.7477 (tp30) cc_final: 0.7009 (tp30) REVERT: G 173 GLN cc_start: 0.8916 (mt0) cc_final: 0.8011 (mp10) REVERT: G 224 LYS cc_start: 0.8425 (ttmt) cc_final: 0.7878 (ttpt) REVERT: G 274 SER cc_start: 0.7895 (p) cc_final: 0.7679 (p) REVERT: H 32 ARG cc_start: 0.6684 (ttt-90) cc_final: 0.5869 (tpt170) REVERT: H 63 LEU cc_start: 0.8939 (tp) cc_final: 0.8735 (tp) REVERT: H 73 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7691 (tpp-160) REVERT: H 94 ARG cc_start: 0.5120 (ttm110) cc_final: 0.4516 (ptt180) REVERT: H 125 GLU cc_start: 0.7551 (tp30) cc_final: 0.7168 (tp30) REVERT: H 144 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8209 (tmm-80) REVERT: H 166 LEU cc_start: 0.8258 (tt) cc_final: 0.7579 (mt) REVERT: H 220 ILE cc_start: 0.8604 (tt) cc_final: 0.8283 (tt) REVERT: H 224 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7812 (ttpt) REVERT: H 231 GLU cc_start: 0.8227 (pp20) cc_final: 0.7926 (tm-30) REVERT: H 234 LYS cc_start: 0.8399 (ttmt) cc_final: 0.7618 (ttpt) REVERT: I 32 ARG cc_start: 0.6960 (ttt-90) cc_final: 0.6436 (tpt170) REVERT: I 63 LEU cc_start: 0.8947 (tp) cc_final: 0.8720 (tp) REVERT: I 125 GLU cc_start: 0.7749 (tp30) cc_final: 0.7456 (tp30) REVERT: I 173 GLN cc_start: 0.8896 (mt0) cc_final: 0.8032 (mt0) REVERT: I 192 PHE cc_start: 0.8615 (t80) cc_final: 0.8332 (t80) REVERT: I 208 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8094 (mtpt) REVERT: I 217 GLU cc_start: 0.8582 (tt0) cc_final: 0.8067 (tt0) REVERT: I 224 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8176 (ttpt) REVERT: I 234 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7611 (tttt) REVERT: I 274 SER cc_start: 0.8359 (p) cc_final: 0.7362 (p) REVERT: J 32 ARG cc_start: 0.7275 (ttt-90) cc_final: 0.6707 (ttt90) REVERT: J 55 PHE cc_start: 0.8977 (m-80) cc_final: 0.8480 (m-80) REVERT: J 63 LEU cc_start: 0.8987 (tp) cc_final: 0.8737 (tp) REVERT: J 73 ARG cc_start: 0.8018 (ttp-110) cc_final: 0.7629 (tpp-160) REVERT: J 94 ARG cc_start: 0.5033 (ttm110) cc_final: 0.4717 (ptt180) REVERT: J 125 GLU cc_start: 0.7548 (tp30) cc_final: 0.7265 (tp30) REVERT: J 173 GLN cc_start: 0.8725 (mt0) cc_final: 0.7821 (mp10) REVERT: J 210 TRP cc_start: 0.8820 (t60) cc_final: 0.8449 (t60) REVERT: J 217 GLU cc_start: 0.8597 (tt0) cc_final: 0.8130 (tt0) REVERT: J 224 LYS cc_start: 0.8377 (ttmt) cc_final: 0.8161 (ttpt) REVERT: J 234 LYS cc_start: 0.8339 (ttmt) cc_final: 0.7689 (tttt) REVERT: J 235 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7938 (tm-30) REVERT: J 236 ASN cc_start: 0.7254 (m-40) cc_final: 0.6498 (m110) REVERT: J 279 TYR cc_start: 0.7577 (t80) cc_final: 0.7148 (t80) outliers start: 0 outliers final: 0 residues processed: 746 average time/residue: 0.3195 time to fit residues: 366.1487 Evaluate side-chains 633 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 633 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 233 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 137 optimal weight: 0.0030 chunk 176 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 203 optimal weight: 0.8980 chunk 135 optimal weight: 0.2980 chunk 240 optimal weight: 0.1980 chunk 150 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN I 175 GLN I 236 ASN J 48 ASN J 206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20010 Z= 0.176 Angle : 0.687 7.240 27200 Z= 0.331 Chirality : 0.038 0.168 3170 Planarity : 0.004 0.041 3350 Dihedral : 4.653 22.164 2690 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.26 % Favored : 92.46 % Rotamer: Outliers : 0.05 % Allowed : 1.25 % Favored : 98.70 % 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: 0.07 (0.17), residues: 2480 helix: 1.16 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -3.77 (0.21), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 257 HIS 0.003 0.001 HIS C 277 PHE 0.017 0.001 PHE F 134 TYR 0.021 0.002 TYR E 264 ARG 0.008 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 753 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7025 (ttt-90) cc_final: 0.6680 (ttt90) REVERT: A 48 ASN cc_start: 0.8231 (t0) cc_final: 0.7821 (t0) REVERT: A 125 GLU cc_start: 0.7314 (tp30) cc_final: 0.7066 (tp30) REVERT: A 166 LEU cc_start: 0.8165 (tt) cc_final: 0.7400 (mt) REVERT: A 234 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7414 (ttpt) REVERT: A 235 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8352 (tm-30) REVERT: A 236 ASN cc_start: 0.7737 (m110) cc_final: 0.7313 (m110) REVERT: A 274 SER cc_start: 0.7848 (p) cc_final: 0.6611 (p) REVERT: B 32 ARG cc_start: 0.6593 (ttt-90) cc_final: 0.6233 (tpt170) REVERT: B 73 ARG cc_start: 0.7907 (ttp-110) cc_final: 0.7648 (tpp-160) REVERT: B 167 LEU cc_start: 0.7720 (pp) cc_final: 0.6853 (tp) REVERT: B 215 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7878 (tm-30) REVERT: B 234 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7600 (tttm) REVERT: B 256 GLU cc_start: 0.8531 (tt0) cc_final: 0.8327 (tt0) REVERT: B 274 SER cc_start: 0.7839 (p) cc_final: 0.7305 (p) REVERT: C 94 ARG cc_start: 0.5170 (ttm110) cc_final: 0.4570 (ptt180) REVERT: C 134 PHE cc_start: 0.8392 (t80) cc_final: 0.8003 (t80) REVERT: C 220 ILE cc_start: 0.8507 (tt) cc_final: 0.8156 (tt) REVERT: C 234 LYS cc_start: 0.8417 (ttmt) cc_final: 0.7664 (ttpt) REVERT: C 258 GLN cc_start: 0.8115 (tt0) cc_final: 0.7885 (tm-30) REVERT: D 32 ARG cc_start: 0.6573 (ttt-90) cc_final: 0.6344 (tpt170) REVERT: D 63 LEU cc_start: 0.8996 (tp) cc_final: 0.8759 (tp) REVERT: D 73 ARG cc_start: 0.5212 (tpp-160) cc_final: 0.4391 (tpt170) REVERT: D 123 PHE cc_start: 0.9060 (m-10) cc_final: 0.8696 (m-80) REVERT: D 125 GLU cc_start: 0.7606 (tp30) cc_final: 0.7166 (tp30) REVERT: D 173 GLN cc_start: 0.8903 (mt0) cc_final: 0.7845 (mp10) REVERT: D 208 LYS cc_start: 0.8355 (mtpp) cc_final: 0.8002 (mtmt) REVERT: D 234 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7692 (tttt) REVERT: D 267 ASN cc_start: 0.8249 (t0) cc_final: 0.7560 (t0) REVERT: E 32 ARG cc_start: 0.7272 (ttt-90) cc_final: 0.6800 (tpp-160) REVERT: E 63 LEU cc_start: 0.9012 (tp) cc_final: 0.8800 (tp) REVERT: E 73 ARG cc_start: 0.7943 (ttp-110) cc_final: 0.7608 (tpp-160) REVERT: E 94 ARG cc_start: 0.5198 (ttm110) cc_final: 0.4766 (ptt180) REVERT: E 111 LEU cc_start: 0.8592 (mt) cc_final: 0.8249 (mt) REVERT: E 173 GLN cc_start: 0.8660 (mt0) cc_final: 0.7790 (mp10) REVERT: E 217 GLU cc_start: 0.8522 (tt0) cc_final: 0.7924 (tt0) REVERT: E 224 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8166 (tttt) REVERT: E 234 LYS cc_start: 0.8397 (ttmt) cc_final: 0.7737 (tttt) REVERT: E 235 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8137 (tm-30) REVERT: E 236 ASN cc_start: 0.7457 (m110) cc_final: 0.7126 (m110) REVERT: E 279 TYR cc_start: 0.7694 (t80) cc_final: 0.7248 (t80) REVERT: F 166 LEU cc_start: 0.8054 (tt) cc_final: 0.7536 (mt) REVERT: F 173 GLN cc_start: 0.8359 (mt0) cc_final: 0.7431 (mt0) REVERT: F 234 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7465 (ttpt) REVERT: F 235 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8358 (tm-30) REVERT: F 274 SER cc_start: 0.8235 (p) cc_final: 0.7080 (p) REVERT: F 279 TYR cc_start: 0.7086 (t80) cc_final: 0.6861 (t80) REVERT: G 32 ARG cc_start: 0.6891 (ttt-90) cc_final: 0.6298 (tpt170) REVERT: G 173 GLN cc_start: 0.8778 (mt0) cc_final: 0.7848 (mp10) REVERT: G 215 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7824 (tp30) REVERT: G 224 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7870 (ttpt) REVERT: G 274 SER cc_start: 0.7865 (p) cc_final: 0.7466 (p) REVERT: G 279 TYR cc_start: 0.7750 (t80) cc_final: 0.7413 (t80) REVERT: H 32 ARG cc_start: 0.6837 (ttt-90) cc_final: 0.5907 (tpt170) REVERT: H 63 LEU cc_start: 0.8936 (tp) cc_final: 0.8720 (tp) REVERT: H 73 ARG cc_start: 0.7958 (ttp-110) cc_final: 0.7691 (tpp-160) REVERT: H 94 ARG cc_start: 0.4963 (ttm110) cc_final: 0.4572 (ptt180) REVERT: H 144 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8157 (tmm-80) REVERT: H 220 ILE cc_start: 0.8577 (tt) cc_final: 0.8231 (tt) REVERT: H 224 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7707 (ttpt) REVERT: H 231 GLU cc_start: 0.8067 (pp20) cc_final: 0.7822 (tm-30) REVERT: H 234 LYS cc_start: 0.8385 (ttmt) cc_final: 0.7559 (ttpt) REVERT: I 32 ARG cc_start: 0.6934 (ttt-90) cc_final: 0.6477 (tpt170) REVERT: I 51 TYR cc_start: 0.8640 (t80) cc_final: 0.8357 (t80) REVERT: I 63 LEU cc_start: 0.8973 (tp) cc_final: 0.8704 (tp) REVERT: I 125 GLU cc_start: 0.7655 (tp30) cc_final: 0.7260 (tp30) REVERT: I 144 ARG cc_start: 0.8472 (tmm-80) cc_final: 0.8115 (ptm-80) REVERT: I 173 GLN cc_start: 0.8852 (mt0) cc_final: 0.7992 (mt0) REVERT: I 192 PHE cc_start: 0.8611 (t80) cc_final: 0.8389 (t80) REVERT: I 208 LYS cc_start: 0.8366 (mtpp) cc_final: 0.8081 (mtpt) REVERT: I 224 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8191 (ttpt) REVERT: I 234 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7488 (tttt) REVERT: I 258 GLN cc_start: 0.8191 (tt0) cc_final: 0.7845 (tm-30) REVERT: J 32 ARG cc_start: 0.7095 (ttt-90) cc_final: 0.6712 (ttt90) REVERT: J 55 PHE cc_start: 0.8991 (m-80) cc_final: 0.8631 (m-80) REVERT: J 63 LEU cc_start: 0.8990 (tp) cc_final: 0.8710 (tp) REVERT: J 73 ARG cc_start: 0.7998 (ttp-110) cc_final: 0.7614 (tpp-160) REVERT: J 94 ARG cc_start: 0.5290 (ttm110) cc_final: 0.4774 (ptt180) REVERT: J 125 GLU cc_start: 0.7309 (tp30) cc_final: 0.7034 (tp30) REVERT: J 144 ARG cc_start: 0.8503 (tmm-80) cc_final: 0.8101 (ptm-80) REVERT: J 173 GLN cc_start: 0.8729 (mt0) cc_final: 0.7790 (mp10) REVERT: J 217 GLU cc_start: 0.8610 (tt0) cc_final: 0.7986 (tt0) REVERT: J 224 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7988 (ttpt) REVERT: J 234 LYS cc_start: 0.8359 (ttmt) cc_final: 0.7716 (tttt) REVERT: J 235 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8181 (tm-30) REVERT: J 236 ASN cc_start: 0.7094 (m-40) cc_final: 0.6826 (m-40) REVERT: J 279 TYR cc_start: 0.7612 (t80) cc_final: 0.7215 (t80) outliers start: 1 outliers final: 0 residues processed: 754 average time/residue: 0.2937 time to fit residues: 337.8402 Evaluate side-chains 639 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 639 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 149 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN J 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20010 Z= 0.208 Angle : 0.701 9.919 27200 Z= 0.343 Chirality : 0.039 0.247 3170 Planarity : 0.004 0.041 3350 Dihedral : 4.690 23.669 2690 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.30 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: 0.09 (0.17), residues: 2480 helix: 1.16 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -3.70 (0.21), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 257 HIS 0.003 0.001 HIS C 245 PHE 0.013 0.001 PHE F 266 TYR 0.032 0.002 TYR A 279 ARG 0.009 0.000 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 734 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7070 (ttt-90) cc_final: 0.6684 (ttt90) REVERT: A 48 ASN cc_start: 0.8251 (t0) cc_final: 0.7731 (t0) REVERT: A 63 LEU cc_start: 0.8868 (tp) cc_final: 0.8654 (tp) REVERT: A 125 GLU cc_start: 0.7553 (tp30) cc_final: 0.7174 (tp30) REVERT: A 144 ARG cc_start: 0.8379 (ttp80) cc_final: 0.7981 (tmm-80) REVERT: A 166 LEU cc_start: 0.8176 (tt) cc_final: 0.7438 (mt) REVERT: A 210 TRP cc_start: 0.8602 (t60) cc_final: 0.8400 (t60) REVERT: A 217 GLU cc_start: 0.8780 (tt0) cc_final: 0.8502 (tt0) REVERT: A 219 GLN cc_start: 0.7634 (tm-30) cc_final: 0.7294 (tm-30) REVERT: A 220 ILE cc_start: 0.8856 (tt) cc_final: 0.8521 (tt) REVERT: A 234 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7488 (ttpt) REVERT: A 235 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 236 ASN cc_start: 0.7672 (m110) cc_final: 0.7245 (m110) REVERT: A 274 SER cc_start: 0.8046 (p) cc_final: 0.7281 (p) REVERT: B 32 ARG cc_start: 0.6661 (ttt-90) cc_final: 0.6258 (tpt170) REVERT: B 73 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7620 (tpp-160) REVERT: B 205 LEU cc_start: 0.8984 (tp) cc_final: 0.8138 (tp) REVERT: B 215 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8028 (tm-30) REVERT: B 217 GLU cc_start: 0.8852 (tt0) cc_final: 0.8548 (tt0) REVERT: B 234 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7612 (tttm) REVERT: B 274 SER cc_start: 0.7714 (p) cc_final: 0.7153 (p) REVERT: C 63 LEU cc_start: 0.8907 (tp) cc_final: 0.8704 (tp) REVERT: C 94 ARG cc_start: 0.5221 (ttm110) cc_final: 0.4589 (ptt180) REVERT: C 134 PHE cc_start: 0.8454 (t80) cc_final: 0.8132 (t80) REVERT: C 220 ILE cc_start: 0.8517 (tt) cc_final: 0.8102 (tt) REVERT: C 231 GLU cc_start: 0.8044 (pp20) cc_final: 0.7805 (tm-30) REVERT: C 234 LYS cc_start: 0.8453 (ttmt) cc_final: 0.7667 (ttpt) REVERT: C 258 GLN cc_start: 0.8309 (tt0) cc_final: 0.7962 (tm-30) REVERT: D 32 ARG cc_start: 0.6840 (ttt-90) cc_final: 0.6341 (tpt170) REVERT: D 63 LEU cc_start: 0.8913 (tp) cc_final: 0.8707 (tp) REVERT: D 73 ARG cc_start: 0.5320 (tpp-160) cc_final: 0.4496 (tpt170) REVERT: D 125 GLU cc_start: 0.7639 (tp30) cc_final: 0.7238 (tp30) REVERT: D 134 PHE cc_start: 0.8237 (t80) cc_final: 0.7723 (t80) REVERT: D 173 GLN cc_start: 0.8884 (mt0) cc_final: 0.7907 (mt0) REVERT: D 208 LYS cc_start: 0.8396 (mtpp) cc_final: 0.7984 (mtmt) REVERT: D 234 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7687 (tttt) REVERT: D 267 ASN cc_start: 0.8405 (t0) cc_final: 0.7752 (t0) REVERT: D 274 SER cc_start: 0.8116 (p) cc_final: 0.7179 (p) REVERT: E 32 ARG cc_start: 0.7140 (ttt-90) cc_final: 0.6734 (ttt90) REVERT: E 55 PHE cc_start: 0.8954 (m-80) cc_final: 0.8613 (m-10) REVERT: E 73 ARG cc_start: 0.7986 (ttp-110) cc_final: 0.7626 (tpp-160) REVERT: E 94 ARG cc_start: 0.5522 (ttm110) cc_final: 0.4857 (ptt180) REVERT: E 144 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7966 (tmm-80) REVERT: E 166 LEU cc_start: 0.8123 (tt) cc_final: 0.7538 (mt) REVERT: E 173 GLN cc_start: 0.8716 (mt0) cc_final: 0.7859 (mp10) REVERT: E 217 GLU cc_start: 0.8559 (tt0) cc_final: 0.8204 (tt0) REVERT: E 234 LYS cc_start: 0.8421 (ttmt) cc_final: 0.7759 (tttt) REVERT: E 235 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8272 (tm-30) REVERT: E 274 SER cc_start: 0.7784 (p) cc_final: 0.5932 (p) REVERT: E 279 TYR cc_start: 0.7507 (t80) cc_final: 0.7154 (t80) REVERT: F 125 GLU cc_start: 0.7646 (tp30) cc_final: 0.7261 (tp30) REVERT: F 166 LEU cc_start: 0.8056 (tt) cc_final: 0.7514 (mt) REVERT: F 173 GLN cc_start: 0.8482 (mt0) cc_final: 0.7526 (mt0) REVERT: F 217 GLU cc_start: 0.8716 (tt0) cc_final: 0.8376 (tt0) REVERT: F 234 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7489 (ttpt) REVERT: F 236 ASN cc_start: 0.7858 (m-40) cc_final: 0.7602 (m-40) REVERT: F 274 SER cc_start: 0.8218 (p) cc_final: 0.7065 (p) REVERT: F 279 TYR cc_start: 0.7312 (t80) cc_final: 0.7003 (t80) REVERT: G 32 ARG cc_start: 0.6875 (ttt-90) cc_final: 0.6348 (tpt170) REVERT: G 144 ARG cc_start: 0.8408 (tmm-80) cc_final: 0.8021 (ptm-80) REVERT: G 166 LEU cc_start: 0.8063 (tt) cc_final: 0.7454 (mt) REVERT: G 173 GLN cc_start: 0.8903 (mt0) cc_final: 0.7863 (mp10) REVERT: G 215 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7788 (tp30) REVERT: G 224 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8035 (ttpt) REVERT: G 274 SER cc_start: 0.7888 (p) cc_final: 0.7589 (p) REVERT: H 32 ARG cc_start: 0.6500 (ttt-90) cc_final: 0.5816 (tpt170) REVERT: H 63 LEU cc_start: 0.8939 (tp) cc_final: 0.8711 (tp) REVERT: H 73 ARG cc_start: 0.7992 (ttp-110) cc_final: 0.7702 (tpp-160) REVERT: H 94 ARG cc_start: 0.5165 (ttm110) cc_final: 0.4524 (ptt180) REVERT: H 144 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8031 (ttp80) REVERT: H 220 ILE cc_start: 0.8601 (tt) cc_final: 0.8167 (tt) REVERT: H 231 GLU cc_start: 0.8209 (pp20) cc_final: 0.7934 (tm-30) REVERT: H 234 LYS cc_start: 0.8414 (ttmt) cc_final: 0.7629 (ttpt) REVERT: I 32 ARG cc_start: 0.6937 (ttt-90) cc_final: 0.6489 (tpt170) REVERT: I 125 GLU cc_start: 0.7717 (tp30) cc_final: 0.7296 (tp30) REVERT: I 144 ARG cc_start: 0.8502 (tmm-80) cc_final: 0.8258 (ptm-80) REVERT: I 173 GLN cc_start: 0.8941 (mt0) cc_final: 0.8169 (mt0) REVERT: I 192 PHE cc_start: 0.8635 (t80) cc_final: 0.8365 (t80) REVERT: I 208 LYS cc_start: 0.8415 (mtpp) cc_final: 0.8069 (mtpt) REVERT: I 217 GLU cc_start: 0.8782 (tt0) cc_final: 0.8522 (tt0) REVERT: I 224 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8264 (ttpt) REVERT: I 234 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7608 (tttt) REVERT: I 279 TYR cc_start: 0.7560 (t80) cc_final: 0.7321 (t80) REVERT: J 32 ARG cc_start: 0.7297 (ttt-90) cc_final: 0.6745 (ttt90) REVERT: J 63 LEU cc_start: 0.9001 (tp) cc_final: 0.8708 (tp) REVERT: J 73 ARG cc_start: 0.8018 (ttp-110) cc_final: 0.7637 (tpp-160) REVERT: J 94 ARG cc_start: 0.5299 (ttm110) cc_final: 0.4791 (ptt180) REVERT: J 125 GLU cc_start: 0.7405 (tp30) cc_final: 0.7154 (tp30) REVERT: J 144 ARG cc_start: 0.8547 (tmm-80) cc_final: 0.8177 (ptm-80) REVERT: J 173 GLN cc_start: 0.8822 (mt0) cc_final: 0.7861 (mp10) REVERT: J 210 TRP cc_start: 0.8693 (t60) cc_final: 0.8492 (t60) REVERT: J 217 GLU cc_start: 0.8594 (tt0) cc_final: 0.8214 (tt0) REVERT: J 224 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8133 (ttpt) REVERT: J 234 LYS cc_start: 0.8365 (ttmt) cc_final: 0.7778 (tttt) REVERT: J 279 TYR cc_start: 0.7682 (t80) cc_final: 0.7306 (t80) outliers start: 0 outliers final: 0 residues processed: 734 average time/residue: 0.2916 time to fit residues: 326.7387 Evaluate side-chains 636 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 636 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 219 optimal weight: 0.9980 chunk 230 optimal weight: 6.9990 chunk 210 optimal weight: 0.4980 chunk 224 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 212 optimal weight: 0.0670 chunk 223 optimal weight: 5.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN C 175 GLN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN E 206 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN ** J 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20010 Z= 0.191 Angle : 0.715 10.133 27200 Z= 0.343 Chirality : 0.040 0.267 3170 Planarity : 0.004 0.042 3350 Dihedral : 4.643 23.021 2690 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.22 % Favored : 92.58 % Rotamer: Outliers : 0.10 % Allowed : 0.43 % Favored : 99.47 % 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: 0.06 (0.17), residues: 2480 helix: 1.09 (0.12), residues: 1910 sheet: None (None), residues: 0 loop : -3.71 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 210 HIS 0.007 0.001 HIS C 245 PHE 0.021 0.001 PHE A 55 TYR 0.025 0.002 TYR G 279 ARG 0.010 0.000 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 740 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6925 (ttt-90) cc_final: 0.6552 (ttt90) REVERT: A 125 GLU cc_start: 0.7546 (tp30) cc_final: 0.7163 (tp30) REVERT: A 134 PHE cc_start: 0.8392 (t80) cc_final: 0.8168 (t80) REVERT: A 144 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7966 (tmm-80) REVERT: A 166 LEU cc_start: 0.8159 (tt) cc_final: 0.7409 (mt) REVERT: A 210 TRP cc_start: 0.8647 (t60) cc_final: 0.8405 (t60) REVERT: A 217 GLU cc_start: 0.8777 (tt0) cc_final: 0.8453 (tt0) REVERT: A 220 ILE cc_start: 0.8884 (tt) cc_final: 0.8654 (tt) REVERT: A 234 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7452 (ttpt) REVERT: A 235 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8420 (tm-30) REVERT: A 274 SER cc_start: 0.8017 (p) cc_final: 0.6719 (p) REVERT: B 32 ARG cc_start: 0.6599 (ttt-90) cc_final: 0.6273 (tpt170) REVERT: B 73 ARG cc_start: 0.7950 (ttp-110) cc_final: 0.7656 (tpp-160) REVERT: B 215 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7942 (tm-30) REVERT: B 220 ILE cc_start: 0.8438 (tt) cc_final: 0.7901 (tt) REVERT: B 234 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7603 (tttm) REVERT: B 256 GLU cc_start: 0.8525 (tt0) cc_final: 0.8169 (tt0) REVERT: B 274 SER cc_start: 0.7598 (p) cc_final: 0.6751 (p) REVERT: B 279 TYR cc_start: 0.7696 (t80) cc_final: 0.7069 (t80) REVERT: C 63 LEU cc_start: 0.8881 (tp) cc_final: 0.8668 (tp) REVERT: C 94 ARG cc_start: 0.5225 (ttm110) cc_final: 0.4551 (ptt180) REVERT: C 134 PHE cc_start: 0.8398 (t80) cc_final: 0.8142 (t80) REVERT: C 177 LEU cc_start: 0.9031 (tp) cc_final: 0.8713 (tp) REVERT: C 220 ILE cc_start: 0.8606 (tt) cc_final: 0.8201 (tt) REVERT: C 231 GLU cc_start: 0.8209 (pp20) cc_final: 0.7822 (tm-30) REVERT: C 234 LYS cc_start: 0.8414 (ttmt) cc_final: 0.7682 (ttpt) REVERT: D 32 ARG cc_start: 0.6784 (ttt-90) cc_final: 0.6384 (tpt170) REVERT: D 51 TYR cc_start: 0.8909 (t80) cc_final: 0.8701 (t80) REVERT: D 55 PHE cc_start: 0.8870 (m-80) cc_final: 0.8578 (m-80) REVERT: D 63 LEU cc_start: 0.8956 (tp) cc_final: 0.8751 (tp) REVERT: D 73 ARG cc_start: 0.5308 (tpp-160) cc_final: 0.4502 (tpt170) REVERT: D 123 PHE cc_start: 0.9054 (m-10) cc_final: 0.8753 (m-80) REVERT: D 125 GLU cc_start: 0.7618 (tp30) cc_final: 0.7204 (tp30) REVERT: D 134 PHE cc_start: 0.8228 (t80) cc_final: 0.7745 (t80) REVERT: D 173 GLN cc_start: 0.8814 (mt0) cc_final: 0.7874 (mt0) REVERT: D 208 LYS cc_start: 0.8342 (mtpp) cc_final: 0.7947 (mtmt) REVERT: D 234 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7684 (tttt) REVERT: D 279 TYR cc_start: 0.7728 (t80) cc_final: 0.7450 (t80) REVERT: E 32 ARG cc_start: 0.7106 (ttt-90) cc_final: 0.6774 (ttt90) REVERT: E 55 PHE cc_start: 0.8933 (m-80) cc_final: 0.8637 (m-10) REVERT: E 73 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.7629 (tpp-160) REVERT: E 94 ARG cc_start: 0.5490 (ttm110) cc_final: 0.4878 (ptt180) REVERT: E 144 ARG cc_start: 0.8377 (ttp80) cc_final: 0.7920 (tmm-80) REVERT: E 166 LEU cc_start: 0.8026 (tt) cc_final: 0.7415 (mt) REVERT: E 173 GLN cc_start: 0.8733 (mt0) cc_final: 0.7829 (mp10) REVERT: E 217 GLU cc_start: 0.8571 (tt0) cc_final: 0.8255 (tt0) REVERT: E 234 LYS cc_start: 0.8437 (ttmt) cc_final: 0.7736 (tttt) REVERT: E 235 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7596 (tm-30) REVERT: E 236 ASN cc_start: 0.7521 (m110) cc_final: 0.6808 (m110) REVERT: E 274 SER cc_start: 0.7748 (p) cc_final: 0.5953 (p) REVERT: E 279 TYR cc_start: 0.7525 (t80) cc_final: 0.7039 (t80) REVERT: F 125 GLU cc_start: 0.7618 (tp30) cc_final: 0.7223 (tp30) REVERT: F 166 LEU cc_start: 0.8050 (tt) cc_final: 0.7519 (mt) REVERT: F 173 GLN cc_start: 0.8459 (mt0) cc_final: 0.7498 (mt0) REVERT: F 219 GLN cc_start: 0.7480 (tm-30) cc_final: 0.7185 (tm-30) REVERT: F 234 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7424 (ttpt) REVERT: F 274 SER cc_start: 0.8193 (p) cc_final: 0.7369 (p) REVERT: F 279 TYR cc_start: 0.7194 (t80) cc_final: 0.6964 (t80) REVERT: G 32 ARG cc_start: 0.6808 (ttt-90) cc_final: 0.6311 (tpt170) REVERT: G 173 GLN cc_start: 0.8854 (mt0) cc_final: 0.7839 (mp10) REVERT: G 215 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7795 (tp30) REVERT: G 224 LYS cc_start: 0.8374 (ttmt) cc_final: 0.7820 (ttpt) REVERT: G 274 SER cc_start: 0.7947 (p) cc_final: 0.7500 (p) REVERT: G 279 TYR cc_start: 0.7600 (t80) cc_final: 0.7397 (t80) REVERT: H 32 ARG cc_start: 0.6689 (ttt-90) cc_final: 0.5838 (tpt170) REVERT: H 63 LEU cc_start: 0.8887 (tp) cc_final: 0.8642 (tp) REVERT: H 73 ARG cc_start: 0.7994 (ttp-110) cc_final: 0.7712 (tpp-160) REVERT: H 94 ARG cc_start: 0.5149 (ttm110) cc_final: 0.4529 (ptt180) REVERT: H 134 PHE cc_start: 0.8527 (t80) cc_final: 0.8257 (t80) REVERT: H 144 ARG cc_start: 0.8382 (ttp80) cc_final: 0.8053 (ttp80) REVERT: H 159 LYS cc_start: 0.6290 (mttt) cc_final: 0.6088 (mmtt) REVERT: H 220 ILE cc_start: 0.8571 (tt) cc_final: 0.8265 (tt) REVERT: H 231 GLU cc_start: 0.8183 (pp20) cc_final: 0.7899 (tm-30) REVERT: H 234 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7605 (ttpt) REVERT: I 32 ARG cc_start: 0.6949 (ttt-90) cc_final: 0.6519 (tpt170) REVERT: I 63 LEU cc_start: 0.8979 (tp) cc_final: 0.8758 (tp) REVERT: I 125 GLU cc_start: 0.7668 (tp30) cc_final: 0.7284 (tp30) REVERT: I 173 GLN cc_start: 0.8952 (mt0) cc_final: 0.8126 (mt0) REVERT: I 192 PHE cc_start: 0.8668 (t80) cc_final: 0.8445 (t80) REVERT: I 208 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8109 (mtpt) REVERT: I 217 GLU cc_start: 0.8681 (tt0) cc_final: 0.8347 (tt0) REVERT: I 224 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8204 (ttpt) REVERT: I 234 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7575 (tttt) REVERT: I 236 ASN cc_start: 0.7946 (m110) cc_final: 0.7728 (m110) REVERT: I 274 SER cc_start: 0.8176 (p) cc_final: 0.6985 (p) REVERT: I 279 TYR cc_start: 0.7559 (t80) cc_final: 0.7322 (t80) REVERT: J 32 ARG cc_start: 0.7298 (ttt-90) cc_final: 0.6748 (ttt90) REVERT: J 63 LEU cc_start: 0.8979 (tp) cc_final: 0.8667 (tp) REVERT: J 73 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.7626 (tpp-160) REVERT: J 94 ARG cc_start: 0.5503 (ttm110) cc_final: 0.4861 (ptt180) REVERT: J 125 GLU cc_start: 0.7389 (tp30) cc_final: 0.7178 (tp30) REVERT: J 144 ARG cc_start: 0.8557 (tmm-80) cc_final: 0.8224 (ptm-80) REVERT: J 173 GLN cc_start: 0.8779 (mt0) cc_final: 0.7824 (mp10) REVERT: J 217 GLU cc_start: 0.8623 (tt0) cc_final: 0.8190 (tt0) REVERT: J 224 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8107 (ttpt) REVERT: J 234 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7717 (tttt) REVERT: J 235 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8060 (tm-30) REVERT: J 274 SER cc_start: 0.7837 (p) cc_final: 0.6363 (p) REVERT: J 279 TYR cc_start: 0.7771 (t80) cc_final: 0.7420 (t80) outliers start: 2 outliers final: 0 residues processed: 742 average time/residue: 0.2959 time to fit residues: 334.4614 Evaluate side-chains 641 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 641 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 147 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 0.0770 chunk 165 optimal weight: 0.5980 chunk 249 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 198 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 121 optimal weight: 0.0980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN C 175 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN ** J 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20010 Z= 0.177 Angle : 0.700 9.105 27200 Z= 0.334 Chirality : 0.038 0.236 3170 Planarity : 0.004 0.045 3350 Dihedral : 4.571 22.930 2690 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.06 % Favored : 92.78 % Rotamer: Outliers : 0.05 % Allowed : 0.14 % Favored : 99.81 % 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: 0.15 (0.17), residues: 2480 helix: 1.14 (0.12), residues: 1910 sheet: None (None), residues: 0 loop : -3.60 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP J 210 HIS 0.005 0.000 HIS C 277 PHE 0.020 0.001 PHE B 134 TYR 0.034 0.002 TYR A 279 ARG 0.011 0.000 ARG C 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 743 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6770 (ttt-90) cc_final: 0.6505 (ttt90) REVERT: A 125 GLU cc_start: 0.7555 (tp30) cc_final: 0.7195 (tp30) REVERT: A 134 PHE cc_start: 0.8347 (t80) cc_final: 0.8145 (t80) REVERT: A 166 LEU cc_start: 0.8034 (tt) cc_final: 0.7262 (mt) REVERT: A 217 GLU cc_start: 0.8756 (tt0) cc_final: 0.8493 (tt0) REVERT: A 234 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7433 (ttpt) REVERT: A 274 SER cc_start: 0.7976 (p) cc_final: 0.6767 (p) REVERT: B 32 ARG cc_start: 0.6625 (ttt-90) cc_final: 0.6250 (tpt170) REVERT: B 73 ARG cc_start: 0.7902 (ttp-110) cc_final: 0.7649 (tpp-160) REVERT: B 234 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7649 (tttm) REVERT: B 256 GLU cc_start: 0.8554 (tt0) cc_final: 0.8139 (tt0) REVERT: B 274 SER cc_start: 0.7666 (p) cc_final: 0.6851 (p) REVERT: B 279 TYR cc_start: 0.7658 (t80) cc_final: 0.7030 (t80) REVERT: C 94 ARG cc_start: 0.5038 (ttm110) cc_final: 0.4647 (ptt180) REVERT: C 134 PHE cc_start: 0.8164 (t80) cc_final: 0.7919 (t80) REVERT: C 177 LEU cc_start: 0.8993 (tp) cc_final: 0.8718 (tp) REVERT: C 220 ILE cc_start: 0.8585 (tt) cc_final: 0.8217 (tt) REVERT: C 231 GLU cc_start: 0.8114 (pp20) cc_final: 0.7785 (tm-30) REVERT: C 234 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7579 (ttpt) REVERT: D 32 ARG cc_start: 0.6757 (ttt-90) cc_final: 0.6392 (tpt170) REVERT: D 73 ARG cc_start: 0.5286 (tpp-160) cc_final: 0.4509 (tpt170) REVERT: D 118 LEU cc_start: 0.8632 (tp) cc_final: 0.8365 (tp) REVERT: D 123 PHE cc_start: 0.9004 (m-10) cc_final: 0.8760 (m-80) REVERT: D 125 GLU cc_start: 0.7610 (tp30) cc_final: 0.7185 (tp30) REVERT: D 134 PHE cc_start: 0.8132 (t80) cc_final: 0.7688 (t80) REVERT: D 173 GLN cc_start: 0.8800 (mt0) cc_final: 0.7879 (mt0) REVERT: D 208 LYS cc_start: 0.8324 (mtpp) cc_final: 0.8025 (mtmt) REVERT: D 234 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7768 (tttt) REVERT: D 258 GLN cc_start: 0.8078 (tt0) cc_final: 0.7762 (tm-30) REVERT: D 279 TYR cc_start: 0.7682 (t80) cc_final: 0.7425 (t80) REVERT: E 32 ARG cc_start: 0.7226 (ttt-90) cc_final: 0.6875 (ttt90) REVERT: E 55 PHE cc_start: 0.8909 (m-80) cc_final: 0.8611 (m-10) REVERT: E 63 LEU cc_start: 0.9021 (tp) cc_final: 0.8808 (tp) REVERT: E 73 ARG cc_start: 0.7959 (ttp-110) cc_final: 0.7643 (tpp-160) REVERT: E 94 ARG cc_start: 0.5437 (ttm110) cc_final: 0.4825 (ptt180) REVERT: E 144 ARG cc_start: 0.8326 (ttp80) cc_final: 0.7882 (tmm-80) REVERT: E 173 GLN cc_start: 0.8712 (mt0) cc_final: 0.7808 (mp10) REVERT: E 234 LYS cc_start: 0.8344 (ttmt) cc_final: 0.7739 (tttt) REVERT: E 279 TYR cc_start: 0.7495 (t80) cc_final: 0.7051 (t80) REVERT: F 166 LEU cc_start: 0.7986 (tt) cc_final: 0.7522 (mt) REVERT: F 173 GLN cc_start: 0.8431 (mt0) cc_final: 0.7503 (mt0) REVERT: F 210 TRP cc_start: 0.8569 (t60) cc_final: 0.8289 (t60) REVERT: F 217 GLU cc_start: 0.8775 (tt0) cc_final: 0.8493 (tt0) REVERT: F 219 GLN cc_start: 0.7446 (tm-30) cc_final: 0.7169 (tm-30) REVERT: F 220 ILE cc_start: 0.8781 (tt) cc_final: 0.8553 (tt) REVERT: F 234 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7362 (ttpt) REVERT: F 274 SER cc_start: 0.7947 (p) cc_final: 0.6621 (p) REVERT: F 279 TYR cc_start: 0.7024 (t80) cc_final: 0.6771 (t80) REVERT: G 32 ARG cc_start: 0.6913 (ttt-90) cc_final: 0.6375 (tpt170) REVERT: G 173 GLN cc_start: 0.8833 (mt0) cc_final: 0.7818 (mp10) REVERT: G 215 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7253 (tp30) REVERT: G 224 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7845 (ttpt) REVERT: G 279 TYR cc_start: 0.7641 (t80) cc_final: 0.7437 (t80) REVERT: H 32 ARG cc_start: 0.6703 (ttt-90) cc_final: 0.5867 (tpt170) REVERT: H 73 ARG cc_start: 0.7995 (ttp-110) cc_final: 0.7710 (tpp-160) REVERT: H 94 ARG cc_start: 0.5043 (ttm110) cc_final: 0.4580 (ptt180) REVERT: H 134 PHE cc_start: 0.8383 (t80) cc_final: 0.8146 (t80) REVERT: H 177 LEU cc_start: 0.9067 (tp) cc_final: 0.8708 (tp) REVERT: H 220 ILE cc_start: 0.8561 (tt) cc_final: 0.8179 (tt) REVERT: H 231 GLU cc_start: 0.7988 (pp20) cc_final: 0.7630 (tm-30) REVERT: H 234 LYS cc_start: 0.8388 (ttmt) cc_final: 0.7535 (ttpt) REVERT: I 63 LEU cc_start: 0.9002 (tp) cc_final: 0.8762 (tp) REVERT: I 125 GLU cc_start: 0.7657 (tp30) cc_final: 0.7261 (tp30) REVERT: I 173 GLN cc_start: 0.8925 (mt0) cc_final: 0.8090 (mt0) REVERT: I 192 PHE cc_start: 0.8636 (t80) cc_final: 0.8404 (t80) REVERT: I 208 LYS cc_start: 0.8342 (mtpp) cc_final: 0.8042 (mtpt) REVERT: I 224 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8148 (ttpt) REVERT: I 234 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7692 (tttt) REVERT: I 258 GLN cc_start: 0.8192 (tt0) cc_final: 0.7847 (tm-30) REVERT: I 274 SER cc_start: 0.8005 (p) cc_final: 0.6979 (p) REVERT: J 32 ARG cc_start: 0.7295 (ttt-90) cc_final: 0.6733 (ttt90) REVERT: J 63 LEU cc_start: 0.8899 (tp) cc_final: 0.8678 (tp) REVERT: J 73 ARG cc_start: 0.7981 (ttp-110) cc_final: 0.7634 (tpp-160) REVERT: J 94 ARG cc_start: 0.5498 (ttm110) cc_final: 0.4823 (ptt180) REVERT: J 125 GLU cc_start: 0.7396 (tp30) cc_final: 0.7124 (tp30) REVERT: J 144 ARG cc_start: 0.8492 (tmm-80) cc_final: 0.8230 (ptm-80) REVERT: J 173 GLN cc_start: 0.8786 (mt0) cc_final: 0.7802 (mp10) REVERT: J 217 GLU cc_start: 0.8624 (tt0) cc_final: 0.8150 (tt0) REVERT: J 234 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7709 (tttt) REVERT: J 235 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8066 (tm-30) REVERT: J 274 SER cc_start: 0.7717 (p) cc_final: 0.6141 (p) REVERT: J 279 TYR cc_start: 0.7737 (t80) cc_final: 0.7390 (t80) outliers start: 1 outliers final: 0 residues processed: 744 average time/residue: 0.2947 time to fit residues: 335.2070 Evaluate side-chains 646 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 646 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 157 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 GLN E 175 GLN ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124472 restraints weight = 35014.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127864 restraints weight = 21383.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130273 restraints weight = 14470.176| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20010 Z= 0.198 Angle : 0.703 9.380 27200 Z= 0.339 Chirality : 0.039 0.225 3170 Planarity : 0.004 0.046 3350 Dihedral : 4.599 22.428 2690 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.22 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.23 (0.18), residues: 2480 helix: 1.16 (0.12), residues: 1910 sheet: None (None), residues: 0 loop : -3.44 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP J 210 HIS 0.004 0.000 HIS C 245 PHE 0.019 0.001 PHE B 134 TYR 0.021 0.002 TYR G 279 ARG 0.011 0.000 ARG C 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5374.39 seconds wall clock time: 97 minutes 32.36 seconds (5852.36 seconds total)