Starting phenix.real_space_refine on Mon Jul 22 22:28:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsi_41593/07_2024/8tsi_41593_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsi_41593/07_2024/8tsi_41593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsi_41593/07_2024/8tsi_41593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsi_41593/07_2024/8tsi_41593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsi_41593/07_2024/8tsi_41593_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsi_41593/07_2024/8tsi_41593_neut.cif" } resolution = 4.4 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= 0.866 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: 7 Type Number sf(0) Gaussians Al 2 5.89 5 P 4 5.49 5 S 98 5.16 5 C 13140 2.51 5 N 3450 2.21 5 O 3546 1.98 5 F 8 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "F GLU 163": "OE1" <-> "OE2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "L GLU 124": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20248 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1700 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 6, 'TRANS': 209} Chain: "C" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2048 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 16, 'TRANS': 240} Chain: "E" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1537 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 177} Chain breaks: 2 Chain: "F" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1606 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain breaks: 2 Chain: "G" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1611 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1590 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1537 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 177} Chain breaks: 2 Chain: "J" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1606 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain breaks: 2 Chain: "K" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1611 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 187} Chain breaks: 2 Chain: "L" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1590 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain breaks: 2 Chain: "D" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2048 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 16, 'TRANS': 240} Chain: "B" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1700 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 6, 'TRANS': 209} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.11, per 1000 atoms: 0.55 Number of scatterers: 20248 At special positions: 0 Unit cell: (135, 130.68, 137.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 98 16.00 P 4 15.00 Al 2 13.00 F 8 9.00 O 3546 8.00 N 3450 7.00 C 13140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS I 138 " - pdb=" SG CYS J 77 " distance=2.03 Simple disulfide: pdb=" SG CYS J 138 " - pdb=" SG CYS K 77 " distance=2.03 Simple disulfide: pdb=" SG CYS K 138 " - pdb=" SG CYS L 77 " distance=2.03 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: 7.59 Conformation dependent library (CDL) restraints added in 3.7 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4716 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 12 sheets defined 65.0% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.694A pdb=" N MET A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.888A pdb=" N TYR A 126 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.777A pdb=" N ARG A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 Processing helix chain 'A' and resid 183 through 191 removed outlier: 3.974A pdb=" N GLU A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 Processing helix chain 'C' and resid 15 through 36 removed outlier: 3.900A pdb=" N THR C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 69 removed outlier: 4.140A pdb=" N PHE C 44 " --> pdb=" O TRP C 40 " (cutoff:3.500A) Proline residue: C 50 - end of helix removed outlier: 6.432A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 94 removed outlier: 3.816A pdb=" N ILE C 79 " --> pdb=" O PRO C 75 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY C 81 " --> pdb=" O PHE C 77 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 96 through 101 removed outlier: 4.015A pdb=" N ASP C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 112 through 143 removed outlier: 3.866A pdb=" N ARG C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 176 Processing helix chain 'C' and resid 177 through 178 No H-bonds generated for 'chain 'C' and resid 177 through 178' Processing helix chain 'C' and resid 179 through 180 No H-bonds generated for 'chain 'C' and resid 179 through 180' Processing helix chain 'C' and resid 181 through 190 removed outlier: 3.979A pdb=" N ILE C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 removed outlier: 3.729A pdb=" N TYR C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.878A pdb=" N THR C 205 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 210 through 216 removed outlier: 3.817A pdb=" N LEU C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 231 Processing helix chain 'C' and resid 242 through 263 Processing helix chain 'E' and resid 13 through 19 removed outlier: 3.596A pdb=" N VAL E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 74 through 84 removed outlier: 4.026A pdb=" N HIS E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 97 Processing helix chain 'E' and resid 97 through 102 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 149 through 180 Processing helix chain 'E' and resid 340 through 361 Processing helix chain 'F' and resid 12 through 19 removed outlier: 4.187A pdb=" N TRP F 16 " --> pdb=" O LYS F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 32 Processing helix chain 'F' and resid 73 through 84 removed outlier: 3.952A pdb=" N HIS F 84 " --> pdb=" O GLN F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 97 Processing helix chain 'F' and resid 97 through 103 removed outlier: 3.706A pdb=" N GLY F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 149 through 175 removed outlier: 3.654A pdb=" N GLN F 154 " --> pdb=" O PRO F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 370 Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 19 through 32 removed outlier: 3.634A pdb=" N MET G 23 " --> pdb=" O VAL G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 84 removed outlier: 4.136A pdb=" N HIS G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 97 Processing helix chain 'G' and resid 97 through 102 removed outlier: 3.760A pdb=" N HIS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 130 Processing helix chain 'G' and resid 149 through 175 removed outlier: 3.940A pdb=" N MET G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 369 Processing helix chain 'H' and resid 11 through 19 Processing helix chain 'H' and resid 19 through 33 Processing helix chain 'H' and resid 72 through 84 removed outlier: 4.228A pdb=" N HIS H 84 " --> pdb=" O GLN H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 97 removed outlier: 3.792A pdb=" N LEU H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 103 Processing helix chain 'H' and resid 118 through 129 Processing helix chain 'H' and resid 149 through 178 removed outlier: 3.744A pdb=" N GLN H 154 " --> pdb=" O PRO H 150 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU H 178 " --> pdb=" O ARG H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 366 Processing helix chain 'I' and resid 13 through 19 Processing helix chain 'I' and resid 19 through 31 removed outlier: 3.908A pdb=" N MET I 23 " --> pdb=" O VAL I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 removed outlier: 4.051A pdb=" N HIS I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 97 Processing helix chain 'I' and resid 97 through 102 Processing helix chain 'I' and resid 118 through 130 Processing helix chain 'I' and resid 149 through 180 Processing helix chain 'I' and resid 340 through 361 Processing helix chain 'J' and resid 7 through 11 removed outlier: 4.102A pdb=" N ALA J 11 " --> pdb=" O ARG J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 19 removed outlier: 4.197A pdb=" N TRP J 16 " --> pdb=" O LYS J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 33 removed outlier: 3.506A pdb=" N MET J 23 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 84 removed outlier: 3.958A pdb=" N HIS J 84 " --> pdb=" O GLN J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 97 Processing helix chain 'J' and resid 97 through 103 removed outlier: 3.707A pdb=" N GLY J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 130 Processing helix chain 'J' and resid 149 through 175 removed outlier: 3.660A pdb=" N GLN J 154 " --> pdb=" O PRO J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 370 Processing helix chain 'K' and resid 13 through 18 Processing helix chain 'K' and resid 19 through 32 removed outlier: 3.790A pdb=" N MET K 23 " --> pdb=" O VAL K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 84 removed outlier: 4.108A pdb=" N HIS K 84 " --> pdb=" O GLN K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 97 Processing helix chain 'K' and resid 97 through 102 removed outlier: 3.754A pdb=" N HIS K 101 " --> pdb=" O LYS K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 130 Processing helix chain 'K' and resid 149 through 175 removed outlier: 3.934A pdb=" N MET K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 369 Processing helix chain 'L' and resid 11 through 19 Processing helix chain 'L' and resid 19 through 33 Processing helix chain 'L' and resid 72 through 84 removed outlier: 4.208A pdb=" N HIS L 84 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 97 removed outlier: 3.810A pdb=" N LEU L 89 " --> pdb=" O SER L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 103 Processing helix chain 'L' and resid 118 through 129 Processing helix chain 'L' and resid 149 through 178 removed outlier: 3.887A pdb=" N GLN L 154 " --> pdb=" O PRO L 150 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 366 Processing helix chain 'D' and resid 15 through 36 removed outlier: 3.900A pdb=" N THR D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 69 removed outlier: 4.140A pdb=" N PHE D 44 " --> pdb=" O TRP D 40 " (cutoff:3.500A) Proline residue: D 50 - end of helix removed outlier: 6.433A pdb=" N LEU D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 94 removed outlier: 3.816A pdb=" N ILE D 79 " --> pdb=" O PRO D 75 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY D 81 " --> pdb=" O PHE D 77 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 96 through 101 removed outlier: 4.015A pdb=" N ASP D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 112 through 143 removed outlier: 3.866A pdb=" N ARG D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 176 Processing helix chain 'D' and resid 177 through 178 No H-bonds generated for 'chain 'D' and resid 177 through 178' Processing helix chain 'D' and resid 179 through 180 No H-bonds generated for 'chain 'D' and resid 179 through 180' Processing helix chain 'D' and resid 181 through 190 removed outlier: 3.979A pdb=" N ILE D 185 " --> pdb=" O GLN D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 197 removed outlier: 3.728A pdb=" N TYR D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 197 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.878A pdb=" N THR D 205 " --> pdb=" O PRO D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 210 through 216 removed outlier: 3.816A pdb=" N LEU D 214 " --> pdb=" O TYR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 231 Processing helix chain 'D' and resid 242 through 263 Processing helix chain 'B' and resid 43 through 53 Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 98 through 113 removed outlier: 3.695A pdb=" N MET B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.888A pdb=" N TYR B 126 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 140 removed outlier: 3.777A pdb=" N ARG B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 171 Processing helix chain 'B' and resid 183 through 191 removed outlier: 3.974A pdb=" N GLU B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 11 removed outlier: 7.497A pdb=" N TYR A 11 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR A 19 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.924A pdb=" N TYR A 147 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A 180 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 149 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 34 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY A 35 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL A 197 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 131 through 135 removed outlier: 7.155A pdb=" N THR E 45 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL E 326 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG E 47 " --> pdb=" O LEU E 324 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU E 324 " --> pdb=" O ARG E 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 131 through 134 removed outlier: 6.931A pdb=" N THR F 45 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL F 326 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG F 47 " --> pdb=" O LEU F 324 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU F 324 " --> pdb=" O ARG F 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 131 through 135 removed outlier: 6.743A pdb=" N VAL G 43 " --> pdb=" O VAL G 327 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.465A pdb=" N VAL H 43 " --> pdb=" O VAL H 327 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG H 47 " --> pdb=" O SER H 323 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER H 323 " --> pdb=" O ARG H 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 131 through 135 removed outlier: 7.113A pdb=" N THR I 45 " --> pdb=" O VAL I 326 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL I 326 " --> pdb=" O THR I 45 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARG I 47 " --> pdb=" O LEU I 324 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU I 324 " --> pdb=" O ARG I 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 131 through 134 removed outlier: 6.938A pdb=" N THR J 45 " --> pdb=" O VAL J 326 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL J 326 " --> pdb=" O THR J 45 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG J 47 " --> pdb=" O LEU J 324 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU J 324 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 131 through 135 removed outlier: 6.740A pdb=" N VAL K 43 " --> pdb=" O VAL K 327 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 130 through 134 removed outlier: 6.931A pdb=" N THR L 45 " --> pdb=" O VAL L 326 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL L 326 " --> pdb=" O THR L 45 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG L 47 " --> pdb=" O LEU L 324 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU L 324 " --> pdb=" O ARG L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 8 through 11 removed outlier: 7.496A pdb=" N TYR B 11 " --> pdb=" O TYR B 19 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR B 19 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.924A pdb=" N TYR B 147 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL B 180 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 149 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE B 34 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY B 35 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL B 197 " --> pdb=" O GLY B 35 " (cutoff:3.500A) 1232 hydrogen bonds defined for protein. 3579 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: 6.26 Time building geometry restraints manager: 8.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6454 1.34 - 1.46: 4851 1.46 - 1.58: 9229 1.58 - 1.70: 6 1.70 - 1.82: 168 Bond restraints: 20708 Sorted by residual: bond pdb=" F1 ALF B 301 " pdb="AL ALF B 301 " ideal model delta sigma weight residual 1.684 1.784 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" F1 ALF A 302 " pdb="AL ALF A 302 " ideal model delta sigma weight residual 1.684 1.784 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" F2 ALF A 302 " pdb="AL ALF A 302 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" F2 ALF B 301 " pdb="AL ALF B 301 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" F3 ALF A 302 " pdb="AL ALF A 302 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 20703 not shown) Histogram of bond angle deviations from ideal: 89.93 - 107.93: 847 107.93 - 125.94: 26921 125.94 - 143.94: 344 143.94 - 161.95: 0 161.95 - 179.95: 4 Bond angle restraints: 28116 Sorted by residual: angle pdb=" F1 ALF A 302 " pdb="AL ALF A 302 " pdb=" F2 ALF A 302 " ideal model delta sigma weight residual 108.68 179.95 -71.27 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F1 ALF B 301 " pdb="AL ALF B 301 " pdb=" F2 ALF B 301 " ideal model delta sigma weight residual 108.68 179.92 -71.24 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F3 ALF A 302 " pdb="AL ALF A 302 " pdb=" F4 ALF A 302 " ideal model delta sigma weight residual 109.63 179.93 -70.30 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F3 ALF B 301 " pdb="AL ALF B 301 " pdb=" F4 ALF B 301 " ideal model delta sigma weight residual 109.63 179.93 -70.30 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F2 ALF A 302 " pdb="AL ALF A 302 " pdb=" F4 ALF A 302 " ideal model delta sigma weight residual 110.21 89.98 20.23 3.00e+00 1.11e-01 4.55e+01 ... (remaining 28111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.19: 11085 24.19 - 48.39: 1115 48.39 - 72.58: 100 72.58 - 96.77: 20 96.77 - 120.96: 6 Dihedral angle restraints: 12326 sinusoidal: 5036 harmonic: 7290 Sorted by residual: dihedral pdb=" CB CYS G 138 " pdb=" SG CYS G 138 " pdb=" SG CYS H 77 " pdb=" CB CYS H 77 " ideal model delta sinusoidal sigma weight residual 93.00 -179.02 -87.98 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS K 138 " pdb=" SG CYS K 138 " pdb=" SG CYS L 77 " pdb=" CB CYS L 77 " ideal model delta sinusoidal sigma weight residual 93.00 -179.43 -87.57 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" C5' ADP B 302 " pdb=" O5' ADP B 302 " pdb=" PA ADP B 302 " pdb=" O2A ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 60.97 -120.96 1 2.00e+01 2.50e-03 3.63e+01 ... (remaining 12323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2495 0.052 - 0.104: 544 0.104 - 0.156: 131 0.156 - 0.208: 30 0.208 - 0.259: 4 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CB THR J 27 " pdb=" CA THR J 27 " pdb=" OG1 THR J 27 " pdb=" CG2 THR J 27 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU F 24 " pdb=" CB LEU F 24 " pdb=" CD1 LEU F 24 " pdb=" CD2 LEU F 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA VAL A 197 " pdb=" N VAL A 197 " pdb=" C VAL A 197 " pdb=" CB VAL A 197 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3201 not shown) Planarity restraints: 3518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 211 " -0.038 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO D 212 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 212 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 212 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 211 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO C 212 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 215 " 0.005 2.00e-02 2.50e+03 1.44e-02 4.15e+00 pdb=" CG TYR B 215 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 215 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 215 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 215 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 215 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 215 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 215 " -0.004 2.00e-02 2.50e+03 ... (remaining 3515 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3217 2.76 - 3.30: 19119 3.30 - 3.83: 33265 3.83 - 4.37: 35672 4.37 - 4.90: 63872 Nonbonded interactions: 155145 Sorted by model distance: nonbonded pdb=" OG1 THR A 83 " pdb=" OE1 GLU A 86 " model vdw 2.225 2.440 nonbonded pdb=" OG1 THR B 83 " pdb=" OE1 GLU B 86 " model vdw 2.225 2.440 nonbonded pdb=" OG SER D 167 " pdb=" OG SER D 252 " model vdw 2.246 2.440 nonbonded pdb=" OG SER C 167 " pdb=" OG SER C 252 " model vdw 2.247 2.440 nonbonded pdb=" O PHE K 30 " pdb=" OG SER K 34 " model vdw 2.247 2.440 ... (remaining 155140 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' and resid 2 through 217) selection = (chain 'B' and resid 2 through 217) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 12 through 175 or resid 322 through 361)) selection = (chain 'F' and (resid 12 through 48 or resid 73 through 361)) selection = (chain 'G' and (resid 12 through 48 or resid 73 through 175 or resid 322 through \ 361)) selection = (chain 'H' and (resid 12 through 48 or resid 73 through 175 or resid 322 through \ 361)) selection = (chain 'I' and (resid 12 through 175 or resid 322 through 361)) selection = (chain 'J' and (resid 12 through 48 or resid 73 through 361)) selection = (chain 'K' and (resid 12 through 48 or resid 73 through 175 or resid 322 through \ 361)) selection = (chain 'L' and (resid 12 through 48 or resid 73 through 175 or resid 322 through \ 361)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 52.920 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 0.100 20708 Z= 0.282 Angle : 1.201 71.270 28116 Z= 0.509 Chirality : 0.049 0.259 3204 Planarity : 0.004 0.065 3518 Dihedral : 17.518 120.963 7592 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.68 % Allowed : 26.73 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.86 (0.17), residues: 2432 helix: 1.42 (0.14), residues: 1422 sheet: 0.75 (0.33), residues: 264 loop : -1.13 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 10 HIS 0.005 0.001 HIS F 369 PHE 0.015 0.001 PHE C 61 TYR 0.033 0.001 TYR B 215 ARG 0.008 0.000 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 456 time to evaluate : 2.158 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.7803 (mtt) cc_final: 0.7465 (mpp) REVERT: A 147 TYR cc_start: 0.7061 (m-10) cc_final: 0.6833 (m-80) REVERT: A 199 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6395 (tp40) REVERT: C 49 GLU cc_start: 0.6135 (tm-30) cc_final: 0.5526 (tm-30) REVERT: C 69 MET cc_start: 0.8685 (ppp) cc_final: 0.8099 (ptt) REVERT: C 96 MET cc_start: 0.8123 (mmm) cc_final: 0.7638 (mmt) REVERT: D 49 GLU cc_start: 0.6145 (tm-30) cc_final: 0.5532 (tm-30) REVERT: D 69 MET cc_start: 0.8648 (ppp) cc_final: 0.8050 (ptt) REVERT: D 96 MET cc_start: 0.8132 (mmm) cc_final: 0.7725 (mmt) REVERT: B 140 MET cc_start: 0.7735 (mtt) cc_final: 0.7386 (mpp) REVERT: B 199 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6464 (tp40) outliers start: 15 outliers final: 6 residues processed: 464 average time/residue: 0.2972 time to fit residues: 212.6804 Evaluate side-chains 448 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 440 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 141 optimal weight: 0.0000 chunk 219 optimal weight: 0.7980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 201 GLN C 204 HIS ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN F 173 HIS H 84 HIS J 173 HIS K 15 GLN L 84 HIS D 204 HIS B 87 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20708 Z= 0.233 Angle : 0.614 12.247 28116 Z= 0.298 Chirality : 0.042 0.173 3204 Planarity : 0.004 0.053 3518 Dihedral : 5.993 117.131 2794 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.18 % Allowed : 3.56 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 2432 helix: 1.86 (0.14), residues: 1426 sheet: 0.79 (0.34), residues: 264 loop : -0.98 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 114 HIS 0.005 0.001 HIS F 173 PHE 0.022 0.001 PHE K 30 TYR 0.026 0.001 TYR A 190 ARG 0.004 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 528 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8795 (mptt) cc_final: 0.8579 (mmtm) REVERT: C 49 GLU cc_start: 0.6636 (tm-30) cc_final: 0.6075 (tm-30) REVERT: C 69 MET cc_start: 0.8403 (ppp) cc_final: 0.7975 (ptt) REVERT: C 87 MET cc_start: 0.7754 (ttm) cc_final: 0.7532 (ttp) REVERT: C 134 ILE cc_start: 0.8636 (tp) cc_final: 0.8205 (tp) REVERT: E 356 TYR cc_start: 0.7889 (t80) cc_final: 0.7628 (t80) REVERT: G 369 HIS cc_start: 0.7568 (t-90) cc_final: 0.7026 (t-90) REVERT: H 80 GLN cc_start: 0.8276 (tm-30) cc_final: 0.8018 (tm-30) REVERT: H 106 LEU cc_start: 0.7868 (mm) cc_final: 0.7618 (pt) REVERT: H 138 CYS cc_start: 0.8188 (m) cc_final: 0.7474 (m) REVERT: K 361 LEU cc_start: 0.8742 (tt) cc_final: 0.8265 (tt) REVERT: L 80 GLN cc_start: 0.8301 (tm-30) cc_final: 0.8018 (tm-30) REVERT: L 106 LEU cc_start: 0.7909 (mm) cc_final: 0.7630 (pt) REVERT: L 138 CYS cc_start: 0.8184 (m) cc_final: 0.7468 (m) REVERT: L 335 ILE cc_start: 0.9104 (tp) cc_final: 0.8858 (tt) REVERT: D 49 GLU cc_start: 0.6679 (tm-30) cc_final: 0.6084 (tm-30) REVERT: D 69 MET cc_start: 0.8360 (ppp) cc_final: 0.7857 (ptt) REVERT: B 48 MET cc_start: 0.8185 (tpt) cc_final: 0.7843 (tpt) REVERT: B 89 LYS cc_start: 0.8900 (mptt) cc_final: 0.8675 (mmtm) outliers start: 4 outliers final: 2 residues processed: 530 average time/residue: 0.3134 time to fit residues: 249.9704 Evaluate side-chains 417 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 415 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 182 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS C 53 HIS C 110 GLN C 204 HIS F 94 GLN H 169 ASN J 94 GLN D 53 HIS D 110 GLN D 204 HIS B 118 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20708 Z= 0.187 Angle : 0.571 15.288 28116 Z= 0.275 Chirality : 0.040 0.199 3204 Planarity : 0.004 0.049 3518 Dihedral : 5.480 115.979 2794 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 2432 helix: 1.90 (0.14), residues: 1446 sheet: 0.87 (0.34), residues: 264 loop : -1.05 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 114 HIS 0.008 0.001 HIS J 369 PHE 0.011 0.001 PHE G 30 TYR 0.022 0.001 TYR B 190 ARG 0.006 0.000 ARG H 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 504 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 33 LYS cc_start: 0.8245 (tptt) cc_final: 0.7846 (tppt) REVERT: C 49 GLU cc_start: 0.6518 (tm-30) cc_final: 0.6064 (tm-30) REVERT: C 69 MET cc_start: 0.8066 (ppp) cc_final: 0.7813 (ptt) REVERT: C 96 MET cc_start: 0.8000 (mmm) cc_final: 0.7766 (mmt) REVERT: C 233 GLN cc_start: 0.7750 (tp40) cc_final: 0.7527 (tp40) REVERT: E 356 TYR cc_start: 0.8025 (t80) cc_final: 0.7689 (t80) REVERT: H 80 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7936 (tm-30) REVERT: H 106 LEU cc_start: 0.7893 (mm) cc_final: 0.7599 (pt) REVERT: I 15 GLN cc_start: 0.8487 (pm20) cc_final: 0.8031 (pm20) REVERT: K 361 LEU cc_start: 0.8574 (tt) cc_final: 0.7969 (tt) REVERT: L 106 LEU cc_start: 0.7903 (mm) cc_final: 0.7650 (pt) REVERT: L 138 CYS cc_start: 0.8175 (m) cc_final: 0.7969 (t) REVERT: L 335 ILE cc_start: 0.9131 (tp) cc_final: 0.8885 (tt) REVERT: D 33 LYS cc_start: 0.8246 (tptt) cc_final: 0.7821 (tppt) REVERT: D 49 GLU cc_start: 0.6555 (tm-30) cc_final: 0.6063 (tm-30) REVERT: D 69 MET cc_start: 0.7934 (ppp) cc_final: 0.7722 (ptt) REVERT: D 96 MET cc_start: 0.8032 (mmm) cc_final: 0.7830 (mmt) REVERT: D 134 ILE cc_start: 0.8661 (tp) cc_final: 0.8327 (tp) REVERT: D 233 GLN cc_start: 0.7792 (tp40) cc_final: 0.7507 (tp40) REVERT: D 257 LEU cc_start: 0.8563 (mt) cc_final: 0.8337 (mt) REVERT: B 48 MET cc_start: 0.8198 (tpp) cc_final: 0.7996 (tpt) outliers start: 2 outliers final: 1 residues processed: 505 average time/residue: 0.3061 time to fit residues: 242.1874 Evaluate side-chains 415 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 414 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 147 optimal weight: 0.0770 chunk 220 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 209 optimal weight: 0.0870 chunk 63 optimal weight: 5.9990 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 53 HIS E 344 ASN ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS B 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20708 Z= 0.237 Angle : 0.574 6.854 28116 Z= 0.281 Chirality : 0.041 0.141 3204 Planarity : 0.004 0.046 3518 Dihedral : 5.285 115.767 2794 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.14 % Allowed : 3.38 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.17), residues: 2432 helix: 1.89 (0.14), residues: 1450 sheet: 0.76 (0.34), residues: 264 loop : -1.21 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 114 HIS 0.005 0.001 HIS K 369 PHE 0.009 0.001 PHE E 30 TYR 0.018 0.001 TYR B 215 ARG 0.006 0.000 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 500 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.6405 (ttt) cc_final: 0.6130 (ttt) REVERT: C 49 GLU cc_start: 0.6429 (tm-30) cc_final: 0.6009 (tm-30) REVERT: C 96 MET cc_start: 0.8213 (mmm) cc_final: 0.7895 (mmt) REVERT: C 150 ARG cc_start: 0.6584 (mtm180) cc_final: 0.6039 (mtm180) REVERT: E 322 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7882 (mttt) REVERT: E 356 TYR cc_start: 0.8081 (t80) cc_final: 0.7832 (t80) REVERT: H 80 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7924 (tm-30) REVERT: H 106 LEU cc_start: 0.7985 (mm) cc_final: 0.7707 (pt) REVERT: I 15 GLN cc_start: 0.8466 (pm20) cc_final: 0.7988 (pm20) REVERT: J 41 GLU cc_start: 0.8513 (tt0) cc_final: 0.8311 (tt0) REVERT: K 361 LEU cc_start: 0.8575 (tt) cc_final: 0.8093 (tt) REVERT: K 369 HIS cc_start: 0.7347 (t-90) cc_final: 0.7072 (t-90) REVERT: L 106 LEU cc_start: 0.7960 (mm) cc_final: 0.7692 (pt) REVERT: L 335 ILE cc_start: 0.9107 (tp) cc_final: 0.8867 (tt) REVERT: D 49 GLU cc_start: 0.6438 (tm-30) cc_final: 0.5405 (tm-30) REVERT: D 96 MET cc_start: 0.8235 (mmm) cc_final: 0.7924 (mmt) REVERT: D 134 ILE cc_start: 0.8707 (tp) cc_final: 0.8357 (tp) REVERT: D 150 ARG cc_start: 0.6593 (mtm180) cc_final: 0.6044 (mtm180) outliers start: 3 outliers final: 2 residues processed: 502 average time/residue: 0.3007 time to fit residues: 232.6806 Evaluate side-chains 406 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 404 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 9.9990 chunk 132 optimal weight: 0.5980 chunk 3 optimal weight: 9.9990 chunk 174 optimal weight: 0.0870 chunk 96 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 HIS F 94 GLN J 94 GLN D 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20708 Z= 0.278 Angle : 0.620 17.738 28116 Z= 0.299 Chirality : 0.042 0.225 3204 Planarity : 0.004 0.045 3518 Dihedral : 5.284 118.638 2794 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.17), residues: 2432 helix: 1.85 (0.14), residues: 1452 sheet: 0.69 (0.33), residues: 264 loop : -1.22 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 114 HIS 0.005 0.001 HIS D 53 PHE 0.016 0.001 PHE F 30 TYR 0.018 0.002 TYR B 190 ARG 0.005 0.000 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.6510 (ttt) cc_final: 0.6281 (ttt) REVERT: C 49 GLU cc_start: 0.6629 (tm-30) cc_final: 0.5926 (tm-30) REVERT: C 57 MET cc_start: 0.8561 (mmm) cc_final: 0.8340 (mmm) REVERT: C 89 ARG cc_start: 0.7323 (ttt180) cc_final: 0.6993 (ttt180) REVERT: C 96 MET cc_start: 0.8229 (mmm) cc_final: 0.8017 (mmt) REVERT: C 134 ILE cc_start: 0.8696 (tp) cc_final: 0.8301 (tp) REVERT: C 150 ARG cc_start: 0.6653 (mtm180) cc_final: 0.6155 (mtm180) REVERT: E 356 TYR cc_start: 0.8098 (t80) cc_final: 0.7822 (t80) REVERT: F 14 LEU cc_start: 0.7207 (pt) cc_final: 0.7001 (tp) REVERT: H 80 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7925 (tm-30) REVERT: H 106 LEU cc_start: 0.7953 (mm) cc_final: 0.7725 (pt) REVERT: H 335 ILE cc_start: 0.9081 (tp) cc_final: 0.8817 (tt) REVERT: I 15 GLN cc_start: 0.8452 (pm20) cc_final: 0.8038 (pm20) REVERT: J 41 GLU cc_start: 0.8516 (tt0) cc_final: 0.8309 (tt0) REVERT: J 134 MET cc_start: 0.8635 (tpp) cc_final: 0.8227 (tpp) REVERT: K 361 LEU cc_start: 0.8509 (tt) cc_final: 0.7997 (tt) REVERT: L 106 LEU cc_start: 0.7889 (mm) cc_final: 0.7637 (pt) REVERT: L 335 ILE cc_start: 0.9166 (tp) cc_final: 0.8944 (tt) REVERT: D 49 GLU cc_start: 0.6642 (tm-30) cc_final: 0.5791 (tm-30) REVERT: D 89 ARG cc_start: 0.7252 (ttt180) cc_final: 0.6941 (ttt180) REVERT: D 96 MET cc_start: 0.8235 (mmm) cc_final: 0.8012 (mmt) REVERT: D 134 ILE cc_start: 0.8713 (tp) cc_final: 0.8357 (tp) REVERT: D 150 ARG cc_start: 0.6667 (mtm180) cc_final: 0.6173 (mtm180) REVERT: B 89 LYS cc_start: 0.9107 (mptt) cc_final: 0.8567 (mmtp) outliers start: 0 outliers final: 0 residues processed: 483 average time/residue: 0.3019 time to fit residues: 223.1100 Evaluate side-chains 386 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 6.9990 chunk 210 optimal weight: 0.7980 chunk 46 optimal weight: 0.0010 chunk 137 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 234 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 204 HIS K 169 ASN D 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20708 Z= 0.220 Angle : 0.579 7.182 28116 Z= 0.279 Chirality : 0.041 0.150 3204 Planarity : 0.004 0.043 3518 Dihedral : 5.215 120.729 2794 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.05 % Allowed : 1.82 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.17), residues: 2432 helix: 1.88 (0.14), residues: 1452 sheet: 0.73 (0.33), residues: 266 loop : -1.24 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 10 HIS 0.012 0.001 HIS D 65 PHE 0.010 0.001 PHE F 30 TYR 0.018 0.001 TYR B 190 ARG 0.004 0.000 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 480 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 GLU cc_start: 0.6662 (tm-30) cc_final: 0.5984 (tm-30) REVERT: C 89 ARG cc_start: 0.7312 (ttt180) cc_final: 0.6954 (ttt180) REVERT: C 96 MET cc_start: 0.8200 (mmm) cc_final: 0.7988 (mmt) REVERT: C 134 ILE cc_start: 0.8684 (tp) cc_final: 0.8275 (tp) REVERT: C 150 ARG cc_start: 0.6552 (mtm180) cc_final: 0.5883 (mpp80) REVERT: E 356 TYR cc_start: 0.8128 (t80) cc_final: 0.7860 (t80) REVERT: F 134 MET cc_start: 0.8702 (tpp) cc_final: 0.8286 (tpp) REVERT: H 80 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7881 (tm-30) REVERT: H 106 LEU cc_start: 0.7940 (mm) cc_final: 0.7707 (pt) REVERT: H 335 ILE cc_start: 0.9101 (tp) cc_final: 0.8832 (tt) REVERT: J 90 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7605 (tp40) REVERT: J 134 MET cc_start: 0.8685 (tpp) cc_final: 0.8307 (tpp) REVERT: K 361 LEU cc_start: 0.8513 (tt) cc_final: 0.8121 (tt) REVERT: L 106 LEU cc_start: 0.7834 (mm) cc_final: 0.7595 (pt) REVERT: L 335 ILE cc_start: 0.9167 (tp) cc_final: 0.8939 (tt) REVERT: D 49 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6953 (tm-30) REVERT: D 89 ARG cc_start: 0.7279 (ttt180) cc_final: 0.6931 (ttt180) REVERT: D 96 MET cc_start: 0.8257 (mmm) cc_final: 0.8045 (mmt) REVERT: D 134 ILE cc_start: 0.8697 (tp) cc_final: 0.8276 (tp) REVERT: D 150 ARG cc_start: 0.6564 (mtm180) cc_final: 0.5872 (mpp80) REVERT: B 89 LYS cc_start: 0.9123 (mptt) cc_final: 0.8527 (mmtp) outliers start: 1 outliers final: 1 residues processed: 481 average time/residue: 0.3029 time to fit residues: 225.6991 Evaluate side-chains 385 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 384 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 233 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 HIS ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS B 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20708 Z= 0.288 Angle : 0.635 16.491 28116 Z= 0.308 Chirality : 0.042 0.173 3204 Planarity : 0.004 0.043 3518 Dihedral : 5.272 124.344 2794 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.05 % Allowed : 1.09 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.17), residues: 2432 helix: 1.83 (0.14), residues: 1438 sheet: 0.63 (0.33), residues: 262 loop : -1.21 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 10 HIS 0.011 0.001 HIS C 65 PHE 0.012 0.001 PHE F 30 TYR 0.018 0.002 TYR B 190 ARG 0.007 0.000 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 473 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.9094 (mptt) cc_final: 0.8890 (mmtm) REVERT: A 105 LYS cc_start: 0.8454 (mttt) cc_final: 0.8233 (mttt) REVERT: A 140 MET cc_start: 0.8235 (mmt) cc_final: 0.7698 (mmt) REVERT: C 49 GLU cc_start: 0.6596 (tm-30) cc_final: 0.5868 (tm-30) REVERT: C 96 MET cc_start: 0.8286 (mmm) cc_final: 0.8018 (mmt) REVERT: C 134 ILE cc_start: 0.8699 (tp) cc_final: 0.8305 (tp) REVERT: C 150 ARG cc_start: 0.6737 (mtm180) cc_final: 0.5993 (mpp80) REVERT: E 356 TYR cc_start: 0.8138 (t80) cc_final: 0.7775 (t80) REVERT: F 134 MET cc_start: 0.8754 (tpp) cc_final: 0.8130 (tpp) REVERT: G 41 GLU cc_start: 0.9133 (tt0) cc_final: 0.8835 (tt0) REVERT: H 106 LEU cc_start: 0.7946 (mm) cc_final: 0.7692 (pt) REVERT: H 335 ILE cc_start: 0.9092 (tp) cc_final: 0.8862 (tt) REVERT: J 19 VAL cc_start: 0.9061 (t) cc_final: 0.8825 (t) REVERT: J 134 MET cc_start: 0.8588 (tpp) cc_final: 0.8066 (tpp) REVERT: K 41 GLU cc_start: 0.9109 (tt0) cc_final: 0.8815 (tt0) REVERT: K 361 LEU cc_start: 0.8509 (tt) cc_final: 0.8101 (tt) REVERT: L 106 LEU cc_start: 0.7855 (mm) cc_final: 0.7629 (pt) REVERT: L 335 ILE cc_start: 0.9182 (tp) cc_final: 0.8913 (tt) REVERT: D 49 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6302 (tm-30) REVERT: D 53 HIS cc_start: 0.6450 (m90) cc_final: 0.6165 (m90) REVERT: D 96 MET cc_start: 0.8340 (mmm) cc_final: 0.8103 (mmt) REVERT: D 134 ILE cc_start: 0.8688 (tp) cc_final: 0.8317 (tp) REVERT: B 89 LYS cc_start: 0.9159 (mptt) cc_final: 0.8616 (mmtp) outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.3052 time to fit residues: 221.7059 Evaluate side-chains 375 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 0.7980 chunk 93 optimal weight: 0.0980 chunk 139 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 212 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 204 HIS ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS B 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20708 Z= 0.175 Angle : 0.587 15.847 28116 Z= 0.280 Chirality : 0.040 0.155 3204 Planarity : 0.003 0.041 3518 Dihedral : 5.084 123.908 2794 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.09 % Allowed : 0.23 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.18), residues: 2432 helix: 1.92 (0.14), residues: 1438 sheet: 0.77 (0.34), residues: 264 loop : -1.15 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 10 HIS 0.009 0.001 HIS C 65 PHE 0.010 0.001 PHE D 171 TYR 0.018 0.001 TYR B 190 ARG 0.010 0.000 ARG F 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 488 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.9099 (mptt) cc_final: 0.8893 (mmtm) REVERT: A 105 LYS cc_start: 0.8397 (mttt) cc_final: 0.8152 (mttt) REVERT: C 49 GLU cc_start: 0.6750 (tm-30) cc_final: 0.6048 (tm-30) REVERT: C 134 ILE cc_start: 0.8676 (tp) cc_final: 0.8247 (tp) REVERT: C 150 ARG cc_start: 0.6477 (mtm180) cc_final: 0.5835 (mpp80) REVERT: E 356 TYR cc_start: 0.8064 (t80) cc_final: 0.7818 (t80) REVERT: G 41 GLU cc_start: 0.9075 (tt0) cc_final: 0.8732 (tt0) REVERT: H 80 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7886 (tm-30) REVERT: H 106 LEU cc_start: 0.7924 (mm) cc_final: 0.7687 (pt) REVERT: H 335 ILE cc_start: 0.9124 (tp) cc_final: 0.8861 (tt) REVERT: J 19 VAL cc_start: 0.8913 (t) cc_final: 0.8588 (t) REVERT: J 134 MET cc_start: 0.8554 (tpp) cc_final: 0.8090 (tpp) REVERT: J 135 ASP cc_start: 0.8655 (t0) cc_final: 0.8395 (t0) REVERT: K 41 GLU cc_start: 0.9071 (tt0) cc_final: 0.8578 (tt0) REVERT: K 361 LEU cc_start: 0.8491 (tt) cc_final: 0.7988 (tt) REVERT: L 23 MET cc_start: 0.7353 (mmt) cc_final: 0.7116 (mmm) REVERT: L 106 LEU cc_start: 0.7815 (mm) cc_final: 0.7591 (pt) REVERT: L 335 ILE cc_start: 0.9157 (tp) cc_final: 0.8926 (tt) REVERT: D 49 GLU cc_start: 0.6830 (tm-30) cc_final: 0.5995 (tm-30) REVERT: D 134 ILE cc_start: 0.8676 (tp) cc_final: 0.8246 (tp) REVERT: D 150 ARG cc_start: 0.6469 (mtm180) cc_final: 0.5856 (mpp80) REVERT: B 89 LYS cc_start: 0.9051 (mptt) cc_final: 0.8592 (mmtp) outliers start: 2 outliers final: 1 residues processed: 489 average time/residue: 0.2972 time to fit residues: 224.6475 Evaluate side-chains 391 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 390 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 0.3980 chunk 203 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 196 optimal weight: 0.9980 chunk 205 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 HIS ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20708 Z= 0.178 Angle : 0.584 7.795 28116 Z= 0.280 Chirality : 0.041 0.163 3204 Planarity : 0.003 0.041 3518 Dihedral : 5.007 123.967 2794 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2432 helix: 1.98 (0.14), residues: 1428 sheet: 0.81 (0.34), residues: 264 loop : -1.10 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 10 HIS 0.015 0.001 HIS C 65 PHE 0.008 0.001 PHE B 136 TYR 0.019 0.001 TYR B 190 ARG 0.006 0.000 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8413 (mttt) cc_final: 0.8133 (mttt) REVERT: C 33 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8362 (mtmm) REVERT: C 49 GLU cc_start: 0.6561 (tm-30) cc_final: 0.5823 (tm-30) REVERT: C 134 ILE cc_start: 0.8680 (tp) cc_final: 0.8257 (tp) REVERT: C 150 ARG cc_start: 0.6358 (mtm180) cc_final: 0.5703 (mpp80) REVERT: E 356 TYR cc_start: 0.8067 (t80) cc_final: 0.7828 (t80) REVERT: G 41 GLU cc_start: 0.9048 (tt0) cc_final: 0.8705 (tt0) REVERT: H 106 LEU cc_start: 0.7934 (mm) cc_final: 0.7678 (pt) REVERT: H 335 ILE cc_start: 0.9136 (tp) cc_final: 0.8895 (tt) REVERT: I 23 MET cc_start: 0.7754 (tpp) cc_final: 0.7513 (tpp) REVERT: J 134 MET cc_start: 0.8557 (tpp) cc_final: 0.8122 (tpp) REVERT: K 41 GLU cc_start: 0.9041 (tt0) cc_final: 0.8663 (tt0) REVERT: K 361 LEU cc_start: 0.8487 (tt) cc_final: 0.7993 (tt) REVERT: L 23 MET cc_start: 0.7402 (mmt) cc_final: 0.7145 (mmm) REVERT: L 106 LEU cc_start: 0.7835 (mm) cc_final: 0.7617 (pt) REVERT: L 335 ILE cc_start: 0.9153 (tp) cc_final: 0.8881 (tt) REVERT: D 49 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6725 (tm-30) REVERT: D 96 MET cc_start: 0.8096 (mmt) cc_final: 0.7801 (mmm) REVERT: D 134 ILE cc_start: 0.8675 (tp) cc_final: 0.8244 (tp) REVERT: D 150 ARG cc_start: 0.6462 (mtm180) cc_final: 0.5840 (mpp80) REVERT: B 89 LYS cc_start: 0.9024 (mptt) cc_final: 0.8599 (mmtp) outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.3045 time to fit residues: 227.6470 Evaluate side-chains 397 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 241 optimal weight: 20.0000 chunk 221 optimal weight: 20.0000 chunk 191 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 152 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 204 HIS ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 ASN I 344 ASN D 204 HIS B 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20708 Z= 0.220 Angle : 0.602 7.963 28116 Z= 0.289 Chirality : 0.041 0.148 3204 Planarity : 0.004 0.041 3518 Dihedral : 5.025 124.589 2794 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2432 helix: 1.97 (0.14), residues: 1426 sheet: 0.79 (0.34), residues: 264 loop : -1.13 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 10 HIS 0.012 0.001 HIS C 65 PHE 0.009 0.001 PHE C 86 TYR 0.018 0.001 TYR E 29 ARG 0.006 0.000 ARG F 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 471 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8400 (mttt) cc_final: 0.8115 (mttt) REVERT: C 49 GLU cc_start: 0.6485 (tm-30) cc_final: 0.5903 (tm-30) REVERT: C 134 ILE cc_start: 0.8695 (tp) cc_final: 0.8260 (tp) REVERT: C 150 ARG cc_start: 0.6363 (mtm180) cc_final: 0.5722 (mpp80) REVERT: E 356 TYR cc_start: 0.8100 (t80) cc_final: 0.7857 (t80) REVERT: G 41 GLU cc_start: 0.9025 (tt0) cc_final: 0.8642 (tt0) REVERT: H 106 LEU cc_start: 0.7965 (mm) cc_final: 0.7699 (pt) REVERT: H 335 ILE cc_start: 0.9101 (tp) cc_final: 0.8880 (tt) REVERT: J 134 MET cc_start: 0.8420 (tpp) cc_final: 0.7998 (tpp) REVERT: K 41 GLU cc_start: 0.9009 (tt0) cc_final: 0.8615 (tt0) REVERT: K 361 LEU cc_start: 0.8439 (tt) cc_final: 0.8110 (tt) REVERT: L 106 LEU cc_start: 0.7826 (mm) cc_final: 0.7611 (pt) REVERT: L 335 ILE cc_start: 0.9174 (tp) cc_final: 0.8885 (tt) REVERT: D 49 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6149 (tm-30) REVERT: D 134 ILE cc_start: 0.8673 (tp) cc_final: 0.8248 (tp) REVERT: D 150 ARG cc_start: 0.6545 (mtm180) cc_final: 0.5885 (mpp80) REVERT: B 89 LYS cc_start: 0.9051 (mptt) cc_final: 0.8612 (mmtp) outliers start: 2 outliers final: 1 residues processed: 472 average time/residue: 0.2972 time to fit residues: 216.7774 Evaluate side-chains 389 residues out of total 2192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 388 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 177 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.0170 chunk 192 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 HIS ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.149386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.140828 restraints weight = 28372.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.126133 restraints weight = 68437.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123142 restraints weight = 59824.501| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20708 Z= 0.171 Angle : 0.602 19.289 28116 Z= 0.284 Chirality : 0.041 0.158 3204 Planarity : 0.003 0.040 3518 Dihedral : 4.971 123.466 2794 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.18), residues: 2432 helix: 1.98 (0.14), residues: 1428 sheet: 0.80 (0.34), residues: 264 loop : -1.09 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 10 HIS 0.012 0.001 HIS C 65 PHE 0.012 0.001 PHE C 171 TYR 0.018 0.001 TYR K 343 ARG 0.005 0.000 ARG F 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4568.08 seconds wall clock time: 81 minutes 53.84 seconds (4913.84 seconds total)