Starting phenix.real_space_refine on Mon Oct 26 03:47:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25sb_80337/10_2026/25sb_80337.cif Found real_map, /net/cci-nas-00/data/ceres_data/25sb_80337/10_2026/25sb_80337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25sb_80337/10_2026/25sb_80337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25sb_80337/10_2026/25sb_80337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25sb_80337/10_2026/25sb_80337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25sb_80337/10_2026/25sb_80337.map" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.717 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 65 5.16 5 C 12080 2.51 5 N 3220 2.21 5 O 3875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19240 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 554 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "B" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1705 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 12, 'TRANS': 210} Chain: "C" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1589 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 197} Chain: "D" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 554 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "H" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1705 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 12, 'TRANS': 210} Chain: "L" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1589 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 197} Chain: "E" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 554 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "I" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1705 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 12, 'TRANS': 210} Chain: "M" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1589 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 197} Chain: "F" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 554 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "J" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1705 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 12, 'TRANS': 210} Chain: "N" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1589 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 197} Chain: "G" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 554 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "K" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1705 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 12, 'TRANS': 210} Chain: "O" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1589 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 197} Time building chain proxies: 3.61, per 1000 atoms: 0.19 Number of scatterers: 19240 At special positions: 0 Unit cell: (177.12, 174.906, 85.608, 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 65 16.00 O 3875 8.00 N 3220 7.00 C 12080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 59 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 103 " distance=2.04 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 209 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 198 " distance=2.04 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 59 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 103 " distance=2.04 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 209 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.04 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 59 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 103 " distance=2.04 Simple disulfide: pdb=" SG CYS I 153 " - pdb=" SG CYS I 209 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.03 Simple disulfide: pdb=" SG CYS M 139 " - pdb=" SG CYS M 198 " distance=2.04 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 59 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 103 " distance=2.04 Simple disulfide: pdb=" SG CYS J 153 " - pdb=" SG CYS J 209 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 139 " - pdb=" SG CYS N 198 " distance=2.04 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 59 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 103 " distance=2.04 Simple disulfide: pdb=" SG CYS K 153 " - pdb=" SG CYS K 209 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.03 Simple disulfide: pdb=" SG CYS O 139 " - pdb=" SG CYS O 198 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 788.6 milliseconds 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 41 sheets defined 9.5% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 37 through 49 removed outlier: 4.148A pdb=" N LEU A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 126 through 132 Processing helix chain 'C' and resid 186 through 193 removed outlier: 3.617A pdb=" N HIS C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 4.045A pdb=" N LEU D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 73 No H-bonds generated for 'chain 'H' and resid 71 through 73' Processing helix chain 'H' and resid 94 through 98 Processing helix chain 'H' and resid 169 through 171 No H-bonds generated for 'chain 'H' and resid 169 through 171' Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 186 through 193 removed outlier: 3.600A pdb=" N HIS L 193 " --> pdb=" O GLN L 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 49 removed outlier: 4.126A pdb=" N LEU E 41 " --> pdb=" O ASN E 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 73 No H-bonds generated for 'chain 'I' and resid 71 through 73' Processing helix chain 'I' and resid 81 through 83 No H-bonds generated for 'chain 'I' and resid 81 through 83' Processing helix chain 'I' and resid 94 through 98 Processing helix chain 'I' and resid 200 through 202 No H-bonds generated for 'chain 'I' and resid 200 through 202' Processing helix chain 'M' and resid 81 through 85 Processing helix chain 'M' and resid 126 through 132 Processing helix chain 'M' and resid 186 through 193 removed outlier: 3.628A pdb=" N HIS M 193 " --> pdb=" O GLN M 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 49 removed outlier: 4.029A pdb=" N LEU F 41 " --> pdb=" O ASN F 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 73 No H-bonds generated for 'chain 'J' and resid 71 through 73' Processing helix chain 'J' and resid 81 through 83 No H-bonds generated for 'chain 'J' and resid 81 through 83' Processing helix chain 'J' and resid 94 through 98 Processing helix chain 'J' and resid 169 through 171 No H-bonds generated for 'chain 'J' and resid 169 through 171' Processing helix chain 'J' and resid 200 through 202 No H-bonds generated for 'chain 'J' and resid 200 through 202' Processing helix chain 'N' and resid 81 through 85 Processing helix chain 'N' and resid 126 through 132 Processing helix chain 'N' and resid 186 through 193 removed outlier: 3.657A pdb=" N HIS N 193 " --> pdb=" O GLN N 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 49 removed outlier: 4.547A pdb=" N SER G 40 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU G 41 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 73 No H-bonds generated for 'chain 'K' and resid 71 through 73' Processing helix chain 'K' and resid 81 through 83 No H-bonds generated for 'chain 'K' and resid 81 through 83' Processing helix chain 'K' and resid 94 through 98 Processing helix chain 'K' and resid 169 through 171 No H-bonds generated for 'chain 'K' and resid 169 through 171' Processing helix chain 'K' and resid 200 through 202 No H-bonds generated for 'chain 'K' and resid 200 through 202' Processing helix chain 'K' and resid 214 through 217 Processing helix chain 'O' and resid 81 through 85 Processing helix chain 'O' and resid 126 through 132 Processing helix chain 'O' and resid 186 through 193 removed outlier: 3.613A pdb=" N HIS O 193 " --> pdb=" O GLN O 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 16 removed outlier: 6.777A pdb=" N LYS A 25 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N THR A 14 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR A 23 " --> pdb=" O THR A 14 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 29 through 33 current: chain 'D' and resid 22 through 26 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 29 through 33 current: chain 'E' and resid 22 through 26 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 29 through 33 current: chain 'F' and resid 22 through 26 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 29 through 33 current: chain 'G' and resid 22 through 26 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 29 through 33 current: chain 'G' and resid 67 through 71 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 11 through 12 current: chain 'B' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 64 through 67 current: chain 'B' and resid 113 through 116 Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 137 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 148 through 158 current: chain 'B' and resid 189 through 198 Processing sheet with id=AA5, first strand: chain 'B' and resid 164 through 167 removed outlier: 4.692A pdb=" N TYR B 207 " --> pdb=" O VAL B 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 9 through 12 current: chain 'C' and resid 47 through 50 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 47 through 50 current: chain 'C' and resid 101 through 102 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 119 through 123 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 135 through 144 current: chain 'C' and resid 177 through 185 Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 160 removed outlier: 4.509A pdb=" N TRP C 153 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 64 through 67 current: chain 'H' and resid 113 through 116 Processing sheet with id=AB3, first strand: chain 'H' and resid 133 through 137 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 148 through 158 current: chain 'H' and resid 189 through 198 Processing sheet with id=AB4, first strand: chain 'H' and resid 164 through 167 removed outlier: 4.667A pdb=" N TYR H 207 " --> pdb=" O VAL H 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 47 through 50 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 47 through 50 current: chain 'L' and resid 101 through 102 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.547A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 135 through 144 current: chain 'L' and resid 177 through 185 Processing sheet with id=AB8, first strand: chain 'L' and resid 158 through 160 removed outlier: 4.484A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'I' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 11 through 12 current: chain 'I' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 64 through 67 current: chain 'I' and resid 113 through 116 Processing sheet with id=AC2, first strand: chain 'I' and resid 133 through 137 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 148 through 158 current: chain 'I' and resid 189 through 198 Processing sheet with id=AC3, first strand: chain 'I' and resid 164 through 167 removed outlier: 4.690A pdb=" N TYR I 207 " --> pdb=" O VAL I 224 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 9 through 12 current: chain 'M' and resid 47 through 50 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 47 through 50 current: chain 'M' and resid 101 through 102 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AC6, first strand: chain 'M' and resid 119 through 123 removed outlier: 3.546A pdb=" N VAL M 138 " --> pdb=" O PHE M 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 135 through 144 current: chain 'M' and resid 177 through 185 Processing sheet with id=AC7, first strand: chain 'M' and resid 158 through 160 removed outlier: 4.451A pdb=" N TRP M 153 " --> pdb=" O VAL M 160 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'J' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 11 through 12 current: chain 'J' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 64 through 67 current: chain 'J' and resid 113 through 116 Processing sheet with id=AD1, first strand: chain 'J' and resid 133 through 137 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 148 through 158 current: chain 'J' and resid 189 through 198 Processing sheet with id=AD2, first strand: chain 'J' and resid 164 through 167 removed outlier: 4.666A pdb=" N TYR J 207 " --> pdb=" O VAL J 224 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 9 through 12 current: chain 'N' and resid 47 through 50 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 47 through 50 current: chain 'N' and resid 101 through 102 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AD5, first strand: chain 'N' and resid 119 through 123 removed outlier: 3.519A pdb=" N VAL N 138 " --> pdb=" O PHE N 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 135 through 144 current: chain 'N' and resid 177 through 185 Processing sheet with id=AD6, first strand: chain 'N' and resid 158 through 160 removed outlier: 4.506A pdb=" N TRP N 153 " --> pdb=" O VAL N 160 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'K' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 11 through 12 current: chain 'K' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 64 through 67 current: chain 'K' and resid 113 through 116 Processing sheet with id=AD9, first strand: chain 'K' and resid 133 through 137 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 148 through 158 current: chain 'K' and resid 189 through 198 Processing sheet with id=AE1, first strand: chain 'K' and resid 164 through 167 removed outlier: 4.678A pdb=" N TYR K 207 " --> pdb=" O VAL K 224 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 9 through 12 current: chain 'O' and resid 47 through 50 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 47 through 50 current: chain 'O' and resid 101 through 102 No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'O' and resid 18 through 23 Processing sheet with id=AE4, first strand: chain 'O' and resid 119 through 123 removed outlier: 3.519A pdb=" N VAL O 138 " --> pdb=" O PHE O 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 135 through 144 current: chain 'O' and resid 177 through 185 Processing sheet with id=AE5, first strand: chain 'O' and resid 158 through 160 removed outlier: 4.458A pdb=" N TRP O 153 " --> pdb=" O VAL O 160 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1170 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: 2.97 Time building geometry restraints manager: 1.80 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: 6111 1.34 - 1.46: 4964 1.46 - 1.58: 8570 1.58 - 1.71: 0 1.71 - 1.83: 80 Bond restraints: 19725 Sorted by residual: bond pdb=" C GLN M 40 " pdb=" N HIS M 41 " ideal model delta sigma weight residual 1.340 1.243 0.098 5.87e-02 2.90e+02 2.77e+00 bond pdb=" C GLY O 112 " pdb=" N GLN O 113 " ideal model delta sigma weight residual 1.331 1.301 0.030 2.07e-02 2.33e+03 2.17e+00 bond pdb=" C GLN N 40 " pdb=" N HIS N 41 " ideal model delta sigma weight residual 1.340 1.257 0.083 5.87e-02 2.90e+02 2.00e+00 bond pdb=" C THR I 111 " pdb=" N PRO I 112 " ideal model delta sigma weight residual 1.338 1.364 -0.026 1.90e-02 2.77e+03 1.86e+00 bond pdb=" C GLN L 40 " pdb=" N HIS L 41 " ideal model delta sigma weight residual 1.340 1.264 0.076 5.87e-02 2.90e+02 1.69e+00 ... (remaining 19720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 26393 1.87 - 3.74: 450 3.74 - 5.62: 42 5.62 - 7.49: 28 7.49 - 9.36: 12 Bond angle restraints: 26925 Sorted by residual: angle pdb=" C THR J 111 " pdb=" N PRO J 112 " pdb=" CA PRO J 112 " ideal model delta sigma weight residual 127.00 135.67 -8.67 2.40e+00 1.74e-01 1.31e+01 angle pdb=" N GLY J 37 " pdb=" CA GLY J 37 " pdb=" C GLY J 37 " ideal model delta sigma weight residual 110.73 117.46 -6.73 1.90e+00 2.77e-01 1.25e+01 angle pdb=" C THR I 111 " pdb=" N PRO I 112 " pdb=" CA PRO I 112 " ideal model delta sigma weight residual 127.00 135.33 -8.33 2.40e+00 1.74e-01 1.20e+01 angle pdb=" N GLY H 37 " pdb=" CA GLY H 37 " pdb=" C GLY H 37 " ideal model delta sigma weight residual 110.73 117.28 -6.55 1.90e+00 2.77e-01 1.19e+01 angle pdb=" C THR H 111 " pdb=" N PRO H 112 " pdb=" CA PRO H 112 " ideal model delta sigma weight residual 127.00 135.25 -8.25 2.40e+00 1.74e-01 1.18e+01 ... (remaining 26920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11131 17.94 - 35.88: 480 35.88 - 53.82: 75 53.82 - 71.76: 16 71.76 - 89.70: 18 Dihedral angle restraints: 11720 sinusoidal: 4380 harmonic: 7340 Sorted by residual: dihedral pdb=" CA TYR B 102 " pdb=" C TYR B 102 " pdb=" N CYS B 103 " pdb=" CA CYS B 103 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA TYR I 102 " pdb=" C TYR I 102 " pdb=" N CYS I 103 " pdb=" CA CYS I 103 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA TYR K 102 " pdb=" C TYR K 102 " pdb=" N CYS K 103 " pdb=" CA CYS K 103 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 11717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1758 0.032 - 0.065: 820 0.065 - 0.097: 325 0.097 - 0.130: 142 0.130 - 0.162: 15 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CA ILE K 39 " pdb=" N ILE K 39 " pdb=" C ILE K 39 " pdb=" CB ILE K 39 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA ILE I 39 " pdb=" N ILE I 39 " pdb=" C ILE I 39 " pdb=" CB ILE I 39 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA ILE H 39 " pdb=" N ILE H 39 " pdb=" C ILE H 39 " pdb=" CB ILE H 39 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 ... (remaining 3057 not shown) Planarity restraints: 3440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 161 " 0.031 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO J 162 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 162 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 162 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU K 161 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO K 162 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO K 162 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO K 162 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 161 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO I 162 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO I 162 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 162 " 0.022 5.00e-02 4.00e+02 ... (remaining 3437 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 10923 3.02 - 3.49: 17173 3.49 - 3.96: 32412 3.96 - 4.43: 37252 4.43 - 4.90: 61195 Nonbonded interactions: 158955 Sorted by model distance: nonbonded pdb=" O GLY M 112 " pdb=" CA GLN M 113 " model vdw 2.551 2.776 nonbonded pdb=" O TYR B 110 " pdb=" OG1 THR B 111 " model vdw 2.564 3.040 nonbonded pdb=" O GLY N 112 " pdb=" CA GLN N 113 " model vdw 2.566 2.776 nonbonded pdb=" O GLY L 112 " pdb=" CA GLN L 113 " model vdw 2.572 2.776 nonbonded pdb=" OG1 THR D 56 " pdb=" O GLY D 64 " model vdw 2.572 3.040 ... (remaining 158950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 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: 0.000 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.620 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 19750 Z= 0.197 Angle : 0.671 9.359 26975 Z= 0.355 Chirality : 0.046 0.162 3060 Planarity : 0.005 0.046 3440 Dihedral : 11.158 89.704 6965 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.00 % Favored : 96.80 % Rotamer: Outliers : 1.78 % Allowed : 5.25 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.16), residues: 2530 helix: 0.12 (0.40), residues: 165 sheet: 1.65 (0.14), residues: 1165 loop : -0.19 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 63 TYR 0.018 0.002 TYR E 13 PHE 0.021 0.003 PHE I 35 TRP 0.013 0.002 TRP B 116 HIS 0.006 0.001 HIS J 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (19725) covalent geometry : angle 0.67015 / 0.35 (26925) SS BOND : bond 0.00672 / 0.43 ( 25) SS BOND : angle 1.19004 / 0.84 ( 50) hydrogen bonds : bond 0.15717 / 10.06 ( 488) hydrogen bonds : angle 6.42575 / 4.45 ( 1170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 324 time to evaluate : 0.760 Fit side-chains REVERT: M 31 ASN cc_start: 0.9130 (t0) cc_final: 0.8874 (t0) REVERT: F 54 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9131 (mm) REVERT: J 194 VAL cc_start: 0.9166 (t) cc_final: 0.8871 (m) REVERT: O 31 ASN cc_start: 0.9147 (t0) cc_final: 0.8899 (t0) outliers start: 39 outliers final: 18 residues processed: 349 average time/residue: 0.5334 time to fit residues: 212.3501 Evaluate side-chains 268 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 249 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 153 CYS Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 142 LYS Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 153 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [216, 98, 194, 227, 107, 10, 66, 247, 130, 124, 103] chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.0050 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS B 1 GLN B 33 ASN B 89 GLN B 212 ASN C 31 ASN D 60 HIS H 1 GLN H 33 ASN H 210 ASN H 212 ASN E 60 HIS I 1 GLN I 33 ASN I 210 ASN I 212 ASN M 41 HIS ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS J 1 GLN J 33 ASN J 212 ASN N 31 ASN N 113 GLN G 60 HIS K 1 GLN K 33 ASN K 210 ASN K 212 ASN O 1 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.044977 restraints weight = 29266.249| |-----------------------------------------------------------------------------| r_work (start): 0.2484 rms_B_bonded: 1.66 r_work: 0.2401 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2307 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9291 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 19750 Z= 0.257 Angle : 0.747 9.876 26975 Z= 0.388 Chirality : 0.049 0.163 3060 Planarity : 0.006 0.071 3440 Dihedral : 6.692 70.712 2770 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.56 % Favored : 96.17 % Rotamer: Outliers : 3.06 % Allowed : 8.49 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.16), residues: 2530 helix: 0.04 (0.39), residues: 165 sheet: 1.60 (0.14), residues: 1160 loop : -0.24 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 63 TYR 0.019 0.003 TYR E 13 PHE 0.022 0.003 PHE I 35 TRP 0.013 0.002 TRP H 36 HIS 0.007 0.002 HIS J 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.26 (19725) covalent geometry : angle 0.74490 / 0.39 (26925) SS BOND : bond 0.00933 / 0.60 ( 25) SS BOND : angle 1.38288 / 0.95 ( 50) hydrogen bonds : bond 0.04939 / 3.24 ( 488) hydrogen bonds : angle 5.25895 / 3.66 ( 1170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 239 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 2 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8167 (ptt) REVERT: D 2 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.7909 (ptp) REVERT: L 209 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8158 (mptm) REVERT: M 31 ASN cc_start: 0.9187 (t0) cc_final: 0.8916 (t0) REVERT: F 2 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8175 (ptt) REVERT: F 54 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9199 (mm) REVERT: O 31 ASN cc_start: 0.9179 (t0) cc_final: 0.8898 (t0) outliers start: 67 outliers final: 33 residues processed: 271 average time/residue: 0.5560 time to fit residues: 171.3216 Evaluate side-chains 267 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain L residue 211 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain M residue 62 ASP Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 142 LYS Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 211 VAL Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 153 CYS Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 211 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [158, 10, 185, 103, 136, 31, 181, 95, 163, 36, 44] chunk 158 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 181 optimal weight: 0.0980 chunk 95 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 1 GLN B 212 ASN ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN H 212 ASN E 60 HIS I 1 GLN I 212 ASN ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS J 1 GLN J 212 ASN N 113 GLN G 60 HIS K 1 GLN K 212 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.047048 restraints weight = 29855.241| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 1.63 r_work: 0.2463 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2371 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9258 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 19750 Z= 0.132 Angle : 0.617 8.404 26975 Z= 0.316 Chirality : 0.044 0.151 3060 Planarity : 0.005 0.049 3440 Dihedral : 6.264 69.543 2768 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.49 % Favored : 97.31 % Rotamer: Outliers : 2.88 % Allowed : 9.45 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2530 helix: 0.20 (0.41), residues: 170 sheet: 1.67 (0.14), residues: 1170 loop : -0.08 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 99 TYR 0.013 0.002 TYR B 60 PHE 0.015 0.002 PHE H 135 TRP 0.010 0.001 TRP H 36 HIS 0.003 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (19725) covalent geometry : angle 0.61622 / 0.32 (26925) SS BOND : bond 0.00505 / 0.33 ( 25) SS BOND : angle 0.78134 / 0.54 ( 50) hydrogen bonds : bond 0.03695 / 2.42 ( 488) hydrogen bonds : angle 4.83990 / 3.37 ( 1170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 0.798 Fit side-chains REVERT: D 2 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8152 (ptp) REVERT: O 31 ASN cc_start: 0.9132 (t0) cc_final: 0.8866 (t0) outliers start: 63 outliers final: 31 residues processed: 278 average time/residue: 0.5786 time to fit residues: 182.2108 Evaluate side-chains 262 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 211 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain M residue 62 ASP Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 142 LYS Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 211 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 211 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [138, 112, 125, 59, 53, 116, 13, 7, 38, 205, 212] chunk 138 optimal weight: 0.0070 chunk 112 optimal weight: 3.9990 chunk 125 optimal weight: 0.0770 chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 1 GLN B 212 ASN C 172 GLN H 1 GLN H 212 ASN E 60 HIS I 1 GLN I 210 ASN I 212 ASN M 31 ASN M 172 GLN J 1 GLN J 212 ASN N 31 ASN N 113 GLN K 1 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.072346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.044531 restraints weight = 29524.445| |-----------------------------------------------------------------------------| r_work (start): 0.2474 rms_B_bonded: 1.65 r_work: 0.2391 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2298 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9297 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 19750 Z= 0.258 Angle : 0.750 10.279 26975 Z= 0.387 Chirality : 0.049 0.160 3060 Planarity : 0.006 0.045 3440 Dihedral : 6.507 66.754 2764 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.68 % Favored : 96.05 % Rotamer: Outliers : 3.42 % Allowed : 10.14 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.17), residues: 2530 helix: 0.03 (0.40), residues: 170 sheet: 1.52 (0.14), residues: 1160 loop : -0.18 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 63 TYR 0.020 0.003 TYR E 13 PHE 0.023 0.003 PHE H 86 TRP 0.013 0.002 TRP H 36 HIS 0.008 0.002 HIS J 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.26 (19725) covalent geometry : angle 0.74894 / 0.39 (26925) SS BOND : bond 0.00971 / 0.62 ( 25) SS BOND : angle 1.34360 / 0.95 ( 50) hydrogen bonds : bond 0.04644 / 3.05 ( 488) hydrogen bonds : angle 4.95874 / 3.47 ( 1170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 231 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 2 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8112 (ptt) REVERT: D 2 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.7902 (ptp) REVERT: E 2 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.7758 (ptp) REVERT: F 2 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8083 (ptp) REVERT: G 2 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8054 (ptp) REVERT: O 31 ASN cc_start: 0.9181 (t0) cc_final: 0.8866 (t0) outliers start: 75 outliers final: 44 residues processed: 269 average time/residue: 0.5395 time to fit residues: 165.1597 Evaluate side-chains 276 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 227 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 211 VAL Chi-restraints excluded: chain E residue 2 MET Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain M residue 62 ASP Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 142 LYS Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 211 VAL Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 211 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [36, 157, 187, 1, 71, 176, 203, 243, 58, 72, 147] chunk 36 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 176 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 chunk 243 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 1 GLN B 212 ASN H 1 GLN H 212 ASN E 60 HIS I 1 GLN I 212 ASN ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 1 GLN J 212 ASN N 113 GLN K 1 GLN K 210 ASN O 172 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.073948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.046379 restraints weight = 29476.527| |-----------------------------------------------------------------------------| r_work (start): 0.2527 rms_B_bonded: 1.62 r_work: 0.2446 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2354 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9268 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 19750 Z= 0.142 Angle : 0.633 8.346 26975 Z= 0.324 Chirality : 0.044 0.155 3060 Planarity : 0.005 0.042 3440 Dihedral : 6.197 66.063 2763 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.45 % Favored : 97.35 % Rotamer: Outliers : 3.33 % Allowed : 10.41 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2530 helix: 0.27 (0.41), residues: 170 sheet: 1.56 (0.14), residues: 1160 loop : -0.09 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 63 TYR 0.013 0.002 TYR E 13 PHE 0.015 0.002 PHE H 86 TRP 0.010 0.001 TRP H 36 HIS 0.004 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (19725) covalent geometry : angle 0.63220 / 0.32 (26925) SS BOND : bond 0.00544 / 0.34 ( 25) SS BOND : angle 1.00673 / 0.70 ( 50) hydrogen bonds : bond 0.03664 / 2.40 ( 488) hydrogen bonds : angle 4.69100 / 3.29 ( 1170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 231 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: C 44 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9133 (mtmm) REVERT: D 2 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.7965 (ptp) REVERT: L 28 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8919 (p0) REVERT: E 30 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.9014 (tt0) REVERT: G 2 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8255 (ptp) REVERT: O 31 ASN cc_start: 0.9151 (t0) cc_final: 0.8877 (t0) outliers start: 73 outliers final: 40 residues processed: 270 average time/residue: 0.5724 time to fit residues: 174.8707 Evaluate side-chains 270 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 211 VAL Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 209 CYS Chi-restraints excluded: chain M residue 62 ASP Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 142 LYS Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain N residue 211 VAL Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 211 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [246, 154, 130, 150, 131, 73, 167, 47, 214, 191, 79] chunk 246 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 1 GLN B 212 ASN H 1 GLN H 212 ASN E 60 HIS I 1 GLN I 210 ASN I 212 ASN M 31 ASN ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 1 GLN J 212 ASN N 31 ASN N 81 GLN N 113 GLN K 1 GLN K 212 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.072266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.044549 restraints weight = 29425.682| |-----------------------------------------------------------------------------| r_work (start): 0.2475 rms_B_bonded: 1.61 r_work: 0.2392 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2298 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9297 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 19750 Z= 0.254 Angle : 0.745 9.838 26975 Z= 0.384 Chirality : 0.049 0.159 3060 Planarity : 0.006 0.044 3440 Dihedral : 6.436 63.603 2763 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.68 % Favored : 96.09 % Rotamer: Outliers : 3.70 % Allowed : 10.59 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.17), residues: 2530 helix: 0.06 (0.40), residues: 170 sheet: 1.46 (0.14), residues: 1155 loop : -0.14 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 63 TYR 0.021 0.003 TYR H 60 PHE 0.022 0.003 PHE H 86 TRP 0.011 0.002 TRP I 36 HIS 0.007 0.002 HIS J 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.25 (19725) covalent geometry : angle 0.74294 / 0.38 (26925) SS BOND : bond 0.00976 / 0.62 ( 25) SS BOND : angle 1.55603 / 1.03 ( 50) hydrogen bonds : bond 0.04501 / 2.96 ( 488) hydrogen bonds : angle 4.83978 / 3.40 ( 1170) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 226 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 2 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8104 (ptt) REVERT: D 2 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.7901 (ptp) REVERT: L 28 ASP cc_start: 0.9225 (OUTLIER) cc_final: 0.9020 (p0) REVERT: E 2 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.7690 (ptp) REVERT: F 2 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8087 (ptp) REVERT: F 54 ILE cc_start: 0.9517 (OUTLIER) cc_final: 0.9235 (mm) REVERT: J 45 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.8980 (mmtm) REVERT: G 2 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.7975 (ptp) REVERT: O 31 ASN cc_start: 0.9181 (t0) cc_final: 0.8869 (t0) outliers start: 81 outliers final: 49 residues processed: 272 average time/residue: 0.5374 time to fit residues: 166.9668 Evaluate side-chains 281 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 211 VAL Chi-restraints excluded: chain E residue 2 MET Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain M residue 62 ASP Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 142 LYS Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 211 VAL Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 211 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [248, 58, 171, 146, 131, 206, 169, 195, 217, 178, 78] chunk 248 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 171 optimal weight: 20.0000 chunk 146 optimal weight: 0.1980 chunk 131 optimal weight: 0.3980 chunk 206 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 1 GLN B 212 ASN H 1 GLN H 212 ASN E 60 HIS I 1 GLN I 212 ASN M 31 ASN ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 1 GLN J 212 ASN N 81 GLN N 113 GLN K 1 GLN K 184 GLN K 210 ASN O 172 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.074817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.047415 restraints weight = 29811.439| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 1.65 r_work: 0.2478 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2388 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9251 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19750 Z= 0.115 Angle : 0.600 8.106 26975 Z= 0.305 Chirality : 0.043 0.152 3060 Planarity : 0.004 0.041 3440 Dihedral : 5.974 63.892 2763 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.29 % Favored : 97.51 % Rotamer: Outliers : 2.51 % Allowed : 11.78 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2530 helix: 0.39 (0.42), residues: 170 sheet: 1.48 (0.14), residues: 1210 loop : -0.05 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 63 TYR 0.012 0.001 TYR H 60 PHE 0.013 0.001 PHE B 86 TRP 0.009 0.001 TRP M 190 HIS 0.003 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.11 (19725) covalent geometry : angle 0.59979 / 0.31 (26925) SS BOND : bond 0.00412 / 0.25 ( 25) SS BOND : angle 0.69686 / 0.48 ( 50) hydrogen bonds : bond 0.03201 / 2.10 ( 488) hydrogen bonds : angle 4.54492 / 3.19 ( 1170) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 2 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8010 (ptt) REVERT: D 2 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8137 (ptp) REVERT: F 54 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9108 (mm) REVERT: G 2 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8263 (ptp) REVERT: O 31 ASN cc_start: 0.9129 (t0) cc_final: 0.8812 (t0) outliers start: 55 outliers final: 26 residues processed: 260 average time/residue: 0.5837 time to fit residues: 171.7953 Evaluate side-chains 253 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain M residue 62 ASP Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 142 LYS Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain O residue 62 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [147, 152, 158, 9, 196, 224, 31, 191, 165, 17, 223] chunk 147 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 31 optimal weight: 0.0770 chunk 191 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 1 GLN B 212 ASN H 1 GLN H 212 ASN E 60 HIS I 1 GLN I 212 ASN ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 1 GLN N 31 ASN N 81 GLN N 113 GLN K 1 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.046313 restraints weight = 29556.131| |-----------------------------------------------------------------------------| r_work (start): 0.2526 rms_B_bonded: 1.61 r_work: 0.2445 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2353 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9270 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 19750 Z= 0.153 Angle : 0.648 8.396 26975 Z= 0.331 Chirality : 0.045 0.152 3060 Planarity : 0.005 0.041 3440 Dihedral : 6.033 63.370 2762 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.20 % Favored : 96.60 % Rotamer: Outliers : 2.51 % Allowed : 12.19 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2530 helix: 0.37 (0.42), residues: 170 sheet: 1.59 (0.14), residues: 1170 loop : -0.00 (0.19), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.016 0.002 TYR H 60 PHE 0.016 0.002 PHE H 86 TRP 0.012 0.001 TRP B 36 HIS 0.004 0.001 HIS J 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (19725) covalent geometry : angle 0.64761 / 0.33 (26925) SS BOND : bond 0.00611 / 0.39 ( 25) SS BOND : angle 0.97928 / 0.65 ( 50) hydrogen bonds : bond 0.03595 / 2.36 ( 488) hydrogen bonds : angle 4.55012 / 3.20 ( 1170) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 224 time to evaluate : 0.716 Fit side-chains REVERT: A 2 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8057 (ptt) REVERT: C 44 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9125 (mtmm) REVERT: D 2 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.7975 (ptp) REVERT: F 54 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9171 (mm) REVERT: G 2 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.7989 (ptp) REVERT: O 31 ASN cc_start: 0.9142 (t0) cc_final: 0.8822 (t0) outliers start: 55 outliers final: 34 residues processed: 257 average time/residue: 0.5753 time to fit residues: 167.2420 Evaluate side-chains 262 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain M residue 62 ASP Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 142 LYS Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [167, 82, 189, 195, 70, 63, 71, 28, 103, 46, 15] chunk 167 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 189 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.2359 > 50:) chunk 195 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 1 GLN B 212 ASN H 1 GLN H 212 ASN E 60 HIS I 1 GLN I 212 ASN M 172 GLN J 1 GLN J 212 ASN N 113 GLN K 1 GLN K 210 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.073434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.045831 restraints weight = 29428.524| |-----------------------------------------------------------------------------| r_work (start): 0.2511 rms_B_bonded: 1.63 r_work: 0.2431 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2339 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9277 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 19750 Z= 0.177 Angle : 0.681 8.595 26975 Z= 0.348 Chirality : 0.045 0.153 3060 Planarity : 0.005 0.041 3440 Dihedral : 6.101 62.441 2761 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.00 % Favored : 96.80 % Rotamer: Outliers : 2.60 % Allowed : 12.19 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2530 helix: 0.30 (0.42), residues: 170 sheet: 1.53 (0.14), residues: 1160 loop : -0.05 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.019 0.002 TYR H 60 PHE 0.018 0.002 PHE H 86 TRP 0.012 0.001 TRP B 36 HIS 0.005 0.001 HIS J 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (19725) covalent geometry : angle 0.67964 / 0.35 (26925) SS BOND : bond 0.00685 / 0.44 ( 25) SS BOND : angle 1.08066 / 0.72 ( 50) hydrogen bonds : bond 0.03838 / 2.51 ( 488) hydrogen bonds : angle 4.59281 / 3.23 ( 1170) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 0.736 Fit side-chains REVERT: A 2 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8076 (ptt) REVERT: C 44 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9125 (mtmm) REVERT: D 2 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.7939 (ptp) REVERT: F 54 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9190 (mm) REVERT: N 63 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8164 (mtm110) REVERT: G 2 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8028 (ptp) REVERT: O 31 ASN cc_start: 0.9148 (t0) cc_final: 0.8824 (t0) outliers start: 57 outliers final: 37 residues processed: 262 average time/residue: 0.5805 time to fit residues: 172.1069 Evaluate side-chains 266 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain M residue 62 ASP Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 142 LYS Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain N residue 63 ARG Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [23, 188, 238, 171, 154, 242, 182, 42, 212, 147, 121] chunk 23 optimal weight: 1.9990 chunk 188 optimal weight: 0.5980 chunk 238 optimal weight: 0.9980 chunk 171 optimal weight: 20.0000 chunk 154 optimal weight: 0.7980 chunk 242 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 121 optimal weight: 20.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 1 GLN B 212 ASN H 1 GLN H 212 ASN E 60 HIS I 1 GLN I 212 ASN ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 1 GLN J 212 ASN N 31 ASN N 113 GLN K 1 GLN K 210 ASN O 172 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.074029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.046530 restraints weight = 29668.116| |-----------------------------------------------------------------------------| r_work (start): 0.2532 rms_B_bonded: 1.65 r_work: 0.2451 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2360 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9265 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 19750 Z= 0.147 Angle : 0.659 9.276 26975 Z= 0.335 Chirality : 0.044 0.152 3060 Planarity : 0.005 0.041 3440 Dihedral : 6.000 62.116 2761 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.89 % Favored : 96.92 % Rotamer: Outliers : 2.15 % Allowed : 12.74 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2530 helix: 0.42 (0.42), residues: 170 sheet: 1.48 (0.14), residues: 1210 loop : -0.05 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.017 0.002 TYR K 60 PHE 0.016 0.002 PHE H 86 TRP 0.011 0.001 TRP B 36 HIS 0.004 0.001 HIS H 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (19725) covalent geometry : angle 0.65816 / 0.33 (26925) SS BOND : bond 0.00559 / 0.36 ( 25) SS BOND : angle 0.89650 / 0.60 ( 50) hydrogen bonds : bond 0.03521 / 2.31 ( 488) hydrogen bonds : angle 4.51551 / 3.18 ( 1170) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 0.725 Fit side-chains REVERT: A 2 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8033 (ptt) REVERT: C 44 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9127 (mtmm) REVERT: D 2 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.7951 (ptp) REVERT: F 54 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9158 (mm) REVERT: G 2 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.7997 (ptp) REVERT: O 31 ASN cc_start: 0.9141 (t0) cc_final: 0.8821 (t0) outliers start: 47 outliers final: 36 residues processed: 249 average time/residue: 0.5757 time to fit residues: 162.2901 Evaluate side-chains 261 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain M residue 62 ASP Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 142 LYS Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 83 LYS Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: [42, 74, 66, 215, 247, 155, 249, 227, 216, 142, 125] chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 249 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 1 GLN B 212 ASN H 1 GLN H 212 ASN E 60 HIS I 1 GLN J 1 GLN J 212 ASN N 113 GLN K 1 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.045133 restraints weight = 29295.016| |-----------------------------------------------------------------------------| r_work (start): 0.2493 rms_B_bonded: 1.59 r_work: 0.2412 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2319 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9288 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 19750 Z= 0.213 Angle : 0.726 9.348 26975 Z= 0.372 Chirality : 0.047 0.155 3060 Planarity : 0.005 0.042 3440 Dihedral : 6.208 60.484 2761 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.48 % Favored : 96.32 % Rotamer: Outliers : 2.65 % Allowed : 12.10 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2530 helix: 0.22 (0.41), residues: 170 sheet: 1.46 (0.14), residues: 1155 loop : -0.07 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 63 TYR 0.022 0.002 TYR K 60 PHE 0.020 0.003 PHE H 86 TRP 0.011 0.002 TRP B 36 HIS 0.006 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.21 (19725) covalent geometry : angle 0.72505 / 0.37 (26925) SS BOND : bond 0.00837 / 0.53 ( 25) SS BOND : angle 1.23984 / 0.82 ( 50) hydrogen bonds : bond 0.04140 / 2.71 ( 488) hydrogen bonds : angle 4.64420 / 3.28 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9963.45 seconds wall clock time: 169 minutes 52.51 seconds (10192.51 seconds total)