Starting phenix.real_space_refine on Wed Nov 20 00:40:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgk_43203/11_2024/8vgk_43203.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgk_43203/11_2024/8vgk_43203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgk_43203/11_2024/8vgk_43203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgk_43203/11_2024/8vgk_43203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgk_43203/11_2024/8vgk_43203.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgk_43203/11_2024/8vgk_43203.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.008 sd= 0.350 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 132 5.16 5 C 12912 2.51 5 N 3488 2.21 5 O 4035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20567 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "B" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "C" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "D" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "E" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "F" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "G" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "H" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "I" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "J" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "K" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "L" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 13.49, per 1000 atoms: 0.66 Number of scatterers: 20567 At special positions: 0 Unit cell: (183, 99, 111, 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 132 16.00 O 4035 8.00 N 3488 7.00 C 12912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 58 " distance=2.04 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 220 " distance=2.04 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 58 " distance=2.04 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 201 " distance=2.04 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 220 " distance=2.04 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 58 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 220 " distance=2.04 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 58 " distance=2.04 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 182 " distance=2.03 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 220 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS E 80 " - pdb=" SG CYS E 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 116 " - pdb=" SG CYS F 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 151 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS F 153 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 201 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.05 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 165 " distance=2.04 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 171 " distance=2.03 Simple disulfide: pdb=" SG CYS G 116 " - pdb=" SG CYS H 141 " distance=2.04 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS H 126 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 11 " - pdb=" SG CYS H 151 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 108 " - pdb=" SG CYS H 153 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 201 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 40 " - pdb=" SG CYS I 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 80 " - pdb=" SG CYS I 171 " distance=2.03 Simple disulfide: pdb=" SG CYS I 116 " - pdb=" SG CYS J 141 " distance=2.04 Simple disulfide: pdb=" SG CYS I 124 " - pdb=" SG CYS J 126 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 Simple disulfide: pdb=" SG CYS J 11 " - pdb=" SG CYS J 151 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 153 " distance=2.03 Simple disulfide: pdb=" SG CYS J 144 " - pdb=" SG CYS J 201 " distance=2.04 Simple disulfide: pdb=" SG CYS K 11 " - pdb=" SG CYS K 151 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 108 " - pdb=" SG CYS K 153 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS L 124 " distance=2.04 Simple disulfide: pdb=" SG CYS K 141 " - pdb=" SG CYS L 116 " distance=2.04 Simple disulfide: pdb=" SG CYS K 144 " - pdb=" SG CYS K 201 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG CYS L 165 " distance=2.04 Simple disulfide: pdb=" SG CYS L 80 " - pdb=" SG CYS L 171 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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: 4.93 Conformation dependent library (CDL) restraints added in 3.1 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 52 sheets defined 7.9% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 60E through 62 No H-bonds generated for 'chain 'A' and resid 60E through 62' Processing helix chain 'A' and resid 164 through 173A Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'B' and resid 60E through 62 No H-bonds generated for 'chain 'B' and resid 60E through 62' Processing helix chain 'B' and resid 164 through 173A Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'C' and resid 60E through 62 No H-bonds generated for 'chain 'C' and resid 60E through 62' Processing helix chain 'C' and resid 164 through 173A Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'D' and resid 60E through 62 No H-bonds generated for 'chain 'D' and resid 60E through 62' Processing helix chain 'D' and resid 164 through 173A Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 122 through 127 Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.570A pdb=" N SER F 65 " --> pdb=" O TRP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'G' and resid 122 through 127 Processing helix chain 'G' and resid 183 through 187 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.566A pdb=" N SER H 65 " --> pdb=" O TRP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'I' and resid 122 through 127 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'J' and resid 62 through 65 removed outlier: 3.570A pdb=" N SER J 65 " --> pdb=" O TRP J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 161 through 163 No H-bonds generated for 'chain 'J' and resid 161 through 163' Processing helix chain 'J' and resid 190 through 194 Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.566A pdb=" N SER K 65 " --> pdb=" O TRP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'K' and resid 190 through 194 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.717A pdb=" N CYS A 42 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 35 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N HIS A 40 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 160 removed outlier: 4.311A pdb=" N CYS A 136 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 139 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 199 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 213 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR A 229 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N CYS A 182 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 21 removed outlier: 4.328A pdb=" N CYS B 136 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 139 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU B 199 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL B 213 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR B 229 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS B 182 " --> pdb=" O MET B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 67 removed outlier: 3.710A pdb=" N CYS B 42 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B 35 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS B 40 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 64 through 67 removed outlier: 3.719A pdb=" N CYS C 42 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL C 35 " --> pdb=" O HIS C 40 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N HIS C 40 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP C 51 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 156 through 160 removed outlier: 4.306A pdb=" N CYS C 136 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR C 139 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU C 199 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL C 213 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N THR C 229 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS C 182 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 64 through 67 removed outlier: 3.719A pdb=" N CYS D 42 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL D 35 " --> pdb=" O HIS D 40 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N HIS D 40 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP D 51 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 156 through 160 removed outlier: 4.312A pdb=" N CYS D 136 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR D 139 " --> pdb=" O PRO D 198 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU D 199 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL D 213 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N THR D 229 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS D 182 " --> pdb=" O MET D 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.719A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LYS E 107 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.719A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LYS E 107 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.931A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN E 160 " --> pdb=" O THR E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.707A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.870A pdb=" N LEU F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 124 through 128 removed outlier: 5.391A pdb=" N TYR F 181 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 124 through 128 removed outlier: 5.391A pdb=" N TYR F 181 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 156 through 159 Processing sheet with id=AC2, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 14 removed outlier: 6.717A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LYS G 107 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA G 13 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 14 removed outlier: 6.717A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LYS G 107 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA G 13 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 114 through 118 removed outlier: 4.061A pdb=" N VAL G 133 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN G 160 " --> pdb=" O THR G 178 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 153 through 154 Processing sheet with id=AC7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.707A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.873A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.397A pdb=" N TYR H 181 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.397A pdb=" N TYR H 181 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 156 through 159 removed outlier: 3.515A pdb=" N THR H 156 " --> pdb=" O ASN H 204 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.723A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LYS I 107 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA I 13 " --> pdb=" O LYS I 107 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.723A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LYS I 107 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA I 13 " --> pdb=" O LYS I 107 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 114 through 118 removed outlier: 4.076A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN I 160 " --> pdb=" O THR I 178 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 153 through 154 Processing sheet with id=AD9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE1, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.697A pdb=" N ALA J 33 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.873A pdb=" N LEU J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 124 through 128 removed outlier: 5.392A pdb=" N TYR J 181 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 124 through 128 removed outlier: 5.392A pdb=" N TYR J 181 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 156 through 159 Processing sheet with id=AE6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.699A pdb=" N ALA K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.870A pdb=" N LEU K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 124 through 128 removed outlier: 5.394A pdb=" N TYR K 181 " --> pdb=" O ASP K 148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 124 through 128 removed outlier: 5.394A pdb=" N TYR K 181 " --> pdb=" O ASP K 148 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 156 through 159 Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.719A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.719A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 114 through 118 removed outlier: 4.067A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN L 160 " --> pdb=" O THR L 178 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 153 through 154 793 hydrogen bonds defined for protein. 1995 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: 7.93 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6547 1.34 - 1.47: 5263 1.47 - 1.59: 8998 1.59 - 1.72: 0 1.72 - 1.85: 152 Bond restraints: 20960 Sorted by residual: bond pdb=" C ALA L 111 " pdb=" N ALA L 112 " ideal model delta sigma weight residual 1.331 1.418 -0.087 2.07e-02 2.33e+03 1.77e+01 bond pdb=" C VAL J 12 " pdb=" N LYS J 13 " ideal model delta sigma weight residual 1.331 1.380 -0.049 2.07e-02 2.33e+03 5.63e+00 bond pdb=" C VAL K 12 " pdb=" N LYS K 13 " ideal model delta sigma weight residual 1.331 1.380 -0.049 2.07e-02 2.33e+03 5.55e+00 bond pdb=" C VAL F 12 " pdb=" N LYS F 13 " ideal model delta sigma weight residual 1.331 1.379 -0.048 2.07e-02 2.33e+03 5.27e+00 bond pdb=" C VAL H 12 " pdb=" N LYS H 13 " ideal model delta sigma weight residual 1.331 1.377 -0.046 2.07e-02 2.33e+03 5.03e+00 ... (remaining 20955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 26713 2.00 - 4.01: 1643 4.01 - 6.01: 194 6.01 - 8.02: 34 8.02 - 10.02: 8 Bond angle restraints: 28592 Sorted by residual: angle pdb=" N PRO B 152A" pdb=" CA PRO B 152A" pdb=" C PRO B 152A" ideal model delta sigma weight residual 110.70 120.72 -10.02 1.22e+00 6.72e-01 6.75e+01 angle pdb=" N PRO D 152A" pdb=" CA PRO D 152A" pdb=" C PRO D 152A" ideal model delta sigma weight residual 110.70 120.44 -9.74 1.22e+00 6.72e-01 6.38e+01 angle pdb=" N PRO A 152A" pdb=" CA PRO A 152A" pdb=" C PRO A 152A" ideal model delta sigma weight residual 110.70 120.06 -9.36 1.22e+00 6.72e-01 5.88e+01 angle pdb=" N PRO C 152A" pdb=" CA PRO C 152A" pdb=" C PRO C 152A" ideal model delta sigma weight residual 110.70 119.97 -9.27 1.22e+00 6.72e-01 5.78e+01 angle pdb=" CA PRO B 152A" pdb=" C PRO B 152A" pdb=" N PRO B 152B" ideal model delta sigma weight residual 117.93 124.06 -6.13 1.20e+00 6.94e-01 2.61e+01 ... (remaining 28587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 11534 17.87 - 35.73: 837 35.73 - 53.60: 114 53.60 - 71.47: 41 71.47 - 89.33: 34 Dihedral angle restraints: 12560 sinusoidal: 4884 harmonic: 7676 Sorted by residual: dihedral pdb=" CA GLU K 152 " pdb=" C GLU K 152 " pdb=" N CYS K 153 " pdb=" CA CYS K 153 " ideal model delta harmonic sigma weight residual -180.00 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLU J 152 " pdb=" C GLU J 152 " pdb=" N CYS J 153 " pdb=" CA CYS J 153 " ideal model delta harmonic sigma weight residual 180.00 -151.14 -28.86 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA CYS E 124 " pdb=" C CYS E 124 " pdb=" N LEU E 125 " pdb=" CA LEU E 125 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 12557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2173 0.055 - 0.111: 831 0.111 - 0.166: 192 0.166 - 0.222: 20 0.222 - 0.277: 4 Chirality restraints: 3220 Sorted by residual: chirality pdb=" CA PRO B 152A" pdb=" N PRO B 152A" pdb=" C PRO B 152A" pdb=" CB PRO B 152A" both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA PRO D 152A" pdb=" N PRO D 152A" pdb=" C PRO D 152A" pdb=" CB PRO D 152A" both_signs ideal model delta sigma weight residual False 2.72 2.44 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA PRO A 152A" pdb=" N PRO A 152A" pdb=" C PRO A 152A" pdb=" CB PRO A 152A" both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 3217 not shown) Planarity restraints: 3648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 181 " -0.008 2.00e-02 2.50e+03 2.42e-02 1.17e+01 pdb=" CG TYR H 181 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR H 181 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR H 181 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR H 181 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR H 181 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 181 " -0.035 2.00e-02 2.50e+03 pdb=" OH TYR H 181 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 181 " -0.008 2.00e-02 2.50e+03 2.36e-02 1.11e+01 pdb=" CG TYR F 181 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR F 181 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR F 181 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR F 181 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR F 181 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 181 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR F 181 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 181 " 0.007 2.00e-02 2.50e+03 2.32e-02 1.08e+01 pdb=" CG TYR J 181 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR J 181 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR J 181 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR J 181 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR J 181 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR J 181 " 0.034 2.00e-02 2.50e+03 pdb=" OH TYR J 181 " -0.032 2.00e-02 2.50e+03 ... (remaining 3645 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 291 2.66 - 3.22: 18633 3.22 - 3.78: 31089 3.78 - 4.34: 45901 4.34 - 4.90: 72755 Nonbonded interactions: 168669 Sorted by model distance: nonbonded pdb=" OE1 GLN D 192 " pdb=" O HOH D 301 " model vdw 2.099 3.040 nonbonded pdb=" OD1 ASP L 170 " pdb=" OG1 THR L 172 " model vdw 2.142 3.040 nonbonded pdb=" OD1 ASP I 170 " pdb=" OG1 THR I 172 " model vdw 2.149 3.040 nonbonded pdb=" O HOH C 330 " pdb=" O HOH C 339 " model vdw 2.150 3.040 nonbonded pdb=" OD1 ASP E 170 " pdb=" OG1 THR E 172 " model vdw 2.152 3.040 ... (remaining 168664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' } 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: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 49.550 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 0.087 20960 Z= 0.357 Angle : 1.040 10.021 28592 Z= 0.593 Chirality : 0.060 0.277 3220 Planarity : 0.010 0.096 3648 Dihedral : 13.841 89.332 7480 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.05 % Favored : 92.35 % Rotamer: Outliers : 0.65 % Allowed : 3.91 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 2640 helix: -2.54 (0.34), residues: 152 sheet: 0.46 (0.16), residues: 876 loop : -1.15 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 159 HIS 0.011 0.003 HIS D 72 PHE 0.022 0.003 PHE G 92 TYR 0.035 0.008 TYR H 181 ARG 0.025 0.004 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 618 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 181 TYR cc_start: 0.8747 (m-80) cc_final: 0.8250 (m-80) REVERT: G 138 ASN cc_start: 0.7702 (m110) cc_final: 0.7246 (m110) REVERT: G 139 PHE cc_start: 0.8407 (p90) cc_final: 0.8080 (p90) REVERT: G 173 TYR cc_start: 0.7482 (p90) cc_final: 0.6147 (p90) REVERT: G 211 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7168 (ttp-170) REVERT: H 6 GLU cc_start: 0.6801 (mp0) cc_final: 0.6598 (mp0) REVERT: H 128 LEU cc_start: 0.7857 (tp) cc_final: 0.7545 (tp) REVERT: H 181 TYR cc_start: 0.8707 (m-80) cc_final: 0.8223 (m-80) REVERT: I 211 ARG cc_start: 0.7434 (ttp80) cc_final: 0.7186 (ttp-170) REVERT: J 128 LEU cc_start: 0.7718 (tp) cc_final: 0.7478 (tp) REVERT: K 128 LEU cc_start: 0.7776 (tp) cc_final: 0.7466 (tp) REVERT: K 149 TYR cc_start: 0.7574 (p90) cc_final: 0.7330 (p90) REVERT: K 181 TYR cc_start: 0.8732 (m-80) cc_final: 0.8373 (m-80) outliers start: 15 outliers final: 3 residues processed: 633 average time/residue: 1.5488 time to fit residues: 1090.6366 Evaluate side-chains 390 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 387 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 4.9990 chunk 200 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 chunk 125 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 20 GLN B 79 GLN B 192 GLN C 192 GLN D 79 GLN D 192 GLN E 3 GLN E 189 HIS F 209 ASN G 3 GLN G 189 HIS H 160 ASN H 209 ASN I 3 GLN I 189 HIS J 76 ASN ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 ASN K 76 ASN K 209 ASN L 3 GLN L 189 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20960 Z= 0.288 Angle : 0.831 12.661 28592 Z= 0.436 Chirality : 0.051 0.208 3220 Planarity : 0.006 0.073 3648 Dihedral : 6.722 48.394 2872 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.13 % Allowed : 14.02 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2640 helix: -0.56 (0.51), residues: 124 sheet: 0.99 (0.17), residues: 888 loop : -0.59 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 215 HIS 0.004 0.001 HIS B 173 PHE 0.022 0.002 PHE L 139 TYR 0.024 0.002 TYR I 140 ARG 0.010 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 469 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.6816 (p0) REVERT: E 173 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6560 (p90) REVERT: F 160 ASN cc_start: 0.8898 (m-40) cc_final: 0.8358 (m110) REVERT: F 209 ASN cc_start: 0.8609 (m110) cc_final: 0.8350 (m-40) REVERT: G 139 PHE cc_start: 0.8266 (p90) cc_final: 0.7927 (p90) REVERT: G 148 TRP cc_start: 0.7631 (m100) cc_final: 0.7283 (m100) REVERT: G 173 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6425 (p90) REVERT: H 105 GLN cc_start: 0.7869 (pm20) cc_final: 0.7629 (pm20) REVERT: H 125 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.7956 (m) REVERT: H 209 ASN cc_start: 0.8479 (m110) cc_final: 0.8249 (m-40) REVERT: H 214 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6985 (ttpp) REVERT: I 139 PHE cc_start: 0.8245 (p90) cc_final: 0.8041 (p90) REVERT: I 148 TRP cc_start: 0.7699 (m100) cc_final: 0.7254 (m100) REVERT: I 173 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.6395 (p90) REVERT: J 152 GLU cc_start: 0.8543 (pm20) cc_final: 0.8304 (pm20) REVERT: J 160 ASN cc_start: 0.8863 (m-40) cc_final: 0.8324 (m110) REVERT: J 181 TYR cc_start: 0.8374 (m-80) cc_final: 0.7539 (m-80) REVERT: K 125 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.8050 (m) REVERT: K 128 LEU cc_start: 0.7721 (tp) cc_final: 0.7470 (tp) REVERT: K 149 TYR cc_start: 0.7704 (p90) cc_final: 0.7441 (p90) REVERT: K 160 ASN cc_start: 0.8889 (m-40) cc_final: 0.8213 (m110) REVERT: K 209 ASN cc_start: 0.8494 (m110) cc_final: 0.8251 (m-40) REVERT: L 139 PHE cc_start: 0.8320 (p90) cc_final: 0.8089 (p90) outliers start: 49 outliers final: 13 residues processed: 506 average time/residue: 1.2735 time to fit residues: 734.0493 Evaluate side-chains 413 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 393 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 183 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 240 optimal weight: 0.0040 chunk 259 optimal weight: 9.9990 chunk 213 optimal weight: 0.9980 chunk 238 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 192 optimal weight: 0.2980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20960 Z= 0.209 Angle : 0.771 11.827 28592 Z= 0.392 Chirality : 0.048 0.164 3220 Planarity : 0.006 0.067 3648 Dihedral : 5.877 25.682 2864 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.87 % Allowed : 17.10 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2640 helix: -0.36 (0.52), residues: 124 sheet: 1.21 (0.17), residues: 916 loop : -0.53 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 215 HIS 0.004 0.001 HIS I 189 PHE 0.023 0.002 PHE E 139 TYR 0.015 0.002 TYR J 99 ARG 0.007 0.001 ARG G 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 429 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.7050 (mtp) cc_final: 0.6503 (mtp) REVERT: E 108 ARG cc_start: 0.7346 (tmm-80) cc_final: 0.7093 (tmm-80) REVERT: E 139 PHE cc_start: 0.8225 (p90) cc_final: 0.7998 (p90) REVERT: E 173 TYR cc_start: 0.6899 (OUTLIER) cc_final: 0.6495 (p90) REVERT: F 128 LEU cc_start: 0.8516 (mp) cc_final: 0.8308 (mm) REVERT: F 148 ASP cc_start: 0.7716 (p0) cc_final: 0.7490 (p0) REVERT: F 152 GLU cc_start: 0.8394 (pm20) cc_final: 0.8182 (pm20) REVERT: F 171 PHE cc_start: 0.8537 (m-80) cc_final: 0.8247 (m-80) REVERT: F 209 ASN cc_start: 0.8633 (m110) cc_final: 0.8396 (m-40) REVERT: G 4 MET cc_start: 0.6978 (mtp) cc_final: 0.6409 (mtp) REVERT: H 6 GLU cc_start: 0.6684 (mp0) cc_final: 0.6397 (mp0) REVERT: H 148 ASP cc_start: 0.7976 (p0) cc_final: 0.7736 (p0) REVERT: H 171 PHE cc_start: 0.8469 (m-80) cc_final: 0.8205 (m-80) REVERT: H 209 ASN cc_start: 0.8637 (m110) cc_final: 0.8405 (m-40) REVERT: I 4 MET cc_start: 0.7019 (mtp) cc_final: 0.6460 (mtp) REVERT: J 171 PHE cc_start: 0.8516 (m-80) cc_final: 0.8256 (m-80) REVERT: K 128 LEU cc_start: 0.7679 (tp) cc_final: 0.7472 (tp) REVERT: K 148 ASP cc_start: 0.7717 (p0) cc_final: 0.7449 (p0) REVERT: K 152 GLU cc_start: 0.8364 (pm20) cc_final: 0.8113 (pm20) REVERT: K 171 PHE cc_start: 0.8480 (m-80) cc_final: 0.8182 (m-80) REVERT: K 209 ASN cc_start: 0.8511 (m110) cc_final: 0.8257 (m-40) REVERT: L 4 MET cc_start: 0.7065 (mtp) cc_final: 0.6459 (mtp) REVERT: L 173 TYR cc_start: 0.7051 (p90) cc_final: 0.6790 (p90) outliers start: 43 outliers final: 25 residues processed: 462 average time/residue: 1.2452 time to fit residues: 657.1625 Evaluate side-chains 407 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 381 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 202 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN G 138 ASN I 30 ASN ** J 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20960 Z= 0.358 Angle : 0.783 10.686 28592 Z= 0.406 Chirality : 0.050 0.173 3220 Planarity : 0.006 0.067 3648 Dihedral : 5.840 25.773 2864 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.95 % Allowed : 18.06 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2640 helix: -0.73 (0.49), residues: 124 sheet: 1.14 (0.16), residues: 928 loop : -0.68 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 148 HIS 0.003 0.001 HIS C 240 PHE 0.025 0.002 PHE F 27 TYR 0.022 0.002 TYR H 181 ARG 0.007 0.001 ARG D 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 392 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 139 PHE cc_start: 0.8284 (p90) cc_final: 0.8014 (p90) REVERT: E 173 TYR cc_start: 0.7181 (p90) cc_final: 0.6796 (p90) REVERT: F 22 CYS cc_start: 0.5851 (t) cc_final: 0.5636 (t) REVERT: F 171 PHE cc_start: 0.8563 (m-80) cc_final: 0.8266 (m-80) REVERT: F 209 ASN cc_start: 0.8899 (m110) cc_final: 0.8680 (m-40) REVERT: G 108 ARG cc_start: 0.7104 (tmm-80) cc_final: 0.6654 (tmm-80) REVERT: G 139 PHE cc_start: 0.8225 (p90) cc_final: 0.7637 (p90) REVERT: G 173 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6847 (p90) REVERT: H 171 PHE cc_start: 0.8530 (m-80) cc_final: 0.8211 (m-80) REVERT: H 209 ASN cc_start: 0.8743 (m110) cc_final: 0.8540 (m-40) REVERT: I 173 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.5983 (p90) REVERT: J 171 PHE cc_start: 0.8493 (m-80) cc_final: 0.8214 (m-80) REVERT: J 200 ILE cc_start: 0.8303 (mp) cc_final: 0.8091 (mp) REVERT: J 202 ASN cc_start: 0.8160 (m-40) cc_final: 0.7220 (t0) REVERT: K 128 LEU cc_start: 0.7918 (tp) cc_final: 0.7701 (mm) REVERT: K 171 PHE cc_start: 0.8475 (m-80) cc_final: 0.8161 (m-80) REVERT: K 209 ASN cc_start: 0.8710 (m110) cc_final: 0.8501 (m-40) REVERT: L 139 PHE cc_start: 0.8305 (p90) cc_final: 0.8015 (p90) outliers start: 45 outliers final: 24 residues processed: 422 average time/residue: 1.2132 time to fit residues: 588.3023 Evaluate side-chains 382 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 356 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 201 CYS Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 202 ASN Chi-restraints excluded: chain L residue 53 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 190 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 229 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 137 ASN F 176 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN I 137 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN L 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20960 Z= 0.395 Angle : 0.773 10.488 28592 Z= 0.405 Chirality : 0.049 0.171 3220 Planarity : 0.006 0.069 3648 Dihedral : 5.785 25.312 2864 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.87 % Allowed : 18.58 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2640 helix: -1.02 (0.46), residues: 124 sheet: 1.19 (0.16), residues: 904 loop : -0.78 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 148 HIS 0.003 0.001 HIS D 173 PHE 0.013 0.002 PHE B 153 TYR 0.023 0.002 TYR H 181 ARG 0.007 0.001 ARG L 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 376 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 88 CYS cc_start: 0.6815 (p) cc_final: 0.6500 (p) REVERT: E 139 PHE cc_start: 0.8432 (p90) cc_final: 0.7847 (p90) REVERT: E 173 TYR cc_start: 0.7519 (p90) cc_final: 0.7280 (p90) REVERT: F 22 CYS cc_start: 0.5945 (t) cc_final: 0.5691 (t) REVERT: F 171 PHE cc_start: 0.8584 (m-80) cc_final: 0.8300 (m-80) REVERT: G 139 PHE cc_start: 0.8262 (p90) cc_final: 0.7701 (p90) REVERT: H 171 PHE cc_start: 0.8544 (m-80) cc_final: 0.8228 (m-80) REVERT: H 209 ASN cc_start: 0.8964 (m110) cc_final: 0.8761 (m-40) REVERT: I 88 CYS cc_start: 0.6779 (p) cc_final: 0.6473 (p) REVERT: I 139 PHE cc_start: 0.8134 (p90) cc_final: 0.7530 (p90) REVERT: J 22 CYS cc_start: 0.6033 (t) cc_final: 0.5813 (t) REVERT: J 148 ASP cc_start: 0.8000 (p0) cc_final: 0.7797 (p0) REVERT: J 171 PHE cc_start: 0.8509 (m-80) cc_final: 0.8242 (m-80) REVERT: K 22 CYS cc_start: 0.5986 (t) cc_final: 0.5770 (t) REVERT: K 128 LEU cc_start: 0.8017 (tp) cc_final: 0.7807 (mm) REVERT: K 171 PHE cc_start: 0.8507 (m-80) cc_final: 0.8220 (m-80) REVERT: L 88 CYS cc_start: 0.6725 (p) cc_final: 0.6393 (p) REVERT: L 139 PHE cc_start: 0.8352 (p90) cc_final: 0.8135 (p90) outliers start: 43 outliers final: 18 residues processed: 408 average time/residue: 1.2165 time to fit residues: 571.4798 Evaluate side-chains 370 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 352 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 201 CYS Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.6980 chunk 229 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 255 optimal weight: 9.9990 chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN E 137 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN G 79 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN I 79 GLN I 137 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20960 Z= 0.245 Angle : 0.760 12.429 28592 Z= 0.393 Chirality : 0.048 0.183 3220 Planarity : 0.006 0.064 3648 Dihedral : 5.496 24.672 2864 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.65 % Allowed : 20.88 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2640 helix: -1.12 (0.47), residues: 124 sheet: 1.39 (0.17), residues: 916 loop : -0.76 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 148 HIS 0.003 0.001 HIS L 198 PHE 0.026 0.002 PHE H 27 TYR 0.027 0.002 TYR H 181 ARG 0.008 0.001 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 376 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 139 PHE cc_start: 0.8263 (p90) cc_final: 0.7593 (p90) REVERT: E 173 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.7232 (p90) REVERT: F 128 LEU cc_start: 0.8343 (mm) cc_final: 0.7831 (mm) REVERT: F 171 PHE cc_start: 0.8599 (m-80) cc_final: 0.8294 (m-80) REVERT: G 117 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8133 (mt) REVERT: G 139 PHE cc_start: 0.8113 (p90) cc_final: 0.7684 (p90) REVERT: H 171 PHE cc_start: 0.8545 (m-80) cc_final: 0.8249 (m-80) REVERT: I 139 PHE cc_start: 0.8032 (p90) cc_final: 0.7686 (p90) REVERT: J 171 PHE cc_start: 0.8484 (m-80) cc_final: 0.8182 (m-80) REVERT: K 171 PHE cc_start: 0.8507 (m-80) cc_final: 0.8193 (m-80) REVERT: L 139 PHE cc_start: 0.8173 (p90) cc_final: 0.7955 (p90) outliers start: 38 outliers final: 23 residues processed: 400 average time/residue: 1.2160 time to fit residues: 557.8421 Evaluate side-chains 379 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 354 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 202 ASN Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 254 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 137 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN H 176 GLN I 137 ASN J 76 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20960 Z= 0.295 Angle : 0.780 12.644 28592 Z= 0.405 Chirality : 0.049 0.166 3220 Planarity : 0.006 0.064 3648 Dihedral : 5.480 23.825 2864 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.87 % Allowed : 20.96 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 2640 helix: -1.22 (0.47), residues: 124 sheet: 1.39 (0.17), residues: 920 loop : -0.84 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 148 HIS 0.003 0.001 HIS L 198 PHE 0.012 0.002 PHE D 153 TYR 0.029 0.002 TYR J 181 ARG 0.008 0.001 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 361 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 MET cc_start: 0.7108 (ttp) cc_final: 0.6779 (ttt) REVERT: E 139 PHE cc_start: 0.8239 (p90) cc_final: 0.7677 (p90) REVERT: E 173 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.7298 (p90) REVERT: F 128 LEU cc_start: 0.8327 (mm) cc_final: 0.7876 (mm) REVERT: F 171 PHE cc_start: 0.8601 (m-80) cc_final: 0.8296 (m-80) REVERT: G 4 MET cc_start: 0.7086 (ttp) cc_final: 0.6764 (ttt) REVERT: G 139 PHE cc_start: 0.8127 (p90) cc_final: 0.7673 (p90) REVERT: H 128 LEU cc_start: 0.8035 (mm) cc_final: 0.7339 (mm) REVERT: H 171 PHE cc_start: 0.8561 (m-80) cc_final: 0.8298 (m-80) REVERT: I 4 MET cc_start: 0.7108 (ttp) cc_final: 0.6778 (ttt) REVERT: I 139 PHE cc_start: 0.8064 (p90) cc_final: 0.7274 (p90) REVERT: I 142 ARG cc_start: 0.8432 (tpp-160) cc_final: 0.8125 (mpp-170) REVERT: J 128 LEU cc_start: 0.8099 (mm) cc_final: 0.7352 (mm) REVERT: J 171 PHE cc_start: 0.8561 (m-80) cc_final: 0.8267 (m-80) REVERT: K 171 PHE cc_start: 0.8541 (m-80) cc_final: 0.8225 (m-80) REVERT: L 4 MET cc_start: 0.7126 (ttp) cc_final: 0.6785 (ttt) REVERT: L 139 PHE cc_start: 0.8225 (p90) cc_final: 0.8010 (p90) outliers start: 43 outliers final: 29 residues processed: 390 average time/residue: 1.3029 time to fit residues: 580.5885 Evaluate side-chains 370 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 340 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN H 176 GLN I 137 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20960 Z= 0.316 Angle : 0.804 13.508 28592 Z= 0.416 Chirality : 0.049 0.186 3220 Planarity : 0.006 0.065 3648 Dihedral : 5.483 23.547 2864 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.56 % Allowed : 22.70 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 2640 helix: -1.37 (0.45), residues: 124 sheet: 1.41 (0.16), residues: 920 loop : -0.86 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 148 HIS 0.003 0.001 HIS L 198 PHE 0.032 0.002 PHE F 27 TYR 0.032 0.002 TYR J 181 ARG 0.008 0.001 ARG L 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 358 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 139 PHE cc_start: 0.8268 (p90) cc_final: 0.7712 (p90) REVERT: E 173 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.7220 (p90) REVERT: F 128 LEU cc_start: 0.8232 (mm) cc_final: 0.7799 (mm) REVERT: F 171 PHE cc_start: 0.8640 (m-80) cc_final: 0.8338 (m-80) REVERT: G 139 PHE cc_start: 0.8049 (p90) cc_final: 0.7654 (p90) REVERT: G 142 ARG cc_start: 0.8465 (tpp-160) cc_final: 0.8140 (mpp-170) REVERT: H 171 PHE cc_start: 0.8601 (m-80) cc_final: 0.8333 (m-80) REVERT: I 117 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8161 (mt) REVERT: I 139 PHE cc_start: 0.8152 (p90) cc_final: 0.7542 (p90) REVERT: J 128 LEU cc_start: 0.8153 (mm) cc_final: 0.7451 (mm) REVERT: J 171 PHE cc_start: 0.8582 (m-80) cc_final: 0.8270 (m-80) REVERT: K 128 LEU cc_start: 0.8264 (mm) cc_final: 0.7730 (mm) REVERT: K 171 PHE cc_start: 0.8579 (m-80) cc_final: 0.8270 (m-80) REVERT: L 139 PHE cc_start: 0.8228 (p90) cc_final: 0.7933 (p90) REVERT: L 173 TYR cc_start: 0.7131 (p90) cc_final: 0.6551 (p90) outliers start: 36 outliers final: 27 residues processed: 383 average time/residue: 1.3148 time to fit residues: 574.5004 Evaluate side-chains 373 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 344 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.0570 chunk 222 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 142 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 186 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN H 176 GLN J 76 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20960 Z= 0.255 Angle : 0.807 13.509 28592 Z= 0.420 Chirality : 0.049 0.223 3220 Planarity : 0.006 0.063 3648 Dihedral : 5.440 25.794 2864 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.69 % Allowed : 23.05 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2640 helix: -1.30 (0.46), residues: 124 sheet: 1.50 (0.17), residues: 916 loop : -0.80 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 148 HIS 0.003 0.001 HIS C 166 PHE 0.031 0.001 PHE H 27 TYR 0.031 0.002 TYR J 181 ARG 0.008 0.001 ARG I 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 362 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 139 PHE cc_start: 0.8230 (p90) cc_final: 0.7691 (p90) REVERT: E 173 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.7161 (p90) REVERT: F 128 LEU cc_start: 0.8269 (mm) cc_final: 0.7877 (mm) REVERT: F 171 PHE cc_start: 0.8649 (m-80) cc_final: 0.8351 (m-80) REVERT: G 139 PHE cc_start: 0.7949 (p90) cc_final: 0.7537 (p90) REVERT: G 142 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8150 (mpp-170) REVERT: H 128 LEU cc_start: 0.8201 (mm) cc_final: 0.7478 (mm) REVERT: H 171 PHE cc_start: 0.8589 (m-80) cc_final: 0.8327 (m-80) REVERT: I 117 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8158 (mt) REVERT: I 139 PHE cc_start: 0.8185 (p90) cc_final: 0.7640 (p90) REVERT: J 171 PHE cc_start: 0.8605 (m-80) cc_final: 0.8297 (m-80) REVERT: K 171 PHE cc_start: 0.8573 (m-80) cc_final: 0.8260 (m-80) REVERT: L 139 PHE cc_start: 0.8087 (p90) cc_final: 0.7849 (p90) outliers start: 39 outliers final: 21 residues processed: 387 average time/residue: 1.2689 time to fit residues: 561.2689 Evaluate side-chains 376 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 353 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.2980 chunk 153 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 174 optimal weight: 7.9990 chunk 263 optimal weight: 0.0170 chunk 242 optimal weight: 0.9980 chunk 209 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20960 Z= 0.230 Angle : 0.819 14.597 28592 Z= 0.420 Chirality : 0.048 0.268 3220 Planarity : 0.006 0.062 3648 Dihedral : 5.351 25.799 2864 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 1.39 % Allowed : 23.74 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2640 helix: -1.26 (0.47), residues: 124 sheet: 1.55 (0.17), residues: 916 loop : -0.74 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 148 HIS 0.003 0.001 HIS C 166 PHE 0.034 0.001 PHE J 27 TYR 0.032 0.002 TYR K 181 ARG 0.005 0.001 ARG E 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 369 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 139 PHE cc_start: 0.8175 (p90) cc_final: 0.7634 (p90) REVERT: E 173 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6990 (p90) REVERT: F 128 LEU cc_start: 0.8335 (mm) cc_final: 0.7947 (mm) REVERT: F 171 PHE cc_start: 0.8631 (m-80) cc_final: 0.8315 (m-80) REVERT: G 139 PHE cc_start: 0.7929 (p90) cc_final: 0.7503 (p90) REVERT: H 128 LEU cc_start: 0.8189 (mm) cc_final: 0.7458 (mm) REVERT: H 171 PHE cc_start: 0.8563 (m-80) cc_final: 0.8292 (m-80) REVERT: I 139 PHE cc_start: 0.8072 (p90) cc_final: 0.7504 (p90) REVERT: J 171 PHE cc_start: 0.8613 (m-80) cc_final: 0.8317 (m-80) REVERT: K 128 LEU cc_start: 0.8276 (mm) cc_final: 0.7573 (mm) REVERT: K 171 PHE cc_start: 0.8570 (m-80) cc_final: 0.8271 (m-80) outliers start: 32 outliers final: 21 residues processed: 391 average time/residue: 1.3028 time to fit residues: 582.3739 Evaluate side-chains 373 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 351 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 0.0570 chunk 209 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 215 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.117069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.066744 restraints weight = 36826.514| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.08 r_work: 0.2608 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4974 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: