Starting phenix.real_space_refine on Wed Nov 20 01:00:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgj_43202/11_2024/8vgj_43202.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgj_43202/11_2024/8vgj_43202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgj_43202/11_2024/8vgj_43202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgj_43202/11_2024/8vgj_43202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgj_43202/11_2024/8vgj_43202.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgj_43202/11_2024/8vgj_43202.cif" } resolution = 2.5 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= -0.009 sd= 0.357 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 116 5.16 5 C 12968 2.51 5 N 3492 2.21 5 O 4003 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20579 Number of models: 1 Model: "" Number of chains: 21 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: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1621 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "F" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1580 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "G" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1621 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "H" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1580 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "I" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1621 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "J" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1580 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "K" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1580 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "L" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1621 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 204} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} 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: "I" 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: 12.45, per 1000 atoms: 0.60 Number of scatterers: 20579 At special positions: 0 Unit cell: (97, 111, 183, 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 116 16.00 O 4003 8.00 N 3492 7.00 C 12968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 58 " distance=2.05 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=2.05 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 201 " distance=2.03 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=2.05 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=2.05 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 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=2.05 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS F 153 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 201 " distance=2.03 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 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=2.05 Simple disulfide: pdb=" SG CYS H 108 " - pdb=" SG CYS H 153 " distance=2.02 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 201 " distance=2.03 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 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=2.05 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 153 " distance=2.02 Simple disulfide: pdb=" SG CYS J 144 " - pdb=" SG CYS J 201 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS K 108 " - pdb=" SG CYS K 153 " distance=2.02 Simple disulfide: pdb=" SG CYS K 144 " - pdb=" SG CYS K 201 " distance=2.03 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: 5.11 Conformation dependent library (CDL) restraints added in 2.9 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: 48 helices and 52 sheets defined 9.3% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.577A pdb=" N CYS A 58 " --> pdb=" O ALA A 55 " (cutoff:3.500A) 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 removed outlier: 3.517A pdb=" N LEU A 173A" --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.576A pdb=" N CYS B 58 " --> pdb=" O ALA B 55 " (cutoff:3.500A) 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 removed outlier: 3.518A pdb=" N LEU B 173A" --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.579A pdb=" N CYS C 58 " --> pdb=" O ALA C 55 " (cutoff:3.500A) 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 removed outlier: 3.518A pdb=" N LEU C 173A" --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.576A pdb=" N CYS D 58 " --> pdb=" O ALA D 55 " (cutoff:3.500A) 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 removed outlier: 3.515A pdb=" N LEU D 173A" --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 121 through 126 removed outlier: 3.627A pdb=" N LEU E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 187 Processing helix 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 192 through 197 removed outlier: 4.651A pdb=" N THR F 196 " --> pdb=" O SER F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.646A pdb=" N LEU G 125 " --> pdb=" O SER G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 187 Processing helix 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 192 through 197 removed outlier: 4.653A pdb=" N THR H 196 " --> pdb=" O SER H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 209 No H-bonds generated for 'chain 'H' and resid 207 through 209' Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'I' and resid 121 through 126 removed outlier: 3.651A pdb=" N LEU I 125 " --> pdb=" O SER I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 187 Processing helix 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 192 through 197 removed outlier: 4.656A pdb=" N THR J 196 " --> pdb=" O SER J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 207 through 209 No H-bonds generated for 'chain 'J' and resid 207 through 209' Processing helix 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 192 through 197 removed outlier: 4.669A pdb=" N THR K 196 " --> pdb=" O SER K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 209 No H-bonds generated for 'chain 'K' and resid 207 through 209' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.631A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 4.177A pdb=" N CYS A 136 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 139 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 199 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL A 213 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR A 229 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS A 182 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.730A pdb=" N CYS A 42 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 35 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS A 40 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 21 removed outlier: 4.177A pdb=" N CYS B 136 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR B 139 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 199 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL B 213 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR B 229 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.541A 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: 3.730A pdb=" N CYS B 42 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 35 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS B 40 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 20 through 21 removed outlier: 4.178A pdb=" N CYS C 136 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR C 139 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 199 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL C 213 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR C 229 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N CYS C 182 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 64 through 67 removed outlier: 3.727A pdb=" N CYS C 42 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 35 " --> pdb=" O HIS C 40 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N HIS C 40 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP C 51 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 20 through 21 removed outlier: 4.180A pdb=" N CYS D 136 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR D 139 " --> pdb=" O PRO D 198 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU D 199 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL D 213 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR D 229 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS D 182 " --> pdb=" O MET D 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 64 through 67 removed outlier: 3.724A pdb=" N CYS D 42 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL D 35 " --> pdb=" O HIS D 40 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS D 40 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP D 51 " --> pdb=" O ILE D 47 " (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: 3.844A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.531A 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: 3.844A 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: 5.228A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (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: 3.856A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.929A 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: 3.554A pdb=" N SER F 124 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY F 143 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL F 187 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU F 145 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER F 185 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS F 147 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU F 183 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 124 through 128 removed outlier: 3.554A pdb=" N SER F 124 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY F 143 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL F 187 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU F 145 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER F 185 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS F 147 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU F 183 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 155 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: 3.843A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.530A 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: 3.843A 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: 5.229A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (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: 3.857A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.930A 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: 3.550A pdb=" N SER H 124 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 4.900A 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: 3.550A pdb=" N SER H 124 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR H 181 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 155 through 159 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: 3.837A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.530A 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: 3.837A 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: 5.224A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (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: 3.857A pdb=" N ALA J 33 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.931A 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: 3.547A pdb=" N SER J 124 " --> pdb=" O LYS J 147 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 4.900A 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: 3.547A pdb=" N SER J 124 " --> pdb=" O LYS J 147 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR J 181 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 155 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: 3.858A pdb=" N ALA K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.930A 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: 3.551A pdb=" N SER K 124 " --> pdb=" O LYS K 147 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY K 143 " --> pdb=" O LEU K 128 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY K 143 " --> pdb=" O VAL K 187 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL K 187 " --> pdb=" O GLY K 143 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU K 145 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER K 185 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS K 147 " --> pdb=" O LEU K 183 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU K 183 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 124 through 128 removed outlier: 3.551A pdb=" N SER K 124 " --> pdb=" O LYS K 147 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY K 143 " --> pdb=" O LEU K 128 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY K 143 " --> pdb=" O VAL K 187 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL K 187 " --> pdb=" O GLY K 143 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU K 145 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER K 185 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS K 147 " --> pdb=" O LEU K 183 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU K 183 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 155 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: 3.839A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.531A 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: 3.839A 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: 5.228A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 153 through 154 792 hydrogen bonds defined for protein. 2016 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: 8.13 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5303 1.33 - 1.46: 5276 1.46 - 1.58: 10301 1.58 - 1.71: 0 1.71 - 1.84: 136 Bond restraints: 21016 Sorted by residual: bond pdb=" C GLU A 21 " pdb=" N ALA A 22 " ideal model delta sigma weight residual 1.331 1.253 0.078 2.07e-02 2.33e+03 1.41e+01 bond pdb=" C GLU B 21 " pdb=" N ALA B 22 " ideal model delta sigma weight residual 1.335 1.252 0.083 3.04e-02 1.08e+03 7.43e+00 bond pdb=" CB ARG J 38 " pdb=" CG ARG J 38 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.52e+00 bond pdb=" CB ARG K 38 " pdb=" CG ARG K 38 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.49e+00 bond pdb=" CB ARG H 38 " pdb=" CG ARG H 38 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.48e+00 ... (remaining 21011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 26767 2.29 - 4.58: 1693 4.58 - 6.87: 153 6.87 - 9.16: 41 9.16 - 11.45: 14 Bond angle restraints: 28668 Sorted by residual: angle pdb=" N PRO D 152A" pdb=" CA PRO D 152A" pdb=" C PRO D 152A" ideal model delta sigma weight residual 110.70 122.15 -11.45 1.22e+00 6.72e-01 8.80e+01 angle pdb=" N PRO B 152A" pdb=" CA PRO B 152A" pdb=" C PRO B 152A" ideal model delta sigma weight residual 110.70 122.05 -11.35 1.22e+00 6.72e-01 8.65e+01 angle pdb=" N PRO C 152A" pdb=" CA PRO C 152A" pdb=" C PRO C 152A" ideal model delta sigma weight residual 110.70 122.03 -11.33 1.22e+00 6.72e-01 8.63e+01 angle pdb=" N PRO A 152A" pdb=" CA PRO A 152A" pdb=" C PRO A 152A" ideal model delta sigma weight residual 110.70 121.67 -10.97 1.22e+00 6.72e-01 8.09e+01 angle pdb=" C PRO D 152 " pdb=" N PRO D 152A" pdb=" CA PRO D 152A" ideal model delta sigma weight residual 120.38 127.54 -7.16 1.03e+00 9.43e-01 4.83e+01 ... (remaining 28663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 11531 17.36 - 34.71: 781 34.71 - 52.07: 148 52.07 - 69.43: 60 69.43 - 86.78: 28 Dihedral angle restraints: 12548 sinusoidal: 4872 harmonic: 7676 Sorted by residual: dihedral pdb=" CA PRO H 123 " pdb=" C PRO H 123 " pdb=" N SER H 124 " pdb=" CA SER H 124 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA PRO F 123 " pdb=" C PRO F 123 " pdb=" N SER F 124 " pdb=" CA SER F 124 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA PRO K 123 " pdb=" C PRO K 123 " pdb=" N SER K 124 " pdb=" CA SER K 124 " ideal model delta harmonic sigma weight residual 180.00 153.66 26.34 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 12545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2143 0.071 - 0.141: 869 0.141 - 0.212: 155 0.212 - 0.283: 44 0.283 - 0.353: 9 Chirality restraints: 3220 Sorted by residual: 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 2.37 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA PRO C 152A" pdb=" N PRO C 152A" pdb=" C PRO C 152A" pdb=" CB PRO C 152A" both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.06e+00 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 2.37 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 3217 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 95 " -0.036 2.00e-02 2.50e+03 2.15e-02 9.23e+00 pdb=" CG TYR B 95 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR B 95 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 95 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 95 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 95 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 95 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 95 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 95 " 0.036 2.00e-02 2.50e+03 2.13e-02 9.07e+00 pdb=" CG TYR A 95 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 95 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 95 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 95 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 95 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 95 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 95 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 95 " 0.035 2.00e-02 2.50e+03 2.12e-02 8.95e+00 pdb=" CG TYR D 95 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR D 95 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 95 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 95 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 95 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 95 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR D 95 " 0.006 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 555 2.68 - 3.24: 19492 3.24 - 3.79: 32253 3.79 - 4.35: 44840 4.35 - 4.90: 72393 Nonbonded interactions: 169533 Sorted by model distance: nonbonded pdb=" OH TYR E 29 " pdb=" NH1 ARG E 94 " model vdw 2.128 3.120 nonbonded pdb=" OH TYR I 29 " pdb=" NH1 ARG I 94 " model vdw 2.129 3.120 nonbonded pdb=" OH TYR G 29 " pdb=" NH1 ARG G 94 " model vdw 2.129 3.120 nonbonded pdb=" OH TYR L 29 " pdb=" NH1 ARG L 94 " model vdw 2.129 3.120 nonbonded pdb=" ND2 ASN G 158 " pdb=" O THR G 180 " model vdw 2.176 3.120 ... (remaining 169528 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: 18.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 46.050 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.011 0.091 21016 Z= 0.743 Angle : 1.203 11.446 28668 Z= 0.662 Chirality : 0.078 0.353 3220 Planarity : 0.012 0.092 3660 Dihedral : 13.485 86.783 7492 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.21 % Favored : 93.48 % Rotamer: Outliers : 1.57 % Allowed : 4.30 % Favored : 94.13 % 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: -1.25 (0.15), residues: 2640 helix: -2.42 (0.32), residues: 144 sheet: 0.15 (0.17), residues: 892 loop : -1.29 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.006 TRP B 141 HIS 0.019 0.005 HIS A 173 PHE 0.027 0.007 PHE I 116 TYR 0.047 0.006 TYR B 95 ARG 0.032 0.004 ARG D 69 *********************** 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 596 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 560 time to evaluate : 2.224 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 82 ASP cc_start: 0.8406 (m-30) cc_final: 0.8198 (m-30) REVERT: E 117 ILE cc_start: 0.9016 (tt) cc_final: 0.8798 (mt) REVERT: E 181 LEU cc_start: 0.8476 (tp) cc_final: 0.8125 (tp) REVERT: E 186 TYR cc_start: 0.9049 (t80) cc_final: 0.8845 (t80) REVERT: F 148 ASP cc_start: 0.8195 (p0) cc_final: 0.7855 (p0) REVERT: F 160 ASN cc_start: 0.8778 (m-40) cc_final: 0.8407 (m-40) REVERT: G 82 ASP cc_start: 0.8420 (m-30) cc_final: 0.8194 (m-30) REVERT: G 117 ILE cc_start: 0.9003 (tt) cc_final: 0.8784 (mt) REVERT: G 181 LEU cc_start: 0.8471 (tp) cc_final: 0.8127 (tp) REVERT: G 186 TYR cc_start: 0.9059 (t80) cc_final: 0.8857 (t80) REVERT: H 148 ASP cc_start: 0.8198 (p0) cc_final: 0.7802 (p0) REVERT: H 160 ASN cc_start: 0.8760 (m-40) cc_final: 0.8402 (m-40) REVERT: I 82 ASP cc_start: 0.8429 (m-30) cc_final: 0.8207 (m-30) REVERT: I 117 ILE cc_start: 0.9006 (tt) cc_final: 0.8794 (mt) REVERT: I 181 LEU cc_start: 0.8477 (tp) cc_final: 0.8126 (tp) REVERT: I 186 TYR cc_start: 0.9050 (t80) cc_final: 0.8848 (t80) REVERT: J 148 ASP cc_start: 0.8185 (p0) cc_final: 0.7789 (p0) REVERT: J 160 ASN cc_start: 0.8749 (m-40) cc_final: 0.8388 (m-40) REVERT: K 148 ASP cc_start: 0.8183 (p0) cc_final: 0.7769 (p0) REVERT: K 160 ASN cc_start: 0.8754 (m-40) cc_final: 0.8368 (m-40) REVERT: K 176 GLN cc_start: 0.8487 (mt0) cc_final: 0.7941 (mt0) REVERT: L 82 ASP cc_start: 0.8423 (m-30) cc_final: 0.7978 (m-30) REVERT: L 117 ILE cc_start: 0.9002 (tt) cc_final: 0.8781 (mt) REVERT: L 181 LEU cc_start: 0.8477 (tp) cc_final: 0.8122 (tp) outliers start: 36 outliers final: 1 residues processed: 584 average time/residue: 1.3146 time to fit residues: 869.3437 Evaluate side-chains 370 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 369 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9990 chunk 200 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 239 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN E 158 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS G 79 GLN G 158 ASN ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 HIS I 79 GLN I 147 GLN I 158 ASN ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 HIS K 169 HIS L 158 ASN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21016 Z= 0.362 Angle : 0.783 9.772 28668 Z= 0.412 Chirality : 0.050 0.140 3220 Planarity : 0.005 0.048 3660 Dihedral : 6.305 102.494 2866 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.35 % Allowed : 14.39 % Favored : 83.26 % 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: -0.28 (0.16), residues: 2640 helix: -1.01 (0.42), residues: 152 sheet: 0.49 (0.16), residues: 932 loop : -0.48 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 148 HIS 0.006 0.001 HIS A 173 PHE 0.031 0.002 PHE D 153 TYR 0.027 0.002 TYR G 140 ARG 0.011 0.001 ARG G 18 *********************** 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 510 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 456 time to evaluate : 2.495 Fit side-chains revert: symmetry clash REVERT: E 95 ASP cc_start: 0.7799 (p0) cc_final: 0.7575 (p0) REVERT: E 210 ASN cc_start: 0.7695 (t0) cc_final: 0.7363 (p0) REVERT: F 26 ARG cc_start: 0.7811 (pmm-80) cc_final: 0.7557 (pmm-80) REVERT: F 105 GLN cc_start: 0.7687 (pm20) cc_final: 0.7365 (pm20) REVERT: F 148 ASP cc_start: 0.8157 (p0) cc_final: 0.7936 (p0) REVERT: F 214 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7924 (ttpt) REVERT: G 95 ASP cc_start: 0.7781 (p0) cc_final: 0.7561 (p0) REVERT: G 173 TYR cc_start: 0.7364 (p90) cc_final: 0.6826 (p90) REVERT: G 210 ASN cc_start: 0.7705 (t0) cc_final: 0.7351 (p0) REVERT: H 26 ARG cc_start: 0.7754 (pmm-80) cc_final: 0.7495 (pmm-80) REVERT: H 105 GLN cc_start: 0.7736 (pm20) cc_final: 0.7396 (pm20) REVERT: H 147 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8822 (tppt) REVERT: H 176 GLN cc_start: 0.8023 (mt0) cc_final: 0.7769 (mt0) REVERT: H 214 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7852 (ttpt) REVERT: I 95 ASP cc_start: 0.7729 (p0) cc_final: 0.7510 (p0) REVERT: I 210 ASN cc_start: 0.7668 (t0) cc_final: 0.7352 (p0) REVERT: J 26 ARG cc_start: 0.7797 (pmm-80) cc_final: 0.7528 (pmm-80) REVERT: J 105 GLN cc_start: 0.7694 (pm20) cc_final: 0.7364 (pm20) REVERT: J 214 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7865 (ttpt) REVERT: K 26 ARG cc_start: 0.7763 (pmm-80) cc_final: 0.7506 (pmm-80) REVERT: K 105 GLN cc_start: 0.7707 (pm20) cc_final: 0.7384 (pm20) REVERT: K 148 ASP cc_start: 0.8135 (p0) cc_final: 0.7861 (p0) REVERT: K 214 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7891 (ttpt) REVERT: L 95 ASP cc_start: 0.7756 (p0) cc_final: 0.7529 (p0) REVERT: L 173 TYR cc_start: 0.7351 (p90) cc_final: 0.6817 (p90) REVERT: L 210 ASN cc_start: 0.7815 (t0) cc_final: 0.7466 (p0) outliers start: 54 outliers final: 12 residues processed: 484 average time/residue: 1.1535 time to fit residues: 643.5650 Evaluate side-chains 409 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 392 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain K residue 214 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 chunk 238 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 192 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 HIS ** I 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 HIS L 79 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21016 Z= 0.306 Angle : 0.727 9.450 28668 Z= 0.383 Chirality : 0.048 0.148 3220 Planarity : 0.005 0.056 3660 Dihedral : 5.667 23.300 2864 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.96 % Allowed : 16.96 % Favored : 80.09 % 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: -0.47 (0.45), residues: 152 sheet: 0.69 (0.16), residues: 920 loop : -0.31 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 148 HIS 0.005 0.001 HIS B 173 PHE 0.021 0.002 PHE L 209 TYR 0.022 0.002 TYR I 140 ARG 0.006 0.001 ARG I 142 *********************** 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 484 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 416 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 148 ASP cc_start: 0.8266 (p0) cc_final: 0.8026 (p0) REVERT: F 160 ASN cc_start: 0.8745 (m-40) cc_final: 0.8490 (m-40) REVERT: H 149 TYR cc_start: 0.8116 (p90) cc_final: 0.7679 (p90) REVERT: H 160 ASN cc_start: 0.8741 (m-40) cc_final: 0.8533 (m-40) REVERT: H 183 LEU cc_start: 0.9255 (tt) cc_final: 0.8808 (mt) REVERT: H 214 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7836 (ttpt) REVERT: J 149 TYR cc_start: 0.8068 (p90) cc_final: 0.7616 (p90) REVERT: J 160 ASN cc_start: 0.8734 (m-40) cc_final: 0.8532 (m-40) REVERT: J 183 LEU cc_start: 0.9287 (tt) cc_final: 0.8825 (mt) REVERT: J 214 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7866 (ttpt) REVERT: K 148 ASP cc_start: 0.8098 (p0) cc_final: 0.7896 (p0) REVERT: K 214 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.7965 (ttpt) REVERT: L 210 ASN cc_start: 0.7780 (t0) cc_final: 0.7228 (p0) outliers start: 68 outliers final: 25 residues processed: 450 average time/residue: 1.1496 time to fit residues: 598.9163 Evaluate side-chains 418 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 390 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 214 LYS Chi-restraints excluded: chain L residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 197 GLN H 202 ASN H 204 ASN J 76 ASN J 176 GLN J 202 ASN ** J 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN K 197 GLN K 202 ASN ** K 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21016 Z= 0.297 Angle : 0.712 9.176 28668 Z= 0.376 Chirality : 0.048 0.170 3220 Planarity : 0.006 0.059 3660 Dihedral : 5.385 25.109 2864 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.65 % Allowed : 17.04 % Favored : 79.30 % 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: 0.10 (0.16), residues: 2640 helix: -0.01 (0.47), residues: 152 sheet: 0.80 (0.16), residues: 920 loop : -0.35 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 148 HIS 0.004 0.001 HIS C 173 PHE 0.022 0.002 PHE E 209 TYR 0.022 0.002 TYR G 140 ARG 0.014 0.001 ARG G 142 *********************** 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 503 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 419 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 210 ASN cc_start: 0.7929 (t0) cc_final: 0.7462 (p0) REVERT: F 3 GLN cc_start: 0.7859 (pm20) cc_final: 0.7647 (pm20) REVERT: F 26 ARG cc_start: 0.7695 (pmm-80) cc_final: 0.7457 (pmm-80) REVERT: F 148 ASP cc_start: 0.8246 (p0) cc_final: 0.8024 (p0) REVERT: G 173 TYR cc_start: 0.6953 (p90) cc_final: 0.6722 (p90) REVERT: G 210 ASN cc_start: 0.7900 (t0) cc_final: 0.7417 (p0) REVERT: H 3 GLN cc_start: 0.7890 (pm20) cc_final: 0.7666 (pm20) REVERT: H 26 ARG cc_start: 0.7688 (pmm-80) cc_final: 0.7457 (pmm-80) REVERT: H 149 TYR cc_start: 0.8042 (p90) cc_final: 0.7573 (p90) REVERT: H 183 LEU cc_start: 0.9209 (tt) cc_final: 0.8807 (mt) REVERT: I 210 ASN cc_start: 0.7870 (t0) cc_final: 0.7419 (p0) REVERT: J 3 GLN cc_start: 0.7896 (pm20) cc_final: 0.7672 (pm20) REVERT: J 26 ARG cc_start: 0.7706 (pmm-80) cc_final: 0.7449 (pmm-80) REVERT: J 149 TYR cc_start: 0.8054 (p90) cc_final: 0.7610 (p90) REVERT: J 183 LEU cc_start: 0.9237 (tt) cc_final: 0.8829 (mt) REVERT: J 214 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7758 (ttpt) REVERT: K 3 GLN cc_start: 0.7850 (pm20) cc_final: 0.7640 (pm20) REVERT: K 26 ARG cc_start: 0.7698 (pmm-80) cc_final: 0.7463 (pmm-80) REVERT: K 148 ASP cc_start: 0.8081 (p0) cc_final: 0.7870 (p0) REVERT: L 139 PHE cc_start: 0.8038 (p90) cc_final: 0.7834 (p90) REVERT: L 173 TYR cc_start: 0.6927 (p90) cc_final: 0.6689 (p90) REVERT: L 210 ASN cc_start: 0.7790 (t0) cc_final: 0.7314 (p0) REVERT: L 211 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7659 (ttm-80) outliers start: 84 outliers final: 32 residues processed: 465 average time/residue: 1.2110 time to fit residues: 646.9906 Evaluate side-chains 414 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 381 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 176 GLN Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER 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: 0.0980 chunk 3 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 229 optimal weight: 0.0470 chunk 64 optimal weight: 0.6980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 221AGLN F 76 ASN F 197 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN J 176 GLN J 197 GLN K 76 ASN ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21016 Z= 0.220 Angle : 0.698 9.095 28668 Z= 0.365 Chirality : 0.046 0.155 3220 Planarity : 0.006 0.060 3660 Dihedral : 5.137 24.851 2864 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.88 % Favored : 96.97 % Rotamer: Outliers : 2.52 % Allowed : 19.26 % Favored : 78.22 % 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: 0.18 (0.16), residues: 2640 helix: -0.02 (0.47), residues: 152 sheet: 0.78 (0.16), residues: 932 loop : -0.24 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 215 HIS 0.004 0.001 HIS C 173 PHE 0.018 0.002 PHE E 209 TYR 0.022 0.002 TYR G 140 ARG 0.011 0.001 ARG I 142 *********************** 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 463 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 405 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 210 ASN cc_start: 0.7942 (t0) cc_final: 0.7352 (p0) REVERT: F 3 GLN cc_start: 0.7843 (pm20) cc_final: 0.7613 (pm20) REVERT: F 26 ARG cc_start: 0.7750 (pmm-80) cc_final: 0.7536 (pmm-80) REVERT: F 148 ASP cc_start: 0.8169 (p0) cc_final: 0.7964 (p0) REVERT: G 210 ASN cc_start: 0.7959 (t0) cc_final: 0.7371 (p0) REVERT: H 3 GLN cc_start: 0.7873 (pm20) cc_final: 0.7630 (pm20) REVERT: H 26 ARG cc_start: 0.7682 (pmm-80) cc_final: 0.7474 (pmm-80) REVERT: H 149 TYR cc_start: 0.8026 (p90) cc_final: 0.7529 (p90) REVERT: H 183 LEU cc_start: 0.9187 (tt) cc_final: 0.8816 (mt) REVERT: I 210 ASN cc_start: 0.7888 (t0) cc_final: 0.7336 (p0) REVERT: J 3 GLN cc_start: 0.7923 (pm20) cc_final: 0.7671 (pm20) REVERT: J 26 ARG cc_start: 0.7698 (pmm-80) cc_final: 0.7466 (pmm-80) REVERT: J 183 LEU cc_start: 0.9170 (tt) cc_final: 0.8873 (mt) REVERT: J 214 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7704 (ttpt) REVERT: K 3 GLN cc_start: 0.7836 (pm20) cc_final: 0.7609 (pm20) REVERT: K 26 ARG cc_start: 0.7692 (pmm-80) cc_final: 0.7487 (pmm-80) REVERT: K 148 ASP cc_start: 0.8122 (p0) cc_final: 0.7919 (p0) REVERT: L 210 ASN cc_start: 0.7774 (t0) cc_final: 0.7216 (p0) outliers start: 58 outliers final: 27 residues processed: 431 average time/residue: 1.1852 time to fit residues: 587.5629 Evaluate side-chains 409 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 381 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 176 GLN Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 171 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 255 optimal weight: 9.9990 chunk 212 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 176 GLN ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN J 176 GLN K 76 ASN ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21016 Z= 0.240 Angle : 0.696 9.018 28668 Z= 0.364 Chirality : 0.046 0.163 3220 Planarity : 0.006 0.061 3660 Dihedral : 5.026 24.028 2864 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.99 % Favored : 96.86 % Rotamer: Outliers : 2.35 % Allowed : 19.70 % Favored : 77.96 % 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: 0.19 (0.16), residues: 2640 helix: -0.16 (0.46), residues: 152 sheet: 0.78 (0.16), residues: 940 loop : -0.21 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 215 HIS 0.003 0.001 HIS C 173 PHE 0.029 0.002 PHE J 27 TYR 0.023 0.002 TYR G 140 ARG 0.016 0.001 ARG L 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 446 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 392 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 185 ASP cc_start: 0.9271 (m-30) cc_final: 0.8488 (p0) REVERT: E 210 ASN cc_start: 0.7945 (t0) cc_final: 0.7342 (p0) REVERT: F 3 GLN cc_start: 0.7899 (pm20) cc_final: 0.7632 (pm20) REVERT: F 26 ARG cc_start: 0.7717 (pmm-80) cc_final: 0.7467 (pmm-80) REVERT: G 173 TYR cc_start: 0.6735 (p90) cc_final: 0.6510 (p90) REVERT: G 185 ASP cc_start: 0.9272 (m-30) cc_final: 0.8501 (p0) REVERT: G 210 ASN cc_start: 0.7946 (t0) cc_final: 0.7354 (p0) REVERT: H 3 GLN cc_start: 0.7931 (pm20) cc_final: 0.7647 (pm20) REVERT: H 26 ARG cc_start: 0.7693 (pmm-80) cc_final: 0.7450 (pmm-80) REVERT: H 149 TYR cc_start: 0.8113 (p90) cc_final: 0.7611 (p90) REVERT: H 183 LEU cc_start: 0.9142 (tt) cc_final: 0.8790 (mt) REVERT: I 185 ASP cc_start: 0.9276 (m-30) cc_final: 0.8495 (p0) REVERT: I 210 ASN cc_start: 0.7949 (t0) cc_final: 0.7410 (p0) REVERT: J 3 GLN cc_start: 0.7979 (pm20) cc_final: 0.7694 (pm20) REVERT: J 26 ARG cc_start: 0.7732 (pmm-80) cc_final: 0.7467 (pmm-80) REVERT: J 183 LEU cc_start: 0.9142 (tt) cc_final: 0.8872 (mt) REVERT: J 214 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7654 (ttpt) REVERT: K 3 GLN cc_start: 0.7889 (pm20) cc_final: 0.7624 (pm20) REVERT: K 26 ARG cc_start: 0.7704 (pmm-80) cc_final: 0.7465 (pmm-80) REVERT: L 185 ASP cc_start: 0.9310 (m-30) cc_final: 0.8531 (p0) REVERT: L 210 ASN cc_start: 0.7867 (t0) cc_final: 0.7178 (p0) outliers start: 54 outliers final: 30 residues processed: 417 average time/residue: 1.2126 time to fit residues: 581.7458 Evaluate side-chains 396 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 365 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 176 GLN Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 171 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 254 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN J 176 GLN K 76 ASN K 160 ASN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21016 Z= 0.329 Angle : 0.743 9.904 28668 Z= 0.384 Chirality : 0.049 0.285 3220 Planarity : 0.006 0.068 3660 Dihedral : 5.048 24.673 2864 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.48 % Favored : 96.36 % Rotamer: Outliers : 2.43 % Allowed : 20.52 % Favored : 77.04 % 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: 0.22 (0.16), residues: 2640 helix: -0.19 (0.45), residues: 152 sheet: 0.86 (0.16), residues: 940 loop : -0.23 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 141 HIS 0.003 0.001 HIS D 173 PHE 0.019 0.002 PHE E 139 TYR 0.025 0.002 TYR G 140 ARG 0.015 0.001 ARG L 18 *********************** 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 432 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 376 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 185 ASP cc_start: 0.9306 (m-30) cc_final: 0.8488 (p0) REVERT: E 210 ASN cc_start: 0.8044 (t0) cc_final: 0.7432 (p0) REVERT: F 3 GLN cc_start: 0.8011 (pm20) cc_final: 0.7718 (pm20) REVERT: F 152 GLU cc_start: 0.7699 (pm20) cc_final: 0.7386 (pm20) REVERT: G 173 TYR cc_start: 0.6782 (p90) cc_final: 0.6556 (p90) REVERT: G 185 ASP cc_start: 0.9308 (m-30) cc_final: 0.8503 (p0) REVERT: G 210 ASN cc_start: 0.8041 (t0) cc_final: 0.7424 (p0) REVERT: H 3 GLN cc_start: 0.8036 (pm20) cc_final: 0.7730 (pm20) REVERT: H 149 TYR cc_start: 0.8206 (p90) cc_final: 0.7735 (p90) REVERT: H 183 LEU cc_start: 0.9128 (tt) cc_final: 0.8764 (mt) REVERT: I 185 ASP cc_start: 0.9304 (m-30) cc_final: 0.8497 (p0) REVERT: I 210 ASN cc_start: 0.7983 (t0) cc_final: 0.7397 (p0) REVERT: J 3 GLN cc_start: 0.8072 (pm20) cc_final: 0.7761 (pm20) REVERT: J 26 ARG cc_start: 0.7773 (pmm-80) cc_final: 0.7565 (pmm-80) REVERT: J 152 GLU cc_start: 0.7767 (pm20) cc_final: 0.7562 (pm20) REVERT: J 183 LEU cc_start: 0.9169 (tt) cc_final: 0.8849 (mt) REVERT: J 214 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7650 (ttpt) REVERT: K 3 GLN cc_start: 0.8003 (pm20) cc_final: 0.7712 (pm20) REVERT: K 152 GLU cc_start: 0.7747 (pm20) cc_final: 0.7481 (pm20) REVERT: L 185 ASP cc_start: 0.9329 (m-30) cc_final: 0.8529 (p0) outliers start: 56 outliers final: 31 residues processed: 404 average time/residue: 1.3292 time to fit residues: 622.5151 Evaluate side-chains 396 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 364 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 176 GLN Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain J residue 214 LYS Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 171 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 5.9990 chunk 101 optimal weight: 0.0050 chunk 151 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 176 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN J 176 GLN K 76 ASN K 160 ASN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21016 Z= 0.227 Angle : 0.748 10.774 28668 Z= 0.383 Chirality : 0.048 0.224 3220 Planarity : 0.006 0.062 3660 Dihedral : 5.012 23.349 2864 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.41 % Favored : 96.44 % Rotamer: Outliers : 1.96 % Allowed : 22.17 % Favored : 75.87 % 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: 0.31 (0.17), residues: 2640 helix: -0.36 (0.44), residues: 152 sheet: 0.97 (0.16), residues: 940 loop : -0.17 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 159 HIS 0.003 0.001 HIS C 173 PHE 0.035 0.002 PHE F 27 TYR 0.025 0.002 TYR G 140 ARG 0.013 0.001 ARG E 18 *********************** 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 432 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 387 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 185 ASP cc_start: 0.9280 (m-30) cc_final: 0.8483 (p0) REVERT: E 210 ASN cc_start: 0.8029 (t0) cc_final: 0.7416 (p0) REVERT: G 139 PHE cc_start: 0.7923 (p90) cc_final: 0.7723 (p90) REVERT: G 173 TYR cc_start: 0.6754 (p90) cc_final: 0.6506 (p90) REVERT: G 185 ASP cc_start: 0.9276 (m-30) cc_final: 0.8500 (p0) REVERT: G 210 ASN cc_start: 0.8025 (t0) cc_final: 0.7406 (p0) REVERT: H 149 TYR cc_start: 0.8211 (p90) cc_final: 0.7789 (p90) REVERT: H 183 LEU cc_start: 0.9082 (tt) cc_final: 0.8736 (mt) REVERT: I 185 ASP cc_start: 0.9279 (m-30) cc_final: 0.8490 (p0) REVERT: I 210 ASN cc_start: 0.7968 (t0) cc_final: 0.7388 (p0) REVERT: J 3 GLN cc_start: 0.8039 (pm20) cc_final: 0.7825 (pm20) REVERT: J 149 TYR cc_start: 0.8168 (p90) cc_final: 0.7532 (p90) REVERT: J 183 LEU cc_start: 0.9154 (tt) cc_final: 0.8858 (mt) REVERT: L 185 ASP cc_start: 0.9298 (m-30) cc_final: 0.8525 (p0) REVERT: L 210 ASN cc_start: 0.8070 (t0) cc_final: 0.7616 (p0) outliers start: 45 outliers final: 25 residues processed: 411 average time/residue: 1.2210 time to fit residues: 575.6083 Evaluate side-chains 385 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 360 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 171 CYS Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 176 GLN Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 171 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 237 optimal weight: 9.9990 chunk 142 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 236 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN K 76 ASN K 160 ASN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21016 Z= 0.334 Angle : 0.796 10.838 28668 Z= 0.413 Chirality : 0.049 0.264 3220 Planarity : 0.006 0.063 3660 Dihedral : 5.247 28.979 2864 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.09 % Favored : 95.76 % Rotamer: Outliers : 2.04 % Allowed : 22.74 % Favored : 75.22 % 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: 0.26 (0.16), residues: 2640 helix: -0.44 (0.44), residues: 152 sheet: 1.02 (0.16), residues: 924 loop : -0.25 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 159 HIS 0.003 0.001 HIS C 173 PHE 0.020 0.002 PHE E 139 TYR 0.024 0.002 TYR F 181 ARG 0.014 0.001 ARG G 18 *********************** 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 422 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 375 time to evaluate : 2.756 Fit side-chains revert: symmetry clash REVERT: E 185 ASP cc_start: 0.9287 (m-30) cc_final: 0.8489 (p0) REVERT: E 210 ASN cc_start: 0.8018 (t0) cc_final: 0.7442 (p0) REVERT: F 152 GLU cc_start: 0.7696 (pm20) cc_final: 0.7455 (pm20) REVERT: G 185 ASP cc_start: 0.9288 (m-30) cc_final: 0.8501 (p0) REVERT: G 210 ASN cc_start: 0.8017 (t0) cc_final: 0.7431 (p0) REVERT: H 149 TYR cc_start: 0.8222 (p90) cc_final: 0.7796 (p90) REVERT: H 183 LEU cc_start: 0.9094 (tt) cc_final: 0.8654 (mt) REVERT: I 173 TYR cc_start: 0.6835 (p90) cc_final: 0.6487 (p90) REVERT: I 185 ASP cc_start: 0.9287 (m-30) cc_final: 0.8497 (p0) REVERT: I 210 ASN cc_start: 0.7985 (t0) cc_final: 0.7403 (p0) REVERT: J 183 LEU cc_start: 0.9160 (tt) cc_final: 0.8842 (mt) REVERT: L 185 ASP cc_start: 0.9310 (m-30) cc_final: 0.8526 (p0) REVERT: L 210 ASN cc_start: 0.8061 (t0) cc_final: 0.7658 (p0) outliers start: 47 outliers final: 23 residues processed: 403 average time/residue: 1.2236 time to fit residues: 566.7539 Evaluate side-chains 383 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 360 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 171 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 4.9990 chunk 153 optimal weight: 0.0040 chunk 118 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 263 optimal weight: 5.9990 chunk 242 optimal weight: 0.4980 chunk 209 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 176 GLN K 76 ASN K 160 ASN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21016 Z= 0.332 Angle : 0.818 10.517 28668 Z= 0.423 Chirality : 0.049 0.256 3220 Planarity : 0.006 0.063 3660 Dihedral : 5.317 27.538 2864 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.86 % Favored : 95.98 % Rotamer: Outliers : 1.65 % Allowed : 23.78 % Favored : 74.57 % 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: 0.21 (0.16), residues: 2640 helix: -0.43 (0.45), residues: 152 sheet: 0.89 (0.16), residues: 940 loop : -0.24 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 159 HIS 0.003 0.001 HIS C 166 PHE 0.042 0.002 PHE F 27 TYR 0.025 0.002 TYR E 49 ARG 0.014 0.001 ARG G 18 ********************** 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 403 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 365 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 185 ASP cc_start: 0.9280 (m-30) cc_final: 0.8491 (OUTLIER) REVERT: E 210 ASN cc_start: 0.8056 (t0) cc_final: 0.7466 (p0) REVERT: F 152 GLU cc_start: 0.7820 (pm20) cc_final: 0.7589 (pm20) REVERT: G 185 ASP cc_start: 0.9283 (m-30) cc_final: 0.8504 (p0) REVERT: G 210 ASN cc_start: 0.8056 (t0) cc_final: 0.7348 (p0) REVERT: I 173 TYR cc_start: 0.6629 (p90) cc_final: 0.6397 (p90) REVERT: I 185 ASP cc_start: 0.9277 (m-30) cc_final: 0.8501 (p0) REVERT: I 210 ASN cc_start: 0.7989 (t0) cc_final: 0.7436 (p0) REVERT: J 149 TYR cc_start: 0.8234 (p90) cc_final: 0.7677 (p90) REVERT: J 183 LEU cc_start: 0.9174 (tt) cc_final: 0.8794 (mt) REVERT: L 185 ASP cc_start: 0.9303 (m-30) cc_final: 0.8536 (p0) REVERT: L 210 ASN cc_start: 0.8105 (t0) cc_final: 0.7671 (p0) outliers start: 38 outliers final: 25 residues processed: 388 average time/residue: 1.1865 time to fit residues: 529.6930 Evaluate side-chains 382 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 358 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 171 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 171 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: