Starting phenix.real_space_refine on Sun Feb 18 20:48:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/02_2024/7jz2_22528_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/02_2024/7jz2_22528.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/7jz2_22528/02_2024/7jz2_22528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/02_2024/7jz2_22528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/02_2024/7jz2_22528_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/02_2024/7jz2_22528_neut_updated.pdb" } 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.172 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 30 7.16 5 P 9 5.49 5 S 186 5.16 5 Na 3 4.78 5 C 14520 2.51 5 N 3921 2.21 5 O 4197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 7": "OE1" <-> "OE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "D ARG 10": "NH1" <-> "NH2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E GLU 425": "OE1" <-> "OE2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E GLU 512": "OE1" <-> "OE2" Residue "E GLU 521": "OE1" <-> "OE2" Residue "E GLU 535": "OE1" <-> "OE2" Residue "E GLU 564": "OE1" <-> "OE2" Residue "E GLU 574": "OE1" <-> "OE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "H ARG 10": "NH1" <-> "NH2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "I GLU 7": "OE1" <-> "OE2" Residue "I GLU 129": "OE1" <-> "OE2" Residue "I GLU 425": "OE1" <-> "OE2" Residue "I GLU 434": "OE1" <-> "OE2" Residue "I GLU 438": "OE1" <-> "OE2" Residue "I GLU 512": "OE1" <-> "OE2" Residue "I GLU 521": "OE1" <-> "OE2" Residue "I GLU 535": "OE1" <-> "OE2" Residue "I GLU 564": "OE1" <-> "OE2" Residue "I GLU 574": "OE1" <-> "OE2" Residue "J GLU 141": "OE1" <-> "OE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 189": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "L ARG 10": "NH1" <-> "NH2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22866 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3707 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 463} Chain breaks: 1 Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 220} Chain: "C" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "D" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 898 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "E" Number of atoms: 3707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3707 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 463} Chain breaks: 1 Chain: "F" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 220} Chain: "G" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 898 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "I" Number of atoms: 3707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3707 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 463} Chain breaks: 1 Chain: "J" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 220} Chain: "K" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 898 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' NA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'HEM': 1, 'UQ2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' NA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'3PE': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'UQ2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' NA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'3PE': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "L" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'UQ2': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4298 SG CYS B 75 79.724 104.845 57.102 1.00 25.54 S ATOM 4931 SG CYS B 155 76.201 91.973 66.627 1.00 22.51 S ATOM 5407 SG CYS B 216 71.860 97.703 66.077 1.00 23.12 S ATOM 4892 SG CYS B 149 73.317 91.509 61.104 1.00 26.11 S ATOM 4914 SG CYS B 152 78.004 96.628 62.112 1.00 22.99 S ATOM 4956 SG CYS B 159 78.230 89.297 74.675 1.00 23.87 S ATOM 11744 SG CYS F 75 29.864 51.387 57.064 1.00 25.46 S ATOM 12377 SG CYS F 155 42.751 54.826 66.599 1.00 22.34 S ATOM 12853 SG CYS F 216 39.979 48.193 66.058 1.00 22.71 S ATOM 12338 SG CYS F 149 44.608 52.556 61.083 1.00 26.26 S ATOM 12360 SG CYS F 152 37.826 54.038 62.080 1.00 22.64 S ATOM 12402 SG CYS F 159 44.035 57.939 74.644 1.00 23.27 S ATOM 19190 SG CYS J 75 101.028 34.907 57.031 1.00 24.60 S ATOM 19823 SG CYS J 155 91.669 44.358 66.618 1.00 22.22 S ATOM 20299 SG CYS J 216 98.798 45.264 66.040 1.00 23.30 S ATOM 19784 SG CYS J 149 92.682 47.102 61.098 1.00 25.85 S ATOM 19806 SG CYS J 152 94.785 40.484 62.081 1.00 23.16 S ATOM 19848 SG CYS J 159 88.372 43.915 74.680 1.00 23.87 S Time building chain proxies: 13.01, per 1000 atoms: 0.57 Number of scatterers: 22866 At special positions: 0 Unit cell: (131.76, 135, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 30 26.01 S 186 16.00 P 9 15.00 Na 3 11.00 O 4197 8.00 N 3921 7.00 C 14520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.33 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 159 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 206 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 212 " pdb=" F3S F 303 " pdb="FE1 F3S F 303 " - pdb=" SG CYS F 159 " pdb="FE3 F3S F 303 " - pdb=" SG CYS F 206 " pdb="FE4 F3S F 303 " - pdb=" SG CYS F 212 " pdb=" F3S J 303 " pdb="FE1 F3S J 303 " - pdb=" SG CYS J 159 " pdb="FE3 F3S J 303 " - pdb=" SG CYS J 206 " pdb="FE4 F3S J 303 " - pdb=" SG CYS J 212 " pdb=" FES B 301 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 75 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 55 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 60 " pdb=" FES F 301 " pdb="FE1 FES F 301 " - pdb=" SG CYS F 75 " pdb="FE2 FES F 301 " - pdb=" SG CYS F 55 " pdb="FE2 FES F 301 " - pdb=" SG CYS F 60 " pdb=" FES J 301 " pdb="FE1 FES J 301 " - pdb=" SG CYS J 75 " pdb="FE2 FES J 301 " - pdb=" SG CYS J 55 " pdb="FE2 FES J 301 " - pdb=" SG CYS J 60 " pdb=" SF4 B 302 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 149 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 216 " pdb=" SF4 F 302 " pdb="FE4 SF4 F 302 " - pdb=" SG CYS F 152 " pdb="FE1 SF4 F 302 " - pdb=" SG CYS F 155 " pdb="FE3 SF4 F 302 " - pdb=" SG CYS F 149 " pdb="FE2 SF4 F 302 " - pdb=" SG CYS F 216 " pdb=" SF4 J 302 " pdb="FE4 SF4 J 302 " - pdb=" SG CYS J 152 " pdb="FE1 SF4 J 302 " - pdb=" SG CYS J 155 " pdb="FE3 SF4 J 302 " - pdb=" SG CYS J 149 " pdb="FE2 SF4 J 302 " - pdb=" SG CYS J 216 " Number of angles added : 75 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5274 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 21 sheets defined 46.7% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 Processing helix chain 'A' and resid 45 through 48 Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 82 through 102 Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 403 through 417 Processing helix chain 'A' and resid 419 through 426 Processing helix chain 'A' and resid 434 through 449 removed outlier: 4.261A pdb=" N GLU A 438 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 477 through 496 removed outlier: 4.197A pdb=" N ASN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'B' and resid 35 through 45 removed outlier: 3.779A pdb=" N LYS B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 79 through 82 No H-bonds generated for 'chain 'B' and resid 79 through 82' Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.787A pdb=" N ILE B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 143 removed outlier: 3.982A pdb=" N LEU B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 190 through 196 Processing helix chain 'B' and resid 212 through 215 No H-bonds generated for 'chain 'B' and resid 212 through 215' Processing helix chain 'B' and resid 222 through 237 Processing helix chain 'C' and resid 22 through 53 removed outlier: 3.954A pdb=" N GLY C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 65 Processing helix chain 'C' and resid 68 through 96 Processing helix chain 'C' and resid 103 through 128 removed outlier: 3.503A pdb=" N LEU C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 39 Processing helix chain 'D' and resid 45 through 52 Processing helix chain 'D' and resid 55 through 83 Processing helix chain 'D' and resid 87 through 112 Processing helix chain 'E' and resid 17 through 29 Processing helix chain 'E' and resid 45 through 48 Processing helix chain 'E' and resid 65 through 75 Processing helix chain 'E' and resid 82 through 102 Proline residue: E 93 - end of helix Processing helix chain 'E' and resid 141 through 156 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 221 through 229 Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 419 through 426 Processing helix chain 'E' and resid 434 through 449 removed outlier: 4.261A pdb=" N GLU E 438 " --> pdb=" O GLU E 434 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU E 444 " --> pdb=" O SER E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 470 Processing helix chain 'E' and resid 477 through 496 removed outlier: 4.196A pdb=" N ASN E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 532 Processing helix chain 'F' and resid 35 through 45 removed outlier: 3.779A pdb=" N LYS F 45 " --> pdb=" O GLN F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 79 through 82 No H-bonds generated for 'chain 'F' and resid 79 through 82' Processing helix chain 'F' and resid 108 through 117 removed outlier: 3.786A pdb=" N ILE F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 143 removed outlier: 3.982A pdb=" N LEU F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 158 No H-bonds generated for 'chain 'F' and resid 156 through 158' Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 172 through 183 Processing helix chain 'F' and resid 190 through 196 Processing helix chain 'F' and resid 212 through 215 No H-bonds generated for 'chain 'F' and resid 212 through 215' Processing helix chain 'F' and resid 222 through 237 Processing helix chain 'G' and resid 22 through 53 removed outlier: 3.954A pdb=" N GLY G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 65 Processing helix chain 'G' and resid 68 through 96 Processing helix chain 'G' and resid 103 through 128 removed outlier: 3.503A pdb=" N LEU G 127 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 39 Processing helix chain 'H' and resid 45 through 52 Processing helix chain 'H' and resid 55 through 83 Processing helix chain 'H' and resid 87 through 112 Processing helix chain 'I' and resid 17 through 29 Processing helix chain 'I' and resid 45 through 48 Processing helix chain 'I' and resid 65 through 75 Processing helix chain 'I' and resid 82 through 102 Proline residue: I 93 - end of helix Processing helix chain 'I' and resid 141 through 156 Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 221 through 229 Processing helix chain 'I' and resid 403 through 417 Processing helix chain 'I' and resid 419 through 426 Processing helix chain 'I' and resid 434 through 449 removed outlier: 4.261A pdb=" N GLU I 438 " --> pdb=" O GLU I 434 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG I 443 " --> pdb=" O ALA I 439 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU I 444 " --> pdb=" O SER I 440 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 470 Processing helix chain 'I' and resid 477 through 496 removed outlier: 4.196A pdb=" N ASN I 496 " --> pdb=" O GLU I 492 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 532 Processing helix chain 'J' and resid 35 through 45 removed outlier: 3.780A pdb=" N LYS J 45 " --> pdb=" O GLN J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 76 No H-bonds generated for 'chain 'J' and resid 74 through 76' Processing helix chain 'J' and resid 79 through 82 No H-bonds generated for 'chain 'J' and resid 79 through 82' Processing helix chain 'J' and resid 108 through 117 removed outlier: 3.787A pdb=" N ILE J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 143 removed outlier: 3.982A pdb=" N LEU J 143 " --> pdb=" O GLN J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 158 No H-bonds generated for 'chain 'J' and resid 156 through 158' Processing helix chain 'J' and resid 160 through 164 Processing helix chain 'J' and resid 172 through 183 Processing helix chain 'J' and resid 190 through 196 Processing helix chain 'J' and resid 212 through 215 No H-bonds generated for 'chain 'J' and resid 212 through 215' Processing helix chain 'J' and resid 222 through 237 Processing helix chain 'K' and resid 22 through 53 removed outlier: 3.955A pdb=" N GLY K 42 " --> pdb=" O PHE K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 65 Processing helix chain 'K' and resid 68 through 96 Processing helix chain 'K' and resid 103 through 128 removed outlier: 3.504A pdb=" N LEU K 127 " --> pdb=" O LEU K 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 39 Processing helix chain 'L' and resid 45 through 52 Processing helix chain 'L' and resid 55 through 83 Processing helix chain 'L' and resid 87 through 112 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 7 removed outlier: 6.203A pdb=" N LEU A 183 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA A 166 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 383 through 385 removed outlier: 6.184A pdb=" N THR A 198 " --> pdb=" O PHE A 384 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL A 11 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR A 159 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 369 through 371 Processing sheet with id= D, first strand: chain 'A' and resid 556 through 560 Processing sheet with id= E, first strand: chain 'A' and resid 239 through 242 removed outlier: 5.742A pdb=" N HIS A 242 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N CYS A 353 " --> pdb=" O HIS A 242 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 19 through 25 removed outlier: 6.144A pdb=" N ILE B 89 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N TYR B 8 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE B 91 " --> pdb=" O TYR B 8 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 64 through 67 Processing sheet with id= H, first strand: chain 'E' and resid 4 through 7 removed outlier: 6.203A pdb=" N LEU E 183 " --> pdb=" O ALA E 166 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA E 166 " --> pdb=" O LEU E 183 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 383 through 385 removed outlier: 6.183A pdb=" N THR E 198 " --> pdb=" O PHE E 384 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL E 11 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR E 159 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 369 through 371 Processing sheet with id= K, first strand: chain 'E' and resid 556 through 560 Processing sheet with id= L, first strand: chain 'E' and resid 239 through 242 removed outlier: 5.741A pdb=" N HIS E 242 " --> pdb=" O CYS E 353 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N CYS E 353 " --> pdb=" O HIS E 242 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 19 through 25 removed outlier: 6.145A pdb=" N ILE F 89 " --> pdb=" O SER F 6 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N TYR F 8 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE F 91 " --> pdb=" O TYR F 8 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 64 through 67 Processing sheet with id= O, first strand: chain 'I' and resid 4 through 7 removed outlier: 6.205A pdb=" N LEU I 183 " --> pdb=" O ALA I 166 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA I 166 " --> pdb=" O LEU I 183 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 383 through 385 removed outlier: 6.183A pdb=" N THR I 198 " --> pdb=" O PHE I 384 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL I 11 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR I 159 " --> pdb=" O LEU I 35 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 369 through 371 Processing sheet with id= R, first strand: chain 'I' and resid 556 through 560 Processing sheet with id= S, first strand: chain 'I' and resid 239 through 242 removed outlier: 5.741A pdb=" N HIS I 242 " --> pdb=" O CYS I 353 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N CYS I 353 " --> pdb=" O HIS I 242 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 19 through 25 removed outlier: 6.144A pdb=" N ILE J 89 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N TYR J 8 " --> pdb=" O ILE J 89 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE J 91 " --> pdb=" O TYR J 8 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 64 through 67 1041 hydrogen bonds defined for protein. 3060 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.51 Time building geometry restraints manager: 10.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.74: 23046 1.74 - 2.29: 321 2.29 - 2.84: 9 2.84 - 3.40: 0 3.40 - 3.95: 9 Bond restraints: 23385 Sorted by residual: bond pdb=" S4 F3S J 303 " pdb="FE1 F3S J 303 " ideal model delta sigma weight residual 2.233 3.935 -1.702 2.00e-02 2.50e+03 7.24e+03 bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.935 -1.702 2.00e-02 2.50e+03 7.24e+03 bond pdb=" S4 F3S F 303 " pdb="FE1 F3S F 303 " ideal model delta sigma weight residual 2.233 3.934 -1.701 2.00e-02 2.50e+03 7.23e+03 bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 3.951 -1.651 2.00e-02 2.50e+03 6.81e+03 bond pdb=" S2 F3S F 303 " pdb="FE3 F3S F 303 " ideal model delta sigma weight residual 2.300 3.950 -1.650 2.00e-02 2.50e+03 6.81e+03 ... (remaining 23380 not shown) Histogram of bond angle deviations from ideal: 41.36 - 68.80: 21 68.80 - 96.24: 75 96.24 - 123.68: 30949 123.68 - 151.12: 719 151.12 - 178.57: 6 Bond angle restraints: 31770 Sorted by residual: angle pdb=" S1 F3S J 303 " pdb="FE4 F3S J 303 " pdb=" S3 F3S J 303 " ideal model delta sigma weight residual 114.75 64.82 49.93 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S1 F3S F 303 " pdb="FE4 F3S F 303 " pdb=" S3 F3S F 303 " ideal model delta sigma weight residual 114.75 64.82 49.93 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 64.83 49.92 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S3 F3S J 303 " pdb="FE1 F3S J 303 " pdb=" S4 F3S J 303 " ideal model delta sigma weight residual 112.59 64.30 48.29 3.00e+00 1.11e-01 2.59e+02 angle pdb=" S3 F3S F 303 " pdb="FE1 F3S F 303 " pdb=" S4 F3S F 303 " ideal model delta sigma weight residual 112.59 64.31 48.28 3.00e+00 1.11e-01 2.59e+02 ... (remaining 31765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 12488 16.63 - 33.25: 972 33.25 - 49.88: 292 49.88 - 66.50: 90 66.50 - 83.13: 36 Dihedral angle restraints: 13878 sinusoidal: 5664 harmonic: 8214 Sorted by residual: dihedral pdb=" C2D HEM K 201 " pdb=" C3D HEM K 201 " pdb=" CAD HEM K 201 " pdb=" CBD HEM K 201 " ideal model delta sinusoidal sigma weight residual 0.00 67.81 -67.81 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" C2D HEM D 201 " pdb=" C3D HEM D 201 " pdb=" CAD HEM D 201 " pdb=" CBD HEM D 201 " ideal model delta sinusoidal sigma weight residual 0.00 67.71 -67.71 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" C2D HEM G 201 " pdb=" C3D HEM G 201 " pdb=" CAD HEM G 201 " pdb=" CBD HEM G 201 " ideal model delta sinusoidal sigma weight residual 0.00 67.70 -67.70 2 2.00e+01 2.50e-03 1.03e+01 ... (remaining 13875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.605: 3504 3.605 - 7.210: 0 7.210 - 10.816: 0 10.816 - 14.421: 0 14.421 - 18.026: 3 Chirality restraints: 3507 Sorted by residual: chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.26 18.03 2.00e-01 2.50e+01 8.12e+03 chirality pdb=" S2 F3S F 303 " pdb="FE1 F3S F 303 " pdb="FE3 F3S F 303 " pdb="FE4 F3S F 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.25 18.02 2.00e-01 2.50e+01 8.12e+03 chirality pdb=" S2 F3S J 303 " pdb="FE1 F3S J 303 " pdb="FE3 F3S J 303 " pdb="FE4 F3S J 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.25 18.02 2.00e-01 2.50e+01 8.12e+03 ... (remaining 3504 not shown) Planarity restraints: 4029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 113 " 0.007 2.00e-02 2.50e+03 5.32e-03 7.07e-01 pdb=" CG TRP L 113 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP L 113 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP L 113 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 113 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 113 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 113 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 113 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 113 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 113 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 109 " 0.004 2.00e-02 2.50e+03 8.38e-03 7.02e-01 pdb=" C PHE D 109 " -0.014 2.00e-02 2.50e+03 pdb=" O PHE D 109 " 0.005 2.00e-02 2.50e+03 pdb=" N VAL D 110 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 109 " -0.004 2.00e-02 2.50e+03 8.36e-03 6.98e-01 pdb=" C PHE L 109 " 0.014 2.00e-02 2.50e+03 pdb=" O PHE L 109 " -0.005 2.00e-02 2.50e+03 pdb=" N VAL L 110 " -0.005 2.00e-02 2.50e+03 ... (remaining 4026 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 419 2.64 - 3.20: 22796 3.20 - 3.77: 37050 3.77 - 4.33: 52424 4.33 - 4.90: 85124 Nonbonded interactions: 197813 Sorted by model distance: nonbonded pdb=" OD1 ASP J 46 " pdb=" OG SER J 48 " model vdw 2.070 2.440 nonbonded pdb=" OD1 ASP F 46 " pdb=" OG SER F 48 " model vdw 2.070 2.440 nonbonded pdb=" OD1 ASP B 46 " pdb=" OG SER B 48 " model vdw 2.070 2.440 nonbonded pdb=" NH1 ARG J 205 " pdb=" OD1 ASP L 82 " model vdw 2.114 2.520 nonbonded pdb=" OE1 GLU E 94 " pdb=" NH1 ARG E 413 " model vdw 2.115 2.520 ... (remaining 197808 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = (chain 'C' and resid 5 through 129) selection = (chain 'G' and resid 5 through 129) selection = (chain 'K' and resid 5 through 129) } ncs_group { reference = (chain 'D' and resid 3 through 115) selection = (chain 'H' and resid 3 through 115) selection = (chain 'L' and resid 3 through 115) } 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: 0.010 Normalize map: mean=0, sd=1: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.940 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 67.710 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 : 0.033 1.702 23385 Z= 1.884 Angle : 1.281 49.935 31770 Z= 0.531 Chirality : 0.528 18.026 3507 Planarity : 0.002 0.019 4029 Dihedral : 14.261 83.128 8604 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 35.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.38 % Allowed : 2.39 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.14), residues: 2841 helix: 0.25 (0.13), residues: 1404 sheet: -3.15 (0.28), residues: 165 loop : -3.27 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 113 HIS 0.003 0.000 HIS E 147 PHE 0.010 0.001 PHE E 411 TYR 0.011 0.001 TYR B 8 ARG 0.002 0.000 ARG E 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 598 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.6830 (mtp) cc_final: 0.6593 (mtp) REVERT: A 227 ILE cc_start: 0.7298 (mt) cc_final: 0.6841 (mt) REVERT: A 236 MET cc_start: 0.7449 (mmp) cc_final: 0.6907 (mmp) REVERT: A 443 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7646 (ttp80) REVERT: B 1 MET cc_start: 0.5214 (ptt) cc_final: 0.4115 (mpp) REVERT: B 41 GLN cc_start: 0.6981 (tt0) cc_final: 0.6644 (mt0) REVERT: D 77 TRP cc_start: 0.7643 (t60) cc_final: 0.7348 (t-100) REVERT: E 209 TYR cc_start: 0.7159 (m-80) cc_final: 0.6879 (m-80) REVERT: E 227 ILE cc_start: 0.7479 (mt) cc_final: 0.7077 (mt) REVERT: E 568 ARG cc_start: 0.7382 (mtt180) cc_final: 0.7083 (mtt180) REVERT: F 9 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.7309 (mmm160) REVERT: F 232 MET cc_start: 0.7783 (mtp) cc_final: 0.7388 (mtp) REVERT: G 93 MET cc_start: 0.6906 (mtp) cc_final: 0.6495 (mtp) REVERT: H 56 PHE cc_start: 0.7072 (t80) cc_final: 0.5613 (m-80) REVERT: I 227 ILE cc_start: 0.7064 (mt) cc_final: 0.6598 (mt) REVERT: I 420 GLN cc_start: 0.6644 (tp40) cc_final: 0.6319 (tp40) REVERT: I 446 ARG cc_start: 0.7473 (tmm160) cc_final: 0.7234 (tmm160) REVERT: I 471 PHE cc_start: 0.6564 (m-80) cc_final: 0.6330 (m-80) REVERT: I 568 ARG cc_start: 0.7437 (mtt180) cc_final: 0.7118 (mtt-85) REVERT: J 67 MET cc_start: 0.6782 (mtm) cc_final: 0.6422 (mtm) REVERT: J 235 GLN cc_start: 0.7010 (mm-40) cc_final: 0.6774 (mm110) REVERT: L 45 TYR cc_start: 0.7261 (t80) cc_final: 0.7059 (t80) REVERT: L 56 PHE cc_start: 0.7054 (t80) cc_final: 0.5779 (m-80) outliers start: 33 outliers final: 7 residues processed: 626 average time/residue: 1.2766 time to fit residues: 915.6714 Evaluate side-chains 492 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 485 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 352 THR Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS A 173 GLN A 214 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 452 ASN A 531 ASN B 71 ASN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS B 237 ASN C 91 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS E 173 GLN E 214 ASN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN E 452 ASN ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 518 ASN E 531 ASN F 71 ASN F 207 HIS F 211 ASN F 228 HIS F 235 GLN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 HIS H 14 HIS ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN I 143 HIS I 214 ASN I 395 HIS I 450 ASN I 452 ASN I 518 ASN I 531 ASN J 71 ASN J 123 ASN J 207 HIS J 228 HIS J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 HIS L 94 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.201 23385 Z= 0.391 Angle : 1.158 53.845 31770 Z= 0.454 Chirality : 0.080 2.307 3507 Planarity : 0.005 0.038 4029 Dihedral : 9.181 76.110 3437 Min Nonbonded Distance : 1.516 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.69 % Allowed : 13.19 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.15), residues: 2841 helix: 0.91 (0.13), residues: 1446 sheet: -2.73 (0.29), residues: 189 loop : -2.64 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 113 HIS 0.007 0.002 HIS H 71 PHE 0.026 0.002 PHE D 60 TYR 0.026 0.002 TYR B 8 ARG 0.004 0.001 ARG F 2 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 519 time to evaluate : 2.605 Fit side-chains REVERT: A 46 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7874 (m) REVERT: A 225 MET cc_start: 0.6961 (mtp) cc_final: 0.6756 (mtp) REVERT: A 443 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7640 (ttp80) REVERT: A 490 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7283 (mp) REVERT: B 1 MET cc_start: 0.5501 (ptt) cc_final: 0.5187 (ptt) REVERT: B 2 ARG cc_start: 0.6641 (ptm160) cc_final: 0.6266 (ptm160) REVERT: C 101 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6916 (mt-10) REVERT: C 123 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7536 (tp) REVERT: D 10 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6809 (mtp180) REVERT: D 77 TRP cc_start: 0.7758 (t60) cc_final: 0.7427 (t-100) REVERT: E 210 GLN cc_start: 0.6782 (tt0) cc_final: 0.6382 (mt0) REVERT: E 227 ILE cc_start: 0.7480 (mt) cc_final: 0.7198 (mt) REVERT: E 352 THR cc_start: 0.7993 (t) cc_final: 0.7679 (m) REVERT: E 449 ASN cc_start: 0.6992 (m-40) cc_final: 0.6731 (m-40) REVERT: E 568 ARG cc_start: 0.7402 (mtt180) cc_final: 0.7088 (mtt180) REVERT: F 9 ARG cc_start: 0.7604 (mmm-85) cc_final: 0.7329 (mmm160) REVERT: F 102 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.7070 (t70) REVERT: F 167 ASP cc_start: 0.6382 (OUTLIER) cc_final: 0.6045 (p0) REVERT: F 168 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7686 (mttt) REVERT: G 93 MET cc_start: 0.6884 (mtp) cc_final: 0.6659 (mtp) REVERT: G 123 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7394 (mp) REVERT: H 10 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6842 (mtp180) REVERT: H 56 PHE cc_start: 0.7250 (t80) cc_final: 0.5732 (m-80) REVERT: I 3 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7679 (mp) REVERT: I 227 ILE cc_start: 0.7329 (mt) cc_final: 0.7071 (mt) REVERT: I 520 MET cc_start: 0.8408 (tpt) cc_final: 0.8011 (tpt) REVERT: J 67 MET cc_start: 0.6881 (mtm) cc_final: 0.6617 (mtm) REVERT: J 102 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.7012 (t70) REVERT: J 235 GLN cc_start: 0.6971 (mm-40) cc_final: 0.6696 (mm110) REVERT: K 101 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6753 (mt-10) REVERT: L 56 PHE cc_start: 0.7313 (t80) cc_final: 0.5917 (m-80) REVERT: L 77 TRP cc_start: 0.7628 (t60) cc_final: 0.7317 (t-100) REVERT: L 90 ARG cc_start: 0.7107 (ttp-110) cc_final: 0.6864 (ttp-110) outliers start: 112 outliers final: 44 residues processed: 564 average time/residue: 1.2640 time to fit residues: 820.5070 Evaluate side-chains 542 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 485 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 10 ARG Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 503 SER Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 256 optimal weight: 0.8980 chunk 277 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 254 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 218 ASN A 367 GLN B 71 ASN B 123 ASN B 133 HIS B 237 ASN C 91 HIS D 94 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN E 496 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN I 173 GLN I 367 GLN I 452 ASN I 470 ASN J 71 ASN J 109 GLN J 123 ASN J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 HIS L 14 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 23385 Z= 0.194 Angle : 1.086 83.718 31770 Z= 0.411 Chirality : 0.058 1.493 3507 Planarity : 0.004 0.042 4029 Dihedral : 7.977 77.204 3433 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.52 % Allowed : 17.09 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2841 helix: 1.44 (0.13), residues: 1452 sheet: -2.21 (0.32), residues: 195 loop : -2.13 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 113 HIS 0.005 0.001 HIS A 68 PHE 0.017 0.001 PHE L 60 TYR 0.030 0.001 TYR H 45 ARG 0.007 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 515 time to evaluate : 2.882 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.5139 (ptt) cc_final: 0.4781 (ptt) REVERT: B 34 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6669 (mmt) REVERT: B 41 GLN cc_start: 0.7181 (tt0) cc_final: 0.6671 (mt0) REVERT: C 123 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7435 (mp) REVERT: E 210 GLN cc_start: 0.6713 (tt0) cc_final: 0.6337 (mt0) REVERT: E 227 ILE cc_start: 0.7399 (mt) cc_final: 0.7153 (mt) REVERT: E 449 ASN cc_start: 0.6916 (m-40) cc_final: 0.6608 (m-40) REVERT: E 568 ARG cc_start: 0.7331 (mtt180) cc_final: 0.7002 (mtt180) REVERT: F 2 ARG cc_start: 0.6556 (ttt90) cc_final: 0.6299 (ttt90) REVERT: F 9 ARG cc_start: 0.7548 (mmm-85) cc_final: 0.7335 (mmm160) REVERT: F 167 ASP cc_start: 0.6283 (OUTLIER) cc_final: 0.5990 (p0) REVERT: F 168 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7627 (mttt) REVERT: H 56 PHE cc_start: 0.7124 (t80) cc_final: 0.5618 (m-80) REVERT: I 210 GLN cc_start: 0.6493 (tt0) cc_final: 0.6214 (mt0) REVERT: I 227 ILE cc_start: 0.7355 (mt) cc_final: 0.7117 (mt) REVERT: I 520 MET cc_start: 0.8421 (tpt) cc_final: 0.8015 (tpt) REVERT: J 9 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7400 (mmm-85) REVERT: J 67 MET cc_start: 0.6848 (mtm) cc_final: 0.6546 (mtm) REVERT: J 214 SER cc_start: 0.6813 (p) cc_final: 0.6552 (m) REVERT: L 56 PHE cc_start: 0.7219 (t80) cc_final: 0.5852 (m-80) REVERT: L 90 ARG cc_start: 0.7025 (ttp-110) cc_final: 0.6775 (ttp-110) outliers start: 84 outliers final: 25 residues processed: 549 average time/residue: 1.3392 time to fit residues: 843.2343 Evaluate side-chains 515 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 486 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 503 SER Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 123 ASN Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 28 optimal weight: 0.0000 chunk 122 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 218 ASN A 367 GLN A 518 ASN B 71 ASN B 123 ASN B 237 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 HIS ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN J 71 ASN J 123 ASN J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 23385 Z= 0.240 Angle : 1.105 84.127 31770 Z= 0.419 Chirality : 0.059 1.453 3507 Planarity : 0.004 0.044 4029 Dihedral : 7.564 78.854 3431 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.82 % Allowed : 18.34 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 2841 helix: 1.52 (0.13), residues: 1449 sheet: -1.90 (0.34), residues: 195 loop : -2.05 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 113 HIS 0.006 0.001 HIS A 143 PHE 0.017 0.002 PHE E 545 TYR 0.037 0.002 TYR L 45 ARG 0.006 0.000 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 496 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.6142 (mt0) REVERT: A 367 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6352 (mt0) REVERT: A 490 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7160 (mp) REVERT: B 1 MET cc_start: 0.5134 (ptt) cc_final: 0.4760 (ptt) REVERT: B 34 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6752 (mmt) REVERT: B 41 GLN cc_start: 0.7136 (tt0) cc_final: 0.6669 (mt0) REVERT: C 101 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6769 (mt-10) REVERT: C 123 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7697 (mm) REVERT: E 210 GLN cc_start: 0.6749 (tt0) cc_final: 0.6371 (mt0) REVERT: E 227 ILE cc_start: 0.7387 (mt) cc_final: 0.7167 (mt) REVERT: E 449 ASN cc_start: 0.6948 (m-40) cc_final: 0.6644 (m-40) REVERT: E 568 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6969 (mtt180) REVERT: F 168 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7649 (mttt) REVERT: H 56 PHE cc_start: 0.7124 (t80) cc_final: 0.5630 (m-80) REVERT: I 210 GLN cc_start: 0.6511 (tt0) cc_final: 0.6233 (mt0) REVERT: I 227 ILE cc_start: 0.7378 (mt) cc_final: 0.7167 (mt) REVERT: I 520 MET cc_start: 0.8399 (tpt) cc_final: 0.8101 (tpt) REVERT: J 2 ARG cc_start: 0.6382 (OUTLIER) cc_final: 0.6146 (ttm-80) REVERT: J 9 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7404 (mmm-85) REVERT: J 67 MET cc_start: 0.6774 (mtm) cc_final: 0.6548 (mtm) REVERT: J 235 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.6296 (mm-40) REVERT: K 101 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6588 (mt-10) REVERT: L 56 PHE cc_start: 0.7275 (t80) cc_final: 0.5895 (m-80) REVERT: L 90 ARG cc_start: 0.7004 (ttp-110) cc_final: 0.6782 (ttp-110) outliers start: 115 outliers final: 47 residues processed: 547 average time/residue: 1.2631 time to fit residues: 793.3773 Evaluate side-chains 538 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 481 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 503 SER Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 123 ASN B 237 ASN D 14 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 HIS E 452 ASN F 237 ASN G 12 ASN ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN I 367 GLN I 452 ASN J 71 ASN J 123 ASN J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 23385 Z= 0.369 Angle : 1.171 84.229 31770 Z= 0.459 Chirality : 0.061 1.426 3507 Planarity : 0.005 0.044 4029 Dihedral : 8.037 78.877 3429 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.69 % Allowed : 19.77 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 2841 helix: 1.19 (0.13), residues: 1449 sheet: -1.80 (0.34), residues: 189 loop : -2.19 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 113 HIS 0.008 0.002 HIS A 143 PHE 0.029 0.002 PHE L 52 TYR 0.034 0.002 TYR L 45 ARG 0.006 0.001 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 479 time to evaluate : 2.547 Fit side-chains revert: symmetry clash REVERT: A 210 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.6124 (mt0) REVERT: A 405 LEU cc_start: 0.7149 (mm) cc_final: 0.6943 (mt) REVERT: A 490 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7341 (mp) REVERT: A 568 ARG cc_start: 0.7405 (mtt180) cc_final: 0.6771 (mtt180) REVERT: B 2 ARG cc_start: 0.6197 (ptm160) cc_final: 0.5968 (ttm-80) REVERT: B 41 GLN cc_start: 0.7194 (tt0) cc_final: 0.6698 (mt0) REVERT: C 101 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6850 (mt-10) REVERT: E 210 GLN cc_start: 0.6858 (tt0) cc_final: 0.6465 (mt0) REVERT: E 568 ARG cc_start: 0.7400 (mtt180) cc_final: 0.7037 (mtt180) REVERT: E 574 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6870 (pp20) REVERT: F 109 GLN cc_start: 0.7631 (mt0) cc_final: 0.7361 (mt0) REVERT: F 168 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7789 (mttt) REVERT: G 123 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7391 (mp) REVERT: H 56 PHE cc_start: 0.7205 (t80) cc_final: 0.5730 (m-80) REVERT: I 156 ASN cc_start: 0.6778 (m110) cc_final: 0.6509 (m110) REVERT: I 227 ILE cc_start: 0.7328 (mt) cc_final: 0.7105 (mt) REVERT: I 490 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7072 (mp) REVERT: J 210 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8173 (mtm) REVERT: J 235 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.6377 (mm-40) REVERT: K 101 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6779 (mt-10) REVERT: L 56 PHE cc_start: 0.7196 (t80) cc_final: 0.5825 (m-80) REVERT: L 90 ARG cc_start: 0.7034 (ttp-110) cc_final: 0.6803 (ttp-170) outliers start: 112 outliers final: 64 residues processed: 537 average time/residue: 1.2108 time to fit residues: 750.4857 Evaluate side-chains 535 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 461 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 503 SER Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 272 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 126 optimal weight: 30.0000 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 218 ASN B 71 ASN B 123 ASN B 237 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 237 ASN H 94 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN J 71 ASN J 123 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 23385 Z= 0.193 Angle : 1.092 84.217 31770 Z= 0.415 Chirality : 0.058 1.451 3507 Planarity : 0.004 0.047 4029 Dihedral : 7.290 79.548 3427 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.27 % Allowed : 22.07 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2841 helix: 1.76 (0.13), residues: 1431 sheet: -1.60 (0.35), residues: 195 loop : -1.87 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 113 HIS 0.004 0.001 HIS I 68 PHE 0.020 0.001 PHE E 545 TYR 0.033 0.001 TYR L 45 ARG 0.008 0.000 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 494 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7747 (mt0) REVERT: A 210 GLN cc_start: 0.6332 (OUTLIER) cc_final: 0.6076 (mt0) REVERT: A 568 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6729 (mtt180) REVERT: B 41 GLN cc_start: 0.7080 (tt0) cc_final: 0.6638 (mt0) REVERT: C 93 MET cc_start: 0.6589 (mtp) cc_final: 0.6376 (mtt) REVERT: C 101 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6599 (mt-10) REVERT: E 210 GLN cc_start: 0.6760 (tt0) cc_final: 0.6459 (mt0) REVERT: E 405 LEU cc_start: 0.6891 (mm) cc_final: 0.6654 (mt) REVERT: E 568 ARG cc_start: 0.7368 (mtt180) cc_final: 0.7008 (mtt180) REVERT: E 574 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6818 (pp20) REVERT: F 168 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7635 (mttt) REVERT: F 214 SER cc_start: 0.6776 (p) cc_final: 0.6517 (m) REVERT: G 123 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7395 (mp) REVERT: H 56 PHE cc_start: 0.7110 (t80) cc_final: 0.5648 (m-80) REVERT: I 490 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.6973 (mp) REVERT: I 574 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6767 (pp20) REVERT: J 210 MET cc_start: 0.8389 (mtp) cc_final: 0.8186 (mtm) REVERT: J 235 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.6269 (mm-40) REVERT: K 101 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6590 (mt-10) REVERT: L 56 PHE cc_start: 0.7210 (t80) cc_final: 0.5862 (m-80) REVERT: L 90 ARG cc_start: 0.7078 (ttp-110) cc_final: 0.6829 (ttp-170) outliers start: 78 outliers final: 32 residues processed: 535 average time/residue: 1.2948 time to fit residues: 794.7138 Evaluate side-chains 521 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 479 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 229 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 123 ASN B 237 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN I 367 GLN I 452 ASN ** J 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 23385 Z= 0.334 Angle : 1.155 84.612 31770 Z= 0.452 Chirality : 0.060 1.413 3507 Planarity : 0.005 0.047 4029 Dihedral : 7.716 80.017 3426 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.61 % Allowed : 22.49 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 2841 helix: 1.34 (0.13), residues: 1449 sheet: -1.55 (0.35), residues: 189 loop : -2.02 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 113 HIS 0.007 0.002 HIS D 71 PHE 0.027 0.002 PHE D 60 TYR 0.036 0.002 TYR L 45 ARG 0.009 0.001 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 475 time to evaluate : 2.447 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: A 210 GLN cc_start: 0.6362 (OUTLIER) cc_final: 0.6130 (mt0) REVERT: A 405 LEU cc_start: 0.7132 (mm) cc_final: 0.6897 (mt) REVERT: A 490 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7339 (mp) REVERT: B 41 GLN cc_start: 0.7148 (tt0) cc_final: 0.6702 (mt0) REVERT: C 101 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6708 (mt-10) REVERT: E 210 GLN cc_start: 0.6785 (tt0) cc_final: 0.6438 (mt0) REVERT: E 398 ASN cc_start: 0.7207 (OUTLIER) cc_final: 0.6968 (t0) REVERT: E 450 ASN cc_start: 0.6686 (OUTLIER) cc_final: 0.6458 (m-40) REVERT: E 568 ARG cc_start: 0.7412 (mtt180) cc_final: 0.7040 (mtt180) REVERT: E 574 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6859 (pp20) REVERT: F 168 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7788 (mttt) REVERT: G 46 TRP cc_start: 0.7032 (t60) cc_final: 0.6800 (t60) REVERT: G 53 SER cc_start: 0.7571 (t) cc_final: 0.7306 (p) REVERT: G 65 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7599 (tpt) REVERT: G 123 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7325 (mp) REVERT: H 56 PHE cc_start: 0.7106 (t80) cc_final: 0.5681 (m-80) REVERT: I 574 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6778 (pp20) REVERT: J 235 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.6315 (mm-40) REVERT: K 101 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6778 (mt-10) REVERT: L 56 PHE cc_start: 0.7215 (t80) cc_final: 0.5895 (m-80) REVERT: L 90 ARG cc_start: 0.7071 (ttp-110) cc_final: 0.6855 (ttp-170) outliers start: 110 outliers final: 63 residues processed: 530 average time/residue: 1.2246 time to fit residues: 749.0560 Evaluate side-chains 546 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 470 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 356 MET Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 503 SER Chi-restraints excluded: chain I residue 567 THR Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 213 optimal weight: 0.0670 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN B 71 ASN B 123 ASN B 237 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 ASN J 71 ASN J 123 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 23385 Z= 0.259 Angle : 1.143 84.385 31770 Z= 0.439 Chirality : 0.060 1.428 3507 Planarity : 0.004 0.055 4029 Dihedral : 7.606 80.596 3426 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.81 % Allowed : 23.20 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2841 helix: 1.44 (0.13), residues: 1449 sheet: -1.62 (0.35), residues: 195 loop : -1.91 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 113 HIS 0.004 0.001 HIS I 68 PHE 0.021 0.002 PHE D 60 TYR 0.037 0.002 TYR H 45 ARG 0.011 0.001 ARG F 2 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 474 time to evaluate : 2.572 Fit side-chains revert: symmetry clash REVERT: A 210 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.6095 (mt0) REVERT: A 405 LEU cc_start: 0.7094 (mm) cc_final: 0.6889 (mt) REVERT: A 490 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7289 (mp) REVERT: A 568 ARG cc_start: 0.7375 (mtt180) cc_final: 0.6822 (mtt180) REVERT: B 41 GLN cc_start: 0.7121 (tt0) cc_final: 0.6678 (mt0) REVERT: C 93 MET cc_start: 0.6675 (mtp) cc_final: 0.6459 (mtt) REVERT: C 101 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6727 (mt-10) REVERT: D 77 TRP cc_start: 0.7739 (t60) cc_final: 0.7359 (t-100) REVERT: E 210 GLN cc_start: 0.6743 (tt0) cc_final: 0.6420 (mt0) REVERT: E 398 ASN cc_start: 0.7123 (OUTLIER) cc_final: 0.6885 (t0) REVERT: E 405 LEU cc_start: 0.6973 (mm) cc_final: 0.6703 (mt) REVERT: E 450 ASN cc_start: 0.6575 (OUTLIER) cc_final: 0.6334 (m-40) REVERT: E 490 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7457 (mp) REVERT: E 568 ARG cc_start: 0.7383 (mtt180) cc_final: 0.7006 (mtt180) REVERT: E 574 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6868 (pp20) REVERT: F 168 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7754 (mtmt) REVERT: F 214 SER cc_start: 0.7014 (p) cc_final: 0.6698 (m) REVERT: G 46 TRP cc_start: 0.7024 (t60) cc_final: 0.6796 (t60) REVERT: G 53 SER cc_start: 0.7573 (t) cc_final: 0.7296 (p) REVERT: G 123 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7277 (mp) REVERT: H 56 PHE cc_start: 0.7047 (t80) cc_final: 0.5630 (m-80) REVERT: I 490 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7095 (mp) REVERT: I 520 MET cc_start: 0.8493 (tpt) cc_final: 0.7888 (tpt) REVERT: I 568 ARG cc_start: 0.7573 (mtt-85) cc_final: 0.6985 (mtt-85) REVERT: I 574 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6769 (pp20) REVERT: J 235 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.6286 (mm-40) REVERT: K 101 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6734 (mt-10) REVERT: L 56 PHE cc_start: 0.7201 (t80) cc_final: 0.5898 (m-80) REVERT: L 90 ARG cc_start: 0.7039 (ttp-110) cc_final: 0.6830 (ttp-170) outliers start: 91 outliers final: 54 residues processed: 526 average time/residue: 1.2492 time to fit residues: 758.9174 Evaluate side-chains 536 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 469 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 503 SER Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 2.9990 chunk 260 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 239 optimal weight: 0.5980 chunk 252 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN B 71 ASN B 123 ASN B 237 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN E 470 ASN ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 ASN J 71 ASN J 123 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 23385 Z= 0.214 Angle : 1.123 84.445 31770 Z= 0.429 Chirality : 0.058 1.425 3507 Planarity : 0.004 0.051 4029 Dihedral : 7.299 81.387 3426 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.10 % Allowed : 23.87 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2841 helix: 1.63 (0.13), residues: 1449 sheet: -1.45 (0.36), residues: 195 loop : -1.82 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 113 HIS 0.004 0.001 HIS I 143 PHE 0.020 0.001 PHE E 471 TYR 0.038 0.002 TYR H 45 ARG 0.009 0.000 ARG F 2 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 482 time to evaluate : 2.498 Fit side-chains revert: symmetry clash REVERT: A 210 GLN cc_start: 0.6303 (OUTLIER) cc_final: 0.6056 (mt0) REVERT: A 490 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7178 (mp) REVERT: A 568 ARG cc_start: 0.7351 (mtt180) cc_final: 0.6779 (mtt180) REVERT: B 41 GLN cc_start: 0.7081 (tt0) cc_final: 0.6639 (mt0) REVERT: C 93 MET cc_start: 0.6650 (mtp) cc_final: 0.6445 (mtt) REVERT: C 101 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6516 (mt-10) REVERT: D 77 TRP cc_start: 0.7801 (t60) cc_final: 0.7367 (t-100) REVERT: E 210 GLN cc_start: 0.6767 (tt0) cc_final: 0.6442 (mt0) REVERT: E 398 ASN cc_start: 0.7076 (OUTLIER) cc_final: 0.6868 (t0) REVERT: E 405 LEU cc_start: 0.6920 (mm) cc_final: 0.6691 (mt) REVERT: E 450 ASN cc_start: 0.6475 (OUTLIER) cc_final: 0.6205 (m-40) REVERT: E 568 ARG cc_start: 0.7352 (mtt180) cc_final: 0.6974 (mtt180) REVERT: E 574 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6911 (pp20) REVERT: F 57 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6979 (tm-30) REVERT: F 168 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7619 (mttt) REVERT: F 214 SER cc_start: 0.6924 (p) cc_final: 0.6654 (m) REVERT: G 46 TRP cc_start: 0.6987 (t60) cc_final: 0.6777 (t60) REVERT: G 53 SER cc_start: 0.7523 (t) cc_final: 0.7250 (p) REVERT: G 123 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7399 (mp) REVERT: H 56 PHE cc_start: 0.7049 (t80) cc_final: 0.5636 (m-80) REVERT: I 50 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7362 (mt0) REVERT: I 490 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7074 (mp) REVERT: I 520 MET cc_start: 0.8411 (tpt) cc_final: 0.7958 (tpt) REVERT: I 568 ARG cc_start: 0.7544 (mtt-85) cc_final: 0.6922 (mtt-85) REVERT: I 574 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6808 (pp20) REVERT: J 210 MET cc_start: 0.8398 (mtp) cc_final: 0.8169 (mtm) REVERT: J 235 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.6242 (mm-40) REVERT: K 101 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6647 (mt-10) REVERT: L 56 PHE cc_start: 0.7187 (t80) cc_final: 0.5877 (m-80) outliers start: 74 outliers final: 46 residues processed: 521 average time/residue: 1.2610 time to fit residues: 755.0322 Evaluate side-chains 529 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 470 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 chunk 163 optimal weight: 0.5980 chunk 127 optimal weight: 9.9990 chunk 186 optimal weight: 0.9990 chunk 280 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN A 470 ASN B 71 ASN B 123 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN ** I 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 ASN J 123 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 23385 Z= 0.200 Angle : 1.122 84.503 31770 Z= 0.426 Chirality : 0.058 1.426 3507 Planarity : 0.004 0.053 4029 Dihedral : 7.094 81.928 3426 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.55 % Allowed : 24.46 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2841 helix: 1.85 (0.13), residues: 1428 sheet: -1.28 (0.37), residues: 195 loop : -1.72 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 113 HIS 0.004 0.001 HIS I 143 PHE 0.023 0.001 PHE I 471 TYR 0.040 0.001 TYR L 45 ARG 0.010 0.000 ARG A 578 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 472 time to evaluate : 2.267 Fit side-chains revert: symmetry clash REVERT: A 210 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.6038 (mt0) REVERT: A 568 ARG cc_start: 0.7341 (mtt180) cc_final: 0.6795 (mtt180) REVERT: B 41 GLN cc_start: 0.7057 (tt0) cc_final: 0.6618 (mt0) REVERT: C 101 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6615 (mt-10) REVERT: D 77 TRP cc_start: 0.7763 (t60) cc_final: 0.7346 (t-100) REVERT: E 28 GLN cc_start: 0.6417 (tm-30) cc_final: 0.6169 (tm-30) REVERT: E 210 GLN cc_start: 0.6724 (tt0) cc_final: 0.6435 (mt0) REVERT: E 568 ARG cc_start: 0.7304 (mtt180) cc_final: 0.6966 (mtt180) REVERT: E 574 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6906 (pp20) REVERT: F 168 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7598 (mttt) REVERT: G 53 SER cc_start: 0.7223 (t) cc_final: 0.6961 (p) REVERT: G 123 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7313 (mp) REVERT: H 56 PHE cc_start: 0.7009 (t80) cc_final: 0.5615 (m-80) REVERT: I 490 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7037 (mp) REVERT: I 520 MET cc_start: 0.8340 (tpt) cc_final: 0.8003 (tpt) REVERT: I 568 ARG cc_start: 0.7525 (mtt-85) cc_final: 0.6892 (mtt-85) REVERT: I 574 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6886 (pp20) REVERT: J 210 MET cc_start: 0.8366 (mtp) cc_final: 0.8147 (mtm) REVERT: J 235 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.6223 (mm-40) REVERT: L 56 PHE cc_start: 0.7188 (t80) cc_final: 0.5880 (m-80) outliers start: 61 outliers final: 35 residues processed: 506 average time/residue: 1.2691 time to fit residues: 747.4140 Evaluate side-chains 507 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 464 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 503 SER Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 503 SER Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 10.0000 chunk 238 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 206 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 28 optimal weight: 0.0770 chunk 41 optimal weight: 8.9990 overall best weight: 4.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 123 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.160681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.144509 restraints weight = 30888.555| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.04 r_work: 0.3692 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 23385 Z= 0.296 Angle : 1.171 84.843 31770 Z= 0.449 Chirality : 0.060 1.414 3507 Planarity : 0.005 0.051 4029 Dihedral : 7.411 81.863 3426 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.97 % Allowed : 24.33 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2841 helix: 1.55 (0.13), residues: 1446 sheet: -1.28 (0.34), residues: 225 loop : -1.83 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 113 HIS 0.005 0.001 HIS I 143 PHE 0.021 0.002 PHE L 60 TYR 0.040 0.002 TYR H 45 ARG 0.012 0.001 ARG I 578 =============================================================================== Job complete usr+sys time: 10945.26 seconds wall clock time: 194 minutes 14.42 seconds (11654.42 seconds total)