Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 11 03:51:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/07_2023/7jz2_22528_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/07_2023/7jz2_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_22528/07_2023/7jz2_22528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/07_2023/7jz2_22528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/07_2023/7jz2_22528_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/07_2023/7jz2_22528_neut_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 11.54, per 1000 atoms: 0.50 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: 10.38 Conformation dependent library (CDL) restraints added in 3.3 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: 1.87 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: 7.56 Time building geometry restraints manager: 10.87 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: 12389 16.63 - 33.25: 939 33.25 - 49.88: 271 49.88 - 66.50: 69 66.50 - 83.13: 33 Dihedral angle restraints: 13701 sinusoidal: 5487 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 13698 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: 0.000 Normalize map: mean=0, sd=1: 0.130 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: 3.100 Check model and map are aligned: 0.360 Set scattering table: 0.200 Process input model: 62.680 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.210 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:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.670 ------------------------------------------------------------------------------- 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 : 13.846 83.128 8427 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 % 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 *********************** 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 : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 7 residues processed: 626 average time/residue: 1.2851 time to fit residues: 922.8485 Evaluate side-chains 487 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 480 time to evaluate : 2.535 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 0.5776 time to fit residues: 5.7002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0470 chunk 73 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 overall best weight: 4.8086 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 228 HIS B 237 ASN C 91 HIS 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 228 HIS F 235 GLN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 HIS H 14 HIS ** I 31 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 ASN I 470 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: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.208 23385 Z= 0.387 Angle : 1.202 54.833 31770 Z= 0.466 Chirality : 0.068 1.811 3507 Planarity : 0.005 0.039 4029 Dihedral : 7.035 76.409 3249 Min Nonbonded Distance : 1.544 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 4.73 % 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: -1.17 (0.15), residues: 2841 helix: 0.89 (0.13), residues: 1446 sheet: -2.72 (0.29), residues: 189 loop : -2.63 (0.16), residues: 1206 *********************** 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 630 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 517 time to evaluate : 2.554 Fit side-chains outliers start: 113 outliers final: 44 residues processed: 561 average time/residue: 1.2751 time to fit residues: 823.7292 Evaluate side-chains 520 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 476 time to evaluate : 2.434 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 18 residues processed: 28 average time/residue: 0.6136 time to fit residues: 25.9303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 213 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 256 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 254 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 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 211 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN ** 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 395 HIS I 450 ASN I 452 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 Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.109 23385 Z= 0.202 Angle : 1.079 82.265 31770 Z= 0.410 Chirality : 0.059 1.526 3507 Planarity : 0.004 0.043 4029 Dihedral : 6.743 77.301 3249 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 3.85 % 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: -0.41 (0.16), residues: 2841 helix: 1.40 (0.13), residues: 1452 sheet: -2.26 (0.32), residues: 195 loop : -2.12 (0.17), residues: 1194 *********************** 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 594 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 502 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 37 residues processed: 548 average time/residue: 1.2381 time to fit residues: 781.3963 Evaluate side-chains 511 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 474 time to evaluate : 2.375 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 27 residues processed: 11 average time/residue: 0.4356 time to fit residues: 10.0116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 257 optimal weight: 8.9990 chunk 272 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 133 HIS B 237 ASN ** 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 531 ASN J 71 ASN J 133 HIS J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 HIS L 94 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2399 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= 0.348 Angle : 1.162 84.068 31770 Z= 0.451 Chirality : 0.061 1.435 3507 Planarity : 0.005 0.046 4029 Dihedral : 6.988 78.572 3249 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 5.15 % 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: -0.65 (0.15), residues: 2841 helix: 1.15 (0.13), residues: 1446 sheet: -1.99 (0.33), residues: 189 loop : -2.21 (0.17), residues: 1206 *********************** 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 607 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 484 time to evaluate : 2.580 Fit side-chains revert: symmetry clash outliers start: 123 outliers final: 59 residues processed: 549 average time/residue: 1.2471 time to fit residues: 793.0747 Evaluate side-chains 530 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 471 time to evaluate : 2.593 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 33 residues processed: 27 average time/residue: 0.7674 time to fit residues: 30.9716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 188 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 68 optimal weight: 0.0980 overall best weight: 5.0188 ------------------------------------------------------------------------------- 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 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN 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 452 ASN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 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 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 ASN I 531 ASN J 71 ASN J 123 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.104 23385 Z= 0.331 Angle : 1.150 84.414 31770 Z= 0.449 Chirality : 0.060 1.416 3507 Planarity : 0.005 0.047 4029 Dihedral : 7.083 78.283 3249 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 4.82 % 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: -0.67 (0.15), residues: 2841 helix: 1.10 (0.13), residues: 1449 sheet: -1.89 (0.34), residues: 189 loop : -2.21 (0.17), residues: 1203 *********************** 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 590 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 475 time to evaluate : 2.749 Fit side-chains outliers start: 115 outliers final: 63 residues processed: 539 average time/residue: 1.2042 time to fit residues: 752.8415 Evaluate side-chains 528 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 465 time to evaluate : 2.409 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 41 residues processed: 24 average time/residue: 0.3422 time to fit residues: 15.9429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 53 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 226 optimal weight: 0.5980 chunk 126 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 143 optimal weight: 0.0570 overall best weight: 0.7102 ------------------------------------------------------------------------------- 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** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN B 71 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 71 ASN F 237 ASN H 94 GLN I 64 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN I 452 ASN I 531 ASN J 71 ASN J 123 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2570 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= 0.186 Angle : 1.089 84.194 31770 Z= 0.414 Chirality : 0.057 1.445 3507 Planarity : 0.004 0.051 4029 Dihedral : 6.683 79.941 3249 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 3.73 % 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: 0.01 (0.16), residues: 2841 helix: 1.71 (0.13), residues: 1434 sheet: -1.68 (0.35), residues: 195 loop : -1.90 (0.17), residues: 1212 *********************** 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 588 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 499 time to evaluate : 2.326 Fit side-chains revert: symmetry clash outliers start: 89 outliers final: 46 residues processed: 555 average time/residue: 1.2253 time to fit residues: 787.7376 Evaluate side-chains 515 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 469 time to evaluate : 2.634 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 36 residues processed: 12 average time/residue: 0.3307 time to fit residues: 9.8242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 155 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 229 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 chunk 165 optimal weight: 0.5980 chunk 125 optimal weight: 7.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- 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** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 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 452 ASN ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN ** I 31 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 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 449 ASN I 452 ASN I 531 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: 0.7135 moved from start: 0.2681 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= 0.326 Angle : 1.149 84.687 31770 Z= 0.450 Chirality : 0.060 1.414 3507 Planarity : 0.005 0.048 4029 Dihedral : 6.943 80.223 3249 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 4.31 % 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: -0.35 (0.15), residues: 2841 helix: 1.32 (0.13), residues: 1449 sheet: -1.56 (0.35), residues: 189 loop : -2.04 (0.17), residues: 1203 *********************** 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 583 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 480 time to evaluate : 2.486 Fit side-chains outliers start: 103 outliers final: 60 residues processed: 539 average time/residue: 1.2459 time to fit residues: 779.0844 Evaluate side-chains 532 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 472 time to evaluate : 2.561 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 41 residues processed: 21 average time/residue: 0.6370 time to fit residues: 20.8592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 53 optimal weight: 0.0670 chunk 52 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN B 41 GLN B 71 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 31 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 420 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: 0.7066 moved from start: 0.2730 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= 0.211 Angle : 1.112 84.295 31770 Z= 0.425 Chirality : 0.058 1.429 3507 Planarity : 0.004 0.050 4029 Dihedral : 6.780 81.443 3249 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 3.35 % 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: 0.01 (0.16), residues: 2841 helix: 1.65 (0.13), residues: 1431 sheet: -1.44 (0.36), residues: 198 loop : -1.84 (0.17), residues: 1212 *********************** 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 556 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 476 time to evaluate : 3.119 Fit side-chains outliers start: 80 outliers final: 47 residues processed: 530 average time/residue: 1.2171 time to fit residues: 748.8321 Evaluate side-chains 513 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 466 time to evaluate : 2.515 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 41 residues processed: 8 average time/residue: 0.4287 time to fit residues: 8.4851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 0.9990 chunk 260 optimal weight: 0.5980 chunk 237 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 110 optimal weight: 0.0870 chunk 198 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 239 optimal weight: 20.0000 chunk 252 optimal weight: 0.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- 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** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN B 71 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 450 ASN E 452 ASN ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN ** I 31 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 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 ASN ** 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: 0.7050 moved from start: 0.2791 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= 0.211 Angle : 1.121 84.449 31770 Z= 0.428 Chirality : 0.058 1.419 3507 Planarity : 0.004 0.051 4029 Dihedral : 6.652 81.783 3249 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 2.81 % 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: 0.13 (0.16), residues: 2841 helix: 1.75 (0.13), residues: 1425 sheet: -1.32 (0.36), residues: 198 loop : -1.78 (0.17), residues: 1218 *********************** 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 542 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 475 time to evaluate : 2.617 Fit side-chains revert: symmetry clash outliers start: 67 outliers final: 48 residues processed: 524 average time/residue: 1.2191 time to fit residues: 742.6502 Evaluate side-chains 515 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 467 time to evaluate : 2.542 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 41 residues processed: 9 average time/residue: 0.6246 time to fit residues: 10.8498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 0.2980 chunk 267 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 280 optimal weight: 9.9990 chunk 258 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 137 optimal weight: 0.0030 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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** A 470 ASN A 507 ASN B 71 ASN E 64 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 496 ASN F 237 ASN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 ASN J 123 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2913 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= 0.184 Angle : 1.108 84.602 31770 Z= 0.422 Chirality : 0.057 1.419 3507 Planarity : 0.004 0.054 4029 Dihedral : 6.410 85.433 3249 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 2.14 % 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 (0.16), residues: 2841 helix: 1.92 (0.13), residues: 1422 sheet: -1.04 (0.35), residues: 228 loop : -1.74 (0.17), residues: 1191 ********************** 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 530 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 479 time to evaluate : 2.337 Fit side-chains outliers start: 51 outliers final: 39 residues processed: 524 average time/residue: 1.1909 time to fit residues: 725.4328 Evaluate side-chains 498 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 459 time to evaluate : 2.454 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 38 residues processed: 3 average time/residue: 0.3096 time to fit residues: 4.8348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 0.1980 chunk 238 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 206 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN B 71 ASN B 123 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** 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 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 448 ASN ** I 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 ASN J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.162062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145151 restraints weight = 30224.636| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.09 r_work: 0.3684 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2919 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= 0.266 Angle : 1.154 84.672 31770 Z= 0.442 Chirality : 0.059 1.410 3507 Planarity : 0.005 0.053 4029 Dihedral : 6.617 85.480 3249 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 2.51 % 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: 0.11 (0.16), residues: 2841 helix: 1.65 (0.13), residues: 1449 sheet: -1.09 (0.34), residues: 228 loop : -1.79 (0.17), residues: 1164 =============================================================================== Job complete usr+sys time: 10766.13 seconds wall clock time: 190 minutes 41.32 seconds (11441.32 seconds total)