Starting phenix.real_space_refine on Mon Apr 8 07:48:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnu_17785/04_2024/8pnu_17785_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnu_17785/04_2024/8pnu_17785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnu_17785/04_2024/8pnu_17785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnu_17785/04_2024/8pnu_17785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnu_17785/04_2024/8pnu_17785_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnu_17785/04_2024/8pnu_17785_updated.pdb" } resolution = 2.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 60 5.16 5 C 8244 2.51 5 N 2112 2.21 5 O 2466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 6": "OE1" <-> "OE2" Residue "G GLU 36": "OE1" <-> "OE2" Residue "G GLU 52": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I GLU 52": "OE1" <-> "OE2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "A GLU 6": "OE1" <-> "OE2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12888 Number of models: 1 Model: "" Number of chains: 30 Chain: "G" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1170 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "H" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1170 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "I" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1170 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "J" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "K" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "L" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "A" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1170 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "B" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1170 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "C" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1170 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "D" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "E" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "F" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'ABN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'ABN': 1, 'HEM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'ABN': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'ABN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'ABN': 1, 'HEM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'ABN': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "L" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 7.29, per 1000 atoms: 0.57 Number of scatterers: 12888 At special positions: 0 Unit cell: (79.2, 81.84, 168.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 6 26.01 S 60 16.00 O 2466 8.00 N 2112 7.00 C 8244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 97 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 97 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 97 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 97 " distance=2.04 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.89 Conformation dependent library (CDL) restraints added in 2.2 seconds 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2796 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 24 sheets defined 43.9% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'G' and resid 4 through 32 removed outlier: 3.524A pdb=" N GLY G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 78 Proline residue: G 61 - end of helix Proline residue: G 76 - end of helix Processing helix chain 'G' and resid 82 through 108 removed outlier: 3.883A pdb=" N ASN G 107 " --> pdb=" O TYR G 103 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 154 Proline residue: G 134 - end of helix removed outlier: 3.659A pdb=" N LEU G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 32 removed outlier: 3.524A pdb=" N GLY H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 78 Proline residue: H 61 - end of helix Proline residue: H 76 - end of helix Processing helix chain 'H' and resid 82 through 108 removed outlier: 3.883A pdb=" N ASN H 107 " --> pdb=" O TYR H 103 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 154 Proline residue: H 134 - end of helix removed outlier: 3.660A pdb=" N LEU H 141 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 32 removed outlier: 3.524A pdb=" N GLY I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 78 Proline residue: I 61 - end of helix Proline residue: I 76 - end of helix Processing helix chain 'I' and resid 82 through 108 removed outlier: 3.884A pdb=" N ASN I 107 " --> pdb=" O TYR I 103 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE I 108 " --> pdb=" O LEU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 154 Proline residue: I 134 - end of helix removed outlier: 3.660A pdb=" N LEU I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 65 No H-bonds generated for 'chain 'J' and resid 63 through 65' Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'K' and resid 63 through 65 No H-bonds generated for 'chain 'K' and resid 63 through 65' Processing helix chain 'K' and resid 89 through 91 No H-bonds generated for 'chain 'K' and resid 89 through 91' Processing helix chain 'L' and resid 63 through 65 No H-bonds generated for 'chain 'L' and resid 63 through 65' Processing helix chain 'L' and resid 89 through 91 No H-bonds generated for 'chain 'L' and resid 89 through 91' Processing helix chain 'A' and resid 4 through 32 removed outlier: 3.524A pdb=" N GLY A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 78 Proline residue: A 61 - end of helix Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 82 through 108 removed outlier: 3.884A pdb=" N ASN A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 154 Proline residue: A 134 - end of helix removed outlier: 3.659A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 32 removed outlier: 3.524A pdb=" N GLY B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 78 Proline residue: B 61 - end of helix Proline residue: B 76 - end of helix Processing helix chain 'B' and resid 82 through 108 removed outlier: 3.884A pdb=" N ASN B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 154 Proline residue: B 134 - end of helix removed outlier: 3.659A pdb=" N LEU B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 32 removed outlier: 3.524A pdb=" N GLY C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 78 Proline residue: C 61 - end of helix Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 82 through 108 removed outlier: 3.884A pdb=" N ASN C 107 " --> pdb=" O TYR C 103 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 154 Proline residue: C 134 - end of helix removed outlier: 3.660A pdb=" N LEU C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing sheet with id= A, first strand: chain 'G' and resid 34 through 38 removed outlier: 7.165A pdb=" N TYR G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 34 through 38 removed outlier: 7.165A pdb=" N TYR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'I' and resid 34 through 38 removed outlier: 7.165A pdb=" N TYR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'J' and resid 6 through 8 Processing sheet with id= E, first strand: chain 'J' and resid 12 through 14 removed outlier: 6.310A pdb=" N THR J 116 " --> pdb=" O VAL J 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'J' and resid 113 through 115 removed outlier: 5.991A pdb=" N ARG J 39 " --> pdb=" O PHE J 48 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE J 48 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 6 through 8 Processing sheet with id= H, first strand: chain 'K' and resid 12 through 14 removed outlier: 6.309A pdb=" N THR K 116 " --> pdb=" O VAL K 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'K' and resid 113 through 115 removed outlier: 5.991A pdb=" N ARG K 39 " --> pdb=" O PHE K 48 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE K 48 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 6 through 8 Processing sheet with id= K, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.309A pdb=" N THR L 116 " --> pdb=" O VAL L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'L' and resid 113 through 115 removed outlier: 5.992A pdb=" N ARG L 39 " --> pdb=" O PHE L 48 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE L 48 " --> pdb=" O ARG L 39 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 34 through 38 removed outlier: 7.165A pdb=" N TYR A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 34 through 38 removed outlier: 7.165A pdb=" N TYR B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 34 through 38 removed outlier: 7.165A pdb=" N TYR C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 6 through 8 Processing sheet with id= Q, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.310A pdb=" N THR D 116 " --> pdb=" O VAL D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 113 through 115 removed outlier: 5.992A pdb=" N ARG D 39 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 6 through 8 Processing sheet with id= T, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.310A pdb=" N THR E 116 " --> pdb=" O VAL E 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 113 through 115 removed outlier: 5.991A pdb=" N ARG E 39 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 6 through 8 Processing sheet with id= W, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.309A pdb=" N THR F 116 " --> pdb=" O VAL F 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 113 through 115 removed outlier: 5.991A pdb=" N ARG F 39 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 2034 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: 4.07 Time building geometry restraints manager: 6.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 5472 1.39 - 1.55: 7416 1.55 - 1.72: 0 1.72 - 1.88: 102 1.88 - 2.05: 24 Bond restraints: 13014 Sorted by residual: bond pdb=" C TYR C 136 " pdb=" O TYR C 136 " ideal model delta sigma weight residual 1.236 1.251 -0.014 1.15e-02 7.56e+03 1.54e+00 bond pdb=" C TYR I 136 " pdb=" O TYR I 136 " ideal model delta sigma weight residual 1.236 1.251 -0.014 1.15e-02 7.56e+03 1.53e+00 bond pdb=" C TYR A 136 " pdb=" O TYR A 136 " ideal model delta sigma weight residual 1.236 1.251 -0.014 1.15e-02 7.56e+03 1.51e+00 bond pdb=" C TYR B 136 " pdb=" O TYR B 136 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.47e+00 bond pdb=" C TYR G 136 " pdb=" O TYR G 136 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.41e+00 ... (remaining 13009 not shown) Histogram of bond angle deviations from ideal: 88.43 - 106.43: 456 106.43 - 124.44: 16700 124.44 - 142.44: 556 142.44 - 160.45: 0 160.45 - 178.45: 12 Bond angle restraints: 17724 Sorted by residual: angle pdb=" C ILE J 52 " pdb=" N ASN J 53 " pdb=" CA ASN J 53 " ideal model delta sigma weight residual 121.06 127.72 -6.66 1.88e+00 2.83e-01 1.25e+01 angle pdb=" C ILE F 52 " pdb=" N ASN F 53 " pdb=" CA ASN F 53 " ideal model delta sigma weight residual 121.06 127.69 -6.63 1.88e+00 2.83e-01 1.24e+01 angle pdb=" C ILE D 52 " pdb=" N ASN D 53 " pdb=" CA ASN D 53 " ideal model delta sigma weight residual 121.06 127.68 -6.62 1.88e+00 2.83e-01 1.24e+01 angle pdb=" C ILE L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.06 127.68 -6.62 1.88e+00 2.83e-01 1.24e+01 angle pdb=" C ILE E 52 " pdb=" N ASN E 53 " pdb=" CA ASN E 53 " ideal model delta sigma weight residual 121.06 127.66 -6.60 1.88e+00 2.83e-01 1.23e+01 ... (remaining 17719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 6270 17.80 - 35.60: 708 35.60 - 53.41: 144 53.41 - 71.21: 96 71.21 - 89.01: 30 Dihedral angle restraints: 7248 sinusoidal: 2778 harmonic: 4470 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 97 " pdb=" CB CYS K 97 " ideal model delta sinusoidal sigma weight residual 93.00 59.91 33.09 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 97 " pdb=" CB CYS E 97 " ideal model delta sinusoidal sigma weight residual 93.00 59.93 33.07 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 97 " pdb=" CB CYS L 97 " ideal model delta sinusoidal sigma weight residual 93.00 59.95 33.05 1 1.00e+01 1.00e-02 1.55e+01 ... (remaining 7245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1032 0.026 - 0.051: 474 0.051 - 0.077: 168 0.077 - 0.102: 85 0.102 - 0.128: 65 Chirality restraints: 1824 Sorted by residual: chirality pdb=" CA ILE B 38 " pdb=" N ILE B 38 " pdb=" C ILE B 38 " pdb=" CB ILE B 38 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE H 38 " pdb=" N ILE H 38 " pdb=" C ILE H 38 " pdb=" CB ILE H 38 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE I 38 " pdb=" N ILE I 38 " pdb=" C ILE I 38 " pdb=" CB ILE I 38 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1821 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP L 63 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO L 64 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO L 64 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 64 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 63 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO J 64 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO J 64 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 64 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 63 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO F 64 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 64 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 64 " -0.041 5.00e-02 4.00e+02 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3222 2.80 - 3.32: 12211 3.32 - 3.85: 22832 3.85 - 4.37: 26968 4.37 - 4.90: 45843 Nonbonded interactions: 111076 Sorted by model distance: nonbonded pdb=" N ABN G 201 " pdb="FE HEM I 202 " model vdw 2.271 3.080 nonbonded pdb=" N ABN A 201 " pdb="FE HEM C 202 " model vdw 2.272 3.080 nonbonded pdb="FE HEM B 201 " pdb=" N ABN B 202 " model vdw 2.272 3.080 nonbonded pdb="FE HEM H 203 " pdb=" N ABN I 201 " model vdw 2.272 3.080 nonbonded pdb="FE HEM B 203 " pdb=" N ABN C 201 " model vdw 2.273 3.080 ... (remaining 111071 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' and resid 2 through 156) selection = (chain 'B' and resid 2 through 156) selection = (chain 'C' and resid 2 through 156) selection = (chain 'G' and resid 2 through 156) selection = (chain 'H' and resid 2 through 156) selection = (chain 'I' and resid 2 through 156) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.790 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: 0.010 Extract box with map and model: 18.560 Check model and map are aligned: 0.190 Set scattering table: 0.140 Process input model: 38.300 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.140 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 : 0.004 0.042 13014 Z= 0.232 Angle : 0.644 6.655 17724 Z= 0.346 Chirality : 0.041 0.128 1824 Planarity : 0.006 0.074 2250 Dihedral : 17.635 89.011 4434 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.87 % Allowed : 19.62 % Favored : 77.51 % 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: 2.57 (0.20), residues: 1602 helix: 3.29 (0.19), residues: 678 sheet: 0.89 (0.31), residues: 228 loop : 0.42 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 28 HIS 0.002 0.001 HIS H 12 PHE 0.012 0.002 PHE K 48 TYR 0.008 0.002 TYR I 103 ARG 0.003 0.000 ARG H 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 296 time to evaluate : 1.396 Fit side-chains REVERT: I 6 GLU cc_start: 0.7852 (mp0) cc_final: 0.7517 (mp0) REVERT: J 12 LEU cc_start: 0.7975 (tp) cc_final: 0.7735 (tm) REVERT: J 53 ASN cc_start: 0.7279 (t0) cc_final: 0.7028 (t0) REVERT: L 12 LEU cc_start: 0.8032 (tp) cc_final: 0.7715 (tm) REVERT: C 6 GLU cc_start: 0.7887 (mp0) cc_final: 0.7527 (mp0) REVERT: F 12 LEU cc_start: 0.7996 (tp) cc_final: 0.7640 (tm) outliers start: 36 outliers final: 10 residues processed: 332 average time/residue: 1.3782 time to fit residues: 495.3618 Evaluate side-chains 249 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 239 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 118 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain E residue 118 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 0.1980 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 4 GLN K 4 GLN K 75 ASN L 4 GLN L 75 ASN D 4 GLN E 4 GLN E 75 ASN F 4 GLN F 75 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13014 Z= 0.199 Angle : 0.574 6.307 17724 Z= 0.290 Chirality : 0.041 0.140 1824 Planarity : 0.004 0.045 2250 Dihedral : 8.780 88.279 1810 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.91 % Allowed : 17.30 % Favored : 80.78 % 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: 2.70 (0.20), residues: 1602 helix: 3.49 (0.18), residues: 678 sheet: 0.86 (0.31), residues: 228 loop : 0.43 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 28 HIS 0.002 0.001 HIS B 58 PHE 0.014 0.001 PHE K 48 TYR 0.009 0.001 TYR C 136 ARG 0.001 0.000 ARG G 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 246 time to evaluate : 1.495 Fit side-chains REVERT: J 53 ASN cc_start: 0.7116 (t0) cc_final: 0.6911 (t0) REVERT: L 12 LEU cc_start: 0.8054 (tp) cc_final: 0.7751 (tm) REVERT: F 12 LEU cc_start: 0.8032 (tp) cc_final: 0.7713 (tm) outliers start: 24 outliers final: 12 residues processed: 264 average time/residue: 1.3414 time to fit residues: 384.2336 Evaluate side-chains 256 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 244 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 126 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 40 GLN K 4 GLN K 40 GLN L 40 GLN D 40 GLN D 53 ASN E 4 GLN E 40 GLN F 40 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13014 Z= 0.209 Angle : 0.596 6.235 17724 Z= 0.303 Chirality : 0.042 0.134 1824 Planarity : 0.004 0.033 2250 Dihedral : 9.390 89.063 1806 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.07 % Allowed : 16.67 % Favored : 81.26 % 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: 2.54 (0.20), residues: 1602 helix: 3.36 (0.18), residues: 678 sheet: 0.83 (0.32), residues: 228 loop : 0.32 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 28 HIS 0.002 0.001 HIS H 58 PHE 0.014 0.002 PHE K 48 TYR 0.010 0.001 TYR L 108 ARG 0.003 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 249 time to evaluate : 1.818 Fit side-chains REVERT: J 40 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: J 53 ASN cc_start: 0.7083 (t0) cc_final: 0.6876 (t0) REVERT: L 12 LEU cc_start: 0.8088 (tp) cc_final: 0.7798 (tm) REVERT: D 40 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: F 12 LEU cc_start: 0.8082 (tp) cc_final: 0.7788 (tm) outliers start: 26 outliers final: 10 residues processed: 269 average time/residue: 1.3447 time to fit residues: 393.0714 Evaluate side-chains 256 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 244 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN K 40 GLN L 40 GLN B 152 GLN D 40 GLN D 53 ASN E 40 GLN F 40 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13014 Z= 0.351 Angle : 0.763 8.464 17724 Z= 0.396 Chirality : 0.048 0.132 1824 Planarity : 0.005 0.034 2250 Dihedral : 8.987 82.875 1806 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.67 % Allowed : 15.23 % Favored : 81.10 % 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: 1.99 (0.20), residues: 1602 helix: 2.90 (0.18), residues: 678 sheet: 0.68 (0.32), residues: 228 loop : -0.03 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP L 37 HIS 0.006 0.002 HIS B 58 PHE 0.018 0.003 PHE D 48 TYR 0.018 0.003 TYR D 108 ARG 0.004 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 241 time to evaluate : 1.559 Fit side-chains REVERT: I 6 GLU cc_start: 0.7996 (mp0) cc_final: 0.7668 (mp0) REVERT: J 40 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: A 2 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6563 (mp) REVERT: C 6 GLU cc_start: 0.7998 (mp0) cc_final: 0.7675 (mp0) REVERT: D 40 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8009 (tt0) outliers start: 46 outliers final: 18 residues processed: 278 average time/residue: 1.3070 time to fit residues: 394.8067 Evaluate side-chains 250 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 229 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN K 40 GLN B 152 GLN D 40 GLN E 40 GLN F 4 GLN F 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13014 Z= 0.233 Angle : 0.638 6.216 17724 Z= 0.329 Chirality : 0.043 0.132 1824 Planarity : 0.004 0.031 2250 Dihedral : 8.613 88.246 1806 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.07 % Allowed : 16.83 % Favored : 81.10 % 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: 2.19 (0.20), residues: 1602 helix: 3.07 (0.18), residues: 678 sheet: 0.66 (0.30), residues: 270 loop : 0.08 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 37 HIS 0.003 0.001 HIS B 58 PHE 0.014 0.002 PHE L 48 TYR 0.010 0.002 TYR L 108 ARG 0.003 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 1.532 Fit side-chains REVERT: I 6 GLU cc_start: 0.7951 (mp0) cc_final: 0.7614 (mp0) REVERT: J 40 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: L 111 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7584 (mptp) REVERT: C 6 GLU cc_start: 0.7952 (mp0) cc_final: 0.7615 (mp0) REVERT: D 40 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8074 (tt0) outliers start: 26 outliers final: 16 residues processed: 268 average time/residue: 1.2695 time to fit residues: 370.3521 Evaluate side-chains 258 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 239 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 4 GLN Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 150 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN L 4 GLN B 152 GLN D 40 GLN F 4 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13014 Z= 0.213 Angle : 0.612 6.165 17724 Z= 0.314 Chirality : 0.042 0.133 1824 Planarity : 0.004 0.031 2250 Dihedral : 8.455 89.676 1806 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.07 % Allowed : 17.70 % Favored : 80.22 % 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: 2.27 (0.20), residues: 1602 helix: 3.16 (0.18), residues: 678 sheet: 0.72 (0.31), residues: 270 loop : 0.09 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 37 HIS 0.002 0.001 HIS B 58 PHE 0.012 0.001 PHE L 48 TYR 0.008 0.001 TYR D 96 ARG 0.004 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 244 time to evaluate : 1.530 Fit side-chains REVERT: I 6 GLU cc_start: 0.7960 (mp0) cc_final: 0.7618 (mp0) REVERT: J 40 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: J 53 ASN cc_start: 0.7089 (t0) cc_final: 0.6884 (t0) REVERT: L 12 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7727 (tp) REVERT: C 6 GLU cc_start: 0.7957 (mp0) cc_final: 0.7616 (mp0) REVERT: D 40 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: D 53 ASN cc_start: 0.7087 (t0) cc_final: 0.6885 (t0) REVERT: F 12 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7747 (tp) outliers start: 26 outliers final: 16 residues processed: 265 average time/residue: 1.3009 time to fit residues: 374.8243 Evaluate side-chains 259 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 239 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 119 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN L 4 GLN B 152 GLN D 40 GLN F 4 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13014 Z= 0.273 Angle : 0.687 6.828 17724 Z= 0.356 Chirality : 0.044 0.132 1824 Planarity : 0.005 0.032 2250 Dihedral : 8.791 85.341 1806 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.63 % Allowed : 16.43 % Favored : 80.94 % 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: 2.03 (0.20), residues: 1602 helix: 2.93 (0.18), residues: 678 sheet: 0.61 (0.30), residues: 270 loop : -0.01 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 37 HIS 0.004 0.001 HIS B 58 PHE 0.014 0.002 PHE K 48 TYR 0.012 0.002 TYR D 108 ARG 0.004 0.001 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 239 time to evaluate : 1.451 Fit side-chains REVERT: I 6 GLU cc_start: 0.7987 (mp0) cc_final: 0.7641 (mp0) REVERT: J 40 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: L 12 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7712 (tp) REVERT: L 111 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7669 (mptp) REVERT: B 8 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8259 (mmtm) REVERT: C 6 GLU cc_start: 0.7991 (mp0) cc_final: 0.7644 (mp0) REVERT: D 40 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: F 12 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7719 (tp) outliers start: 33 outliers final: 21 residues processed: 266 average time/residue: 1.3035 time to fit residues: 376.9871 Evaluate side-chains 263 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 236 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 119 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.0270 chunk 89 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 40 GLN L 4 GLN D 40 GLN E 83 GLN F 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13014 Z= 0.202 Angle : 0.594 6.302 17724 Z= 0.303 Chirality : 0.041 0.134 1824 Planarity : 0.004 0.031 2250 Dihedral : 8.176 89.960 1806 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.31 % Allowed : 16.59 % Favored : 81.10 % 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: 2.29 (0.20), residues: 1602 helix: 3.25 (0.18), residues: 678 sheet: 0.65 (0.30), residues: 276 loop : 0.03 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 37 HIS 0.001 0.000 HIS A 3 PHE 0.011 0.001 PHE F 48 TYR 0.007 0.001 TYR D 96 ARG 0.006 0.000 ARG I 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 240 time to evaluate : 1.527 Fit side-chains REVERT: H 86 ARG cc_start: 0.7449 (mtp85) cc_final: 0.7199 (mtt90) REVERT: J 40 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: L 12 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7717 (tp) REVERT: B 86 ARG cc_start: 0.7445 (mtp85) cc_final: 0.7196 (mtt90) REVERT: D 40 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8021 (tt0) outliers start: 29 outliers final: 17 residues processed: 264 average time/residue: 1.2808 time to fit residues: 368.7061 Evaluate side-chains 254 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 234 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 119 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN J 53 ASN L 4 GLN B 152 GLN D 40 GLN D 53 ASN F 4 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13014 Z= 0.215 Angle : 0.614 6.593 17724 Z= 0.314 Chirality : 0.042 0.132 1824 Planarity : 0.004 0.031 2250 Dihedral : 8.389 89.804 1806 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.23 % Allowed : 16.51 % Favored : 81.26 % 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: 2.25 (0.20), residues: 1602 helix: 3.18 (0.18), residues: 678 sheet: 0.75 (0.30), residues: 270 loop : 0.01 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 37 HIS 0.002 0.001 HIS B 58 PHE 0.011 0.001 PHE F 48 TYR 0.008 0.001 TYR L 108 ARG 0.006 0.000 ARG I 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 239 time to evaluate : 1.489 Fit side-chains REVERT: J 40 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: L 12 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7724 (tp) REVERT: D 40 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8095 (tt0) outliers start: 28 outliers final: 19 residues processed: 262 average time/residue: 1.3129 time to fit residues: 374.3671 Evaluate side-chains 259 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 237 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 119 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 12 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN L 4 GLN B 152 GLN D 40 GLN F 4 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 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 0.054 13014 Z= 0.224 Angle : 0.632 6.759 17724 Z= 0.325 Chirality : 0.042 0.131 1824 Planarity : 0.004 0.034 2250 Dihedral : 8.423 89.362 1806 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.39 % Allowed : 16.99 % Favored : 80.62 % 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: 2.21 (0.20), residues: 1602 helix: 3.14 (0.18), residues: 678 sheet: 0.75 (0.30), residues: 270 loop : -0.03 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 37 HIS 0.003 0.001 HIS B 58 PHE 0.012 0.002 PHE L 48 TYR 0.008 0.001 TYR L 108 ARG 0.006 0.000 ARG I 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 238 time to evaluate : 1.329 Fit side-chains REVERT: H 86 ARG cc_start: 0.7478 (mtp85) cc_final: 0.7243 (mtt90) REVERT: I 6 GLU cc_start: 0.7950 (mp0) cc_final: 0.7579 (mp0) REVERT: J 40 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: L 12 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7691 (tp) REVERT: B 86 ARG cc_start: 0.7479 (mtp85) cc_final: 0.7243 (mtt90) REVERT: C 6 GLU cc_start: 0.7947 (mp0) cc_final: 0.7582 (mp0) REVERT: D 40 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: F 111 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7646 (mptp) outliers start: 30 outliers final: 20 residues processed: 262 average time/residue: 1.3189 time to fit residues: 374.9904 Evaluate side-chains 262 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 119 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 18 optimal weight: 0.0570 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN L 4 GLN B 152 GLN D 40 GLN F 4 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.129517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.103804 restraints weight = 11471.579| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.03 r_work: 0.3060 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13014 Z= 0.236 Angle : 0.651 6.740 17724 Z= 0.335 Chirality : 0.042 0.130 1824 Planarity : 0.004 0.035 2250 Dihedral : 8.514 88.404 1806 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.39 % Allowed : 17.15 % Favored : 80.46 % 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: 2.14 (0.20), residues: 1602 helix: 3.08 (0.18), residues: 678 sheet: 0.73 (0.30), residues: 270 loop : -0.06 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 37 HIS 0.003 0.001 HIS B 58 PHE 0.013 0.002 PHE F 48 TYR 0.009 0.002 TYR F 108 ARG 0.006 0.000 ARG I 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6314.23 seconds wall clock time: 113 minutes 46.98 seconds (6826.98 seconds total)