Starting phenix.real_space_refine on Mon Apr 8 09:26:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnv_17786/04_2024/8pnv_17786_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnv_17786/04_2024/8pnv_17786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.048 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnv_17786/04_2024/8pnv_17786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnv_17786/04_2024/8pnv_17786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnv_17786/04_2024/8pnv_17786_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnv_17786/04_2024/8pnv_17786_updated.pdb" } resolution = 2.048 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 8202 2.51 5 N 2106 2.21 5 O 2724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 52": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 107": "OE1" <-> "OE2" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 52": "OE1" <-> "OE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "I GLU 52": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 107": "OE1" <-> "OE2" Residue "K TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13098 Number of models: 1 Model: "" Number of chains: 30 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: 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Time building chain proxies: 7.36, per 1000 atoms: 0.56 Number of scatterers: 13098 At special positions: 0 Unit cell: (79.2, 81.18, 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 2724 8.00 N 2106 7.00 C 8202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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 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 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: 6.06 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: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 4 through 32 removed outlier: 3.543A 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: 3.906A pdb=" N ASN A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 4.313A 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: 3.654A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 32 removed outlier: 3.543A 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: 3.906A pdb=" N ASN B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 4.314A 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: 3.654A pdb=" N LEU B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 32 removed outlier: 3.543A 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: 3.906A pdb=" N ASN C 107 " --> pdb=" O TYR C 103 " (cutoff:3.500A) removed outlier: 4.314A 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: 3.654A 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 helix chain 'G' and resid 4 through 32 removed outlier: 3.543A 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: 3.906A pdb=" N ASN G 107 " --> pdb=" O TYR G 103 " (cutoff:3.500A) removed outlier: 4.313A 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: 3.654A pdb=" N LEU G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 32 removed outlier: 3.543A 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: 3.906A pdb=" N ASN H 107 " --> pdb=" O TYR H 103 " (cutoff:3.500A) removed outlier: 4.314A 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: 3.654A pdb=" N LEU H 141 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 32 removed outlier: 3.543A 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: 3.906A pdb=" N ASN I 107 " --> pdb=" O TYR I 103 " (cutoff:3.500A) removed outlier: 4.313A 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: 3.655A 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 sheet with id= A, first strand: chain 'A' and resid 34 through 38 removed outlier: 7.019A pdb=" N TYR A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 34 through 38 removed outlier: 7.020A pdb=" N TYR B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 34 through 38 removed outlier: 7.019A pdb=" N TYR C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 6 through 8 Processing sheet with id= E, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.344A pdb=" N THR D 116 " --> pdb=" O VAL D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 113 through 115 removed outlier: 5.962A pdb=" N ARG D 39 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 6 through 8 Processing sheet with id= H, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.344A pdb=" N THR E 116 " --> pdb=" O VAL E 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'E' and resid 113 through 115 removed outlier: 5.962A pdb=" N ARG E 39 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 6 through 8 Processing sheet with id= K, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.345A pdb=" N THR F 116 " --> pdb=" O VAL F 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 113 through 115 removed outlier: 5.962A pdb=" N ARG F 39 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N PHE F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 34 through 38 removed outlier: 7.019A pdb=" N TYR G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 34 through 38 removed outlier: 7.019A pdb=" N TYR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 34 through 38 removed outlier: 7.019A pdb=" N TYR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 6 through 8 Processing sheet with id= Q, first strand: chain 'J' and resid 12 through 14 removed outlier: 6.345A pdb=" N THR J 116 " --> pdb=" O VAL J 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'J' and resid 113 through 115 removed outlier: 5.962A pdb=" N ARG J 39 " --> pdb=" O PHE J 48 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE J 48 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 6 through 8 Processing sheet with id= T, first strand: chain 'K' and resid 12 through 14 removed outlier: 6.344A pdb=" N THR K 116 " --> pdb=" O VAL K 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'K' and resid 113 through 115 removed outlier: 5.962A pdb=" N ARG K 39 " --> pdb=" O PHE K 48 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE K 48 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 6 through 8 Processing sheet with id= W, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.345A pdb=" N THR L 116 " --> pdb=" O VAL L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 113 through 115 removed outlier: 5.962A pdb=" N ARG L 39 " --> pdb=" O PHE L 48 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N PHE L 48 " --> pdb=" O ARG L 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: 4.40 Time building geometry restraints manager: 6.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 5428 1.39 - 1.55: 7412 1.55 - 1.72: 0 1.72 - 1.88: 102 1.88 - 2.05: 24 Bond restraints: 12966 Sorted by residual: bond pdb=" CB ASN L 53 " pdb=" CG ASN L 53 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.58e+00 bond pdb=" CB ASN F 53 " pdb=" CG ASN F 53 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.55e+00 bond pdb=" CB ASN K 53 " pdb=" CG ASN K 53 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.49e+00 bond pdb=" CB ASN E 53 " pdb=" CG ASN E 53 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.48e+00 bond pdb=" CB ASN D 53 " pdb=" CG ASN D 53 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.44e+00 ... (remaining 12961 not shown) Histogram of bond angle deviations from ideal: 88.24 - 106.32: 456 106.32 - 124.40: 16636 124.40 - 142.49: 566 142.49 - 160.57: 0 160.57 - 178.65: 12 Bond angle restraints: 17670 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 121.06 128.01 -6.95 1.88e+00 2.83e-01 1.37e+01 angle pdb=" C ILE D 52 " pdb=" N ASN D 53 " pdb=" CA ASN D 53 " ideal model delta sigma weight residual 121.06 128.01 -6.95 1.88e+00 2.83e-01 1.36e+01 angle pdb=" C ILE K 52 " pdb=" N ASN K 53 " pdb=" CA ASN K 53 " ideal model delta sigma weight residual 121.06 127.97 -6.91 1.88e+00 2.83e-01 1.35e+01 angle pdb=" C ILE E 52 " pdb=" N ASN E 53 " pdb=" CA ASN E 53 " ideal model delta sigma weight residual 121.06 127.97 -6.91 1.88e+00 2.83e-01 1.35e+01 angle pdb=" C ILE L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.06 127.96 -6.90 1.88e+00 2.83e-01 1.35e+01 ... (remaining 17665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 6192 17.03 - 34.07: 768 34.07 - 51.10: 144 51.10 - 68.14: 108 68.14 - 85.17: 30 Dihedral angle restraints: 7242 sinusoidal: 2772 harmonic: 4470 Sorted by residual: 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 60.59 32.41 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 97 " pdb=" CB CYS F 97 " ideal model delta sinusoidal sigma weight residual 93.00 60.59 32.41 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 97 " pdb=" CB CYS J 97 " ideal model delta sinusoidal sigma weight residual 93.00 60.59 32.41 1 1.00e+01 1.00e-02 1.49e+01 ... (remaining 7239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1075 0.030 - 0.059: 444 0.059 - 0.089: 200 0.089 - 0.119: 84 0.119 - 0.148: 21 Chirality restraints: 1824 Sorted by residual: chirality pdb=" CA ILE H 43 " pdb=" N ILE H 43 " pdb=" C ILE H 43 " pdb=" CB ILE H 43 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE A 43 " pdb=" N ILE A 43 " pdb=" C ILE A 43 " pdb=" CB ILE A 43 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE G 43 " pdb=" N ILE G 43 " pdb=" C ILE G 43 " pdb=" CB ILE G 43 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 1821 not shown) Planarity restraints: 2244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP L 63 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO L 64 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO L 64 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 64 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 63 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO D 64 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 63 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.11e+00 pdb=" N PRO E 64 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " 0.037 5.00e-02 4.00e+02 ... (remaining 2241 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 971 2.73 - 3.27: 13095 3.27 - 3.82: 23782 3.82 - 4.36: 28599 4.36 - 4.90: 47853 Nonbonded interactions: 114300 Sorted by model distance: nonbonded pdb=" O HOH L 214 " pdb=" O HOH L 244 " model vdw 2.188 2.440 nonbonded pdb=" O HOH F 214 " pdb=" O HOH F 244 " model vdw 2.188 2.440 nonbonded pdb=" O HOH K 214 " pdb=" O HOH K 244 " model vdw 2.189 2.440 nonbonded pdb=" O HOH D 214 " pdb=" O HOH D 244 " model vdw 2.189 2.440 nonbonded pdb=" O HOH J 214 " pdb=" O HOH J 244 " model vdw 2.189 2.440 ... (remaining 114295 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 'B' selection = chain 'C' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 5.960 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: 19.360 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 38.760 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 0.044 12966 Z= 0.259 Angle : 0.662 6.948 17670 Z= 0.340 Chirality : 0.043 0.148 1824 Planarity : 0.006 0.067 2244 Dihedral : 17.458 85.170 4428 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 3.28 (0.19), residues: 678 sheet: 0.89 (0.31), residues: 228 loop : 0.43 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 28 HIS 0.002 0.001 HIS I 12 PHE 0.016 0.002 PHE L 48 TYR 0.013 0.002 TYR A 103 ARG 0.003 0.000 ARG G 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 296 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 260 time to evaluate : 1.594 Fit side-chains revert: symmetry clash REVERT: F 107 GLU cc_start: 0.6856 (tt0) cc_final: 0.6574 (tt0) REVERT: J 107 GLU cc_start: 0.6895 (tt0) cc_final: 0.6589 (tt0) outliers start: 36 outliers final: 32 residues processed: 296 average time/residue: 1.2586 time to fit residues: 406.1447 Evaluate side-chains 286 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 254 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 118 SER Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 66 LYS Chi-restraints excluded: chain L 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: 2.9990 chunk 118 optimal weight: 0.0970 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN C 30 ASN D 86 ASN G 30 ASN I 30 ASN K 86 ASN L 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12966 Z= 0.358 Angle : 0.741 9.227 17670 Z= 0.389 Chirality : 0.047 0.153 1824 Planarity : 0.006 0.056 2244 Dihedral : 10.379 84.513 1850 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.47 % Allowed : 15.79 % Favored : 79.74 % 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: 2.12 (0.20), residues: 1602 helix: 2.87 (0.19), residues: 678 sheet: 0.32 (0.30), residues: 270 loop : 0.38 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 37 HIS 0.003 0.001 HIS H 12 PHE 0.018 0.003 PHE E 48 TYR 0.017 0.003 TYR I 103 ARG 0.005 0.001 ARG L 28 *********************** 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 303 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 247 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7242 (mtt-85) REVERT: B 86 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7242 (mtt-85) REVERT: E 93 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7242 (p0) REVERT: F 107 GLU cc_start: 0.7103 (tt0) cc_final: 0.6844 (tt0) REVERT: H 86 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7271 (mtt-85) REVERT: I 86 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7238 (mtt-85) REVERT: L 93 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7243 (p0) outliers start: 56 outliers final: 33 residues processed: 291 average time/residue: 1.3550 time to fit residues: 427.6048 Evaluate side-chains 282 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 243 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 66 LYS Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN K 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12966 Z= 0.241 Angle : 0.624 7.164 17670 Z= 0.320 Chirality : 0.043 0.136 1824 Planarity : 0.005 0.047 2244 Dihedral : 9.356 81.946 1834 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.15 % Allowed : 15.07 % 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: 2.22 (0.20), residues: 1602 helix: 3.08 (0.19), residues: 678 sheet: 0.29 (0.29), residues: 270 loop : 0.32 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 37 HIS 0.002 0.001 HIS F 58 PHE 0.016 0.002 PHE E 48 TYR 0.009 0.002 TYR L 96 ARG 0.003 0.000 ARG A 112 *********************** 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 298 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 246 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7146 (mtt-85) REVERT: D 93 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7307 (p0) REVERT: F 93 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7174 (p0) REVERT: F 107 GLU cc_start: 0.6897 (tt0) cc_final: 0.6604 (tt0) REVERT: I 86 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7148 (mtt-85) REVERT: J 53 ASN cc_start: 0.7041 (t0) cc_final: 0.6814 (t0) REVERT: J 93 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7175 (p0) REVERT: K 93 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7309 (p0) outliers start: 52 outliers final: 24 residues processed: 282 average time/residue: 1.3104 time to fit residues: 401.3547 Evaluate side-chains 272 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 242 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L 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: 0.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN K 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12966 Z= 0.249 Angle : 0.637 7.329 17670 Z= 0.326 Chirality : 0.043 0.136 1824 Planarity : 0.005 0.044 2244 Dihedral : 8.915 82.200 1812 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.99 % Allowed : 15.71 % Favored : 80.30 % 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: 2.11 (0.20), residues: 1602 helix: 3.02 (0.19), residues: 678 sheet: 0.22 (0.29), residues: 270 loop : 0.21 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 37 HIS 0.002 0.001 HIS I 58 PHE 0.015 0.002 PHE E 48 TYR 0.009 0.002 TYR D 96 ARG 0.003 0.000 ARG H 112 *********************** 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 293 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 243 time to evaluate : 1.419 Fit side-chains REVERT: B 86 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7148 (mtt-85) REVERT: D 53 ASN cc_start: 0.7096 (t0) cc_final: 0.6884 (t0) REVERT: D 93 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7330 (p0) REVERT: E 93 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7159 (p0) REVERT: F 93 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7174 (p0) REVERT: F 107 GLU cc_start: 0.6914 (tt0) cc_final: 0.6621 (tt0) REVERT: I 86 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7168 (mtt-85) REVERT: J 53 ASN cc_start: 0.7071 (t0) cc_final: 0.6794 (t0) REVERT: J 93 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7159 (p0) REVERT: K 93 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7335 (p0) REVERT: L 93 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7151 (p0) outliers start: 50 outliers final: 30 residues processed: 276 average time/residue: 1.3412 time to fit residues: 402.7155 Evaluate side-chains 278 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 240 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L 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: 0.9990 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN K 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12966 Z= 0.234 Angle : 0.616 6.804 17670 Z= 0.313 Chirality : 0.042 0.136 1824 Planarity : 0.005 0.043 2244 Dihedral : 8.526 81.599 1804 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.51 % Allowed : 16.03 % 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: 2.12 (0.20), residues: 1602 helix: 3.08 (0.19), residues: 678 sheet: 0.35 (0.30), residues: 234 loop : 0.10 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 37 HIS 0.001 0.001 HIS F 58 PHE 0.014 0.002 PHE L 48 TYR 0.009 0.002 TYR L 96 ARG 0.002 0.000 ARG H 112 *********************** 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 284 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 240 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7053 (mtt-85) REVERT: D 53 ASN cc_start: 0.7067 (t0) cc_final: 0.6822 (t0) REVERT: D 93 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7300 (p0) REVERT: E 93 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7133 (p0) REVERT: F 93 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7158 (p0) REVERT: F 107 GLU cc_start: 0.6871 (tt0) cc_final: 0.6573 (tt0) REVERT: I 86 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7079 (mtt-85) REVERT: J 53 ASN cc_start: 0.7022 (t0) cc_final: 0.6736 (t0) REVERT: J 93 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7158 (p0) REVERT: K 93 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7298 (p0) REVERT: L 93 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7133 (p0) outliers start: 44 outliers final: 25 residues processed: 269 average time/residue: 1.3507 time to fit residues: 394.0834 Evaluate side-chains 270 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 237 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L 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: 7.9990 chunk 29 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12966 Z= 0.255 Angle : 0.645 7.417 17670 Z= 0.330 Chirality : 0.043 0.136 1824 Planarity : 0.005 0.044 2244 Dihedral : 8.579 82.392 1802 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.51 % Allowed : 16.03 % 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: 2.03 (0.20), residues: 1602 helix: 2.96 (0.19), residues: 678 sheet: 0.20 (0.29), residues: 270 loop : 0.16 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 37 HIS 0.002 0.001 HIS I 58 PHE 0.015 0.002 PHE L 48 TYR 0.009 0.002 TYR B 103 ARG 0.003 0.000 ARG A 112 *********************** 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 286 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 242 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7100 (mtt-85) REVERT: D 93 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7338 (p0) REVERT: E 93 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7156 (p0) REVERT: F 93 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7155 (p0) REVERT: F 107 GLU cc_start: 0.6961 (tt0) cc_final: 0.6688 (tt0) REVERT: I 86 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7085 (mtt-85) REVERT: J 93 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7157 (p0) REVERT: K 53 ASN cc_start: 0.7050 (t0) cc_final: 0.6849 (t0) REVERT: K 93 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7339 (p0) REVERT: L 93 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7155 (p0) outliers start: 44 outliers final: 26 residues processed: 269 average time/residue: 1.3192 time to fit residues: 385.4467 Evaluate side-chains 272 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 238 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12966 Z= 0.225 Angle : 0.607 6.467 17670 Z= 0.307 Chirality : 0.042 0.136 1824 Planarity : 0.004 0.043 2244 Dihedral : 8.419 81.132 1802 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.55 % Allowed : 16.83 % 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: 2.14 (0.20), residues: 1602 helix: 3.11 (0.19), residues: 678 sheet: 0.39 (0.30), residues: 234 loop : 0.09 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 37 HIS 0.001 0.000 HIS J 58 PHE 0.014 0.002 PHE E 48 TYR 0.009 0.002 TYR L 96 ARG 0.002 0.000 ARG H 112 *********************** 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 268 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.7010 (mtt-85) REVERT: D 53 ASN cc_start: 0.7042 (t0) cc_final: 0.6791 (t0) REVERT: E 93 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7122 (p0) REVERT: F 20 ARG cc_start: 0.7919 (ttt-90) cc_final: 0.7353 (ttt180) REVERT: F 93 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7141 (p0) REVERT: F 107 GLU cc_start: 0.6852 (tt0) cc_final: 0.6576 (tt0) REVERT: I 86 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6994 (mtt-85) REVERT: J 20 ARG cc_start: 0.7919 (ttt-90) cc_final: 0.7348 (ttt180) REVERT: J 93 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7137 (p0) REVERT: L 93 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7125 (p0) outliers start: 32 outliers final: 19 residues processed: 256 average time/residue: 1.3633 time to fit residues: 378.5079 Evaluate side-chains 260 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 235 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR 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 I residue 38 ILE Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12966 Z= 0.228 Angle : 0.617 8.858 17670 Z= 0.310 Chirality : 0.042 0.135 1824 Planarity : 0.004 0.042 2244 Dihedral : 8.377 81.103 1802 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.63 % Allowed : 16.75 % 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: 2.15 (0.20), residues: 1602 helix: 3.11 (0.19), residues: 678 sheet: 0.43 (0.30), residues: 234 loop : 0.10 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 37 HIS 0.001 0.000 HIS F 58 PHE 0.014 0.002 PHE E 48 TYR 0.008 0.001 TYR L 96 ARG 0.002 0.000 ARG H 112 *********************** 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 272 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 239 time to evaluate : 1.676 Fit side-chains revert: symmetry clash REVERT: D 53 ASN cc_start: 0.7026 (t0) cc_final: 0.6776 (t0) REVERT: E 93 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7118 (p0) REVERT: F 20 ARG cc_start: 0.7921 (ttt-90) cc_final: 0.7360 (ttt180) REVERT: F 93 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7137 (p0) REVERT: F 107 GLU cc_start: 0.6868 (tt0) cc_final: 0.6598 (tt0) REVERT: J 20 ARG cc_start: 0.7944 (ttt-90) cc_final: 0.7353 (ttt180) REVERT: J 93 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7136 (p0) REVERT: L 93 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7123 (p0) outliers start: 33 outliers final: 22 residues processed: 263 average time/residue: 1.3659 time to fit residues: 389.7678 Evaluate side-chains 262 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 236 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR 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 I residue 38 ILE Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 144 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12966 Z= 0.207 Angle : 0.577 6.651 17670 Z= 0.289 Chirality : 0.041 0.134 1824 Planarity : 0.004 0.040 2244 Dihedral : 8.213 80.407 1802 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.99 % Allowed : 17.07 % 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: 2.29 (0.20), residues: 1602 helix: 3.23 (0.19), residues: 678 sheet: 0.56 (0.30), residues: 234 loop : 0.14 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 37 HIS 0.001 0.000 HIS J 58 PHE 0.013 0.001 PHE E 48 TYR 0.008 0.001 TYR L 96 ARG 0.001 0.000 ARG H 112 *********************** 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 259 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 234 time to evaluate : 1.437 Fit side-chains REVERT: E 93 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7090 (p0) REVERT: F 20 ARG cc_start: 0.7945 (ttt-90) cc_final: 0.7372 (ttt180) REVERT: F 93 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.7094 (p0) REVERT: F 107 GLU cc_start: 0.6819 (tt0) cc_final: 0.6576 (tt0) REVERT: G 86 ARG cc_start: 0.7174 (mtt-85) cc_final: 0.6908 (mtm110) REVERT: J 20 ARG cc_start: 0.7940 (ttt-90) cc_final: 0.7370 (ttt180) REVERT: J 93 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7093 (p0) REVERT: L 93 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.7089 (p0) outliers start: 25 outliers final: 20 residues processed: 253 average time/residue: 1.3358 time to fit residues: 366.9225 Evaluate side-chains 256 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 232 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR 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 I residue 38 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 155 optimal weight: 0.0060 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12966 Z= 0.237 Angle : 0.623 8.206 17670 Z= 0.316 Chirality : 0.042 0.137 1824 Planarity : 0.004 0.042 2244 Dihedral : 8.404 81.677 1802 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.99 % Allowed : 17.15 % Favored : 80.86 % 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: 2.12 (0.20), residues: 1602 helix: 3.05 (0.19), residues: 678 sheet: 0.44 (0.30), residues: 234 loop : 0.10 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 37 HIS 0.002 0.001 HIS I 58 PHE 0.013 0.002 PHE E 48 TYR 0.009 0.002 TYR L 96 ARG 0.002 0.000 ARG A 112 ********************** 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 264 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 239 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: D 53 ASN cc_start: 0.7070 (t0) cc_final: 0.6818 (t0) REVERT: E 93 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7133 (p0) REVERT: F 20 ARG cc_start: 0.7927 (ttt-90) cc_final: 0.7344 (ttt180) REVERT: F 93 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7150 (p0) REVERT: F 107 GLU cc_start: 0.6915 (tt0) cc_final: 0.6632 (tt0) REVERT: J 20 ARG cc_start: 0.7950 (ttt-90) cc_final: 0.7342 (ttt180) REVERT: J 93 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7139 (p0) REVERT: L 93 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7132 (p0) outliers start: 25 outliers final: 21 residues processed: 258 average time/residue: 1.3391 time to fit residues: 374.7566 Evaluate side-chains 261 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 236 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR 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 I residue 38 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.120174 restraints weight = 10652.451| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 0.93 r_work: 0.3218 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12966 Z= 0.228 Angle : 0.619 9.896 17670 Z= 0.312 Chirality : 0.042 0.135 1824 Planarity : 0.004 0.042 2244 Dihedral : 8.354 81.085 1802 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.91 % Allowed : 17.07 % Favored : 81.02 % 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: 2.13 (0.20), residues: 1602 helix: 3.08 (0.19), residues: 678 sheet: 0.47 (0.30), residues: 234 loop : 0.08 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 37 HIS 0.001 0.000 HIS B 58 PHE 0.013 0.002 PHE L 48 TYR 0.009 0.001 TYR L 96 ARG 0.002 0.000 ARG A 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6304.09 seconds wall clock time: 113 minutes 28.56 seconds (6808.56 seconds total)