Starting phenix.real_space_refine on Sun Aug 24 11:19:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5kel_8240/08_2025/5kel_8240.cif Found real_map, /net/cci-nas-00/data/ceres_data/5kel_8240/08_2025/5kel_8240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5kel_8240/08_2025/5kel_8240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5kel_8240/08_2025/5kel_8240.map" model { file = "/net/cci-nas-00/data/ceres_data/5kel_8240/08_2025/5kel_8240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5kel_8240/08_2025/5kel_8240.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 12147 2.51 5 N 3210 2.21 5 O 3837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19278 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1828 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 889 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 952 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 102} Chain: "C" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 930 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: E, F, G, I, P, Q, T, U, J, M, N, O, W, a, X, b, Y, c, Z, d Time building chain proxies: 2.79, per 1000 atoms: 0.14 Number of scatterers: 19278 At special positions: 0 Unit cell: (150.65, 148.03, 145.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3837 8.00 N 3210 7.00 C 12147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=2.02 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.19 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.21 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.14 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS G 609 " distance=2.02 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS I 609 " distance=2.02 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.02 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS F 135 " distance=2.02 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 121 " - pdb=" SG CYS F 147 " distance=2.03 Simple disulfide: pdb=" SG CYS G 511 " - pdb=" SG CYS G 556 " distance=2.03 Simple disulfide: pdb=" SG CYS I 511 " - pdb=" SG CYS I 556 " distance=2.03 Simple disulfide: pdb=" SG CYS G 601 " - pdb=" SG CYS G 608 " distance=2.04 Simple disulfide: pdb=" SG CYS I 601 " - pdb=" SG CYS I 608 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.19 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.19 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.21 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.21 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.15 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.15 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA V 3 " - " MAN V 5 " " BMA Z 3 " - " MAN Z 5 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 603 " - " ASN A 238 " " NAG E 603 " - " ASN E 238 " " NAG F 603 " - " ASN F 238 " " NAG K 1 " - " ASN A 228 " " NAG R 1 " - " ASN A 268 " " NAG S 1 " - " ASN A 257 " " NAG V 1 " - " ASN B 563 " " NAG W 1 " - " ASN E 228 " " NAG X 1 " - " ASN E 268 " " NAG Y 1 " - " ASN E 257 " " NAG Z 1 " - " ASN G 563 " " NAG a 1 " - " ASN F 228 " " NAG b 1 " - " ASN F 268 " " NAG c 1 " - " ASN F 257 " " NAG d 1 " - " ASN I 563 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 733.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 51 sheets defined 15.2% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.810A pdb=" N LEU B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 597 removed outlier: 3.580A pdb=" N ARG B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 100 through 101 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 40 through 43 Processing helix chain 'C' and resid 60 through 65 removed outlier: 4.411A pdb=" N SER C 65 " --> pdb=" O PRO C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 85 Processing helix chain 'E' and resid 210 through 215 Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'E' and resid 256 through 260 Processing helix chain 'G' and resid 527 through 532 Processing helix chain 'G' and resid 550 through 552 No H-bonds generated for 'chain 'G' and resid 550 through 552' Processing helix chain 'G' and resid 553 through 576 removed outlier: 3.810A pdb=" N LEU G 571 " --> pdb=" O GLN G 567 " (cutoff:3.500A) Processing helix chain 'G' and resid 584 through 597 removed outlier: 3.579A pdb=" N ARG G 596 " --> pdb=" O PHE G 592 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 52A through 54 Processing helix chain 'P' and resid 100 through 101 Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'J' and resid 40 through 43 Processing helix chain 'J' and resid 60 through 65 removed outlier: 4.410A pdb=" N SER J 65 " --> pdb=" O PRO J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 71 through 74 Processing helix chain 'F' and resid 78 through 85 Processing helix chain 'F' and resid 210 through 215 Processing helix chain 'F' and resid 249 through 255 Processing helix chain 'F' and resid 256 through 260 Processing helix chain 'I' and resid 527 through 532 Processing helix chain 'I' and resid 550 through 552 No H-bonds generated for 'chain 'I' and resid 550 through 552' Processing helix chain 'I' and resid 553 through 576 removed outlier: 3.810A pdb=" N LEU I 571 " --> pdb=" O GLN I 567 " (cutoff:3.500A) Processing helix chain 'I' and resid 584 through 597 removed outlier: 3.580A pdb=" N ARG I 596 " --> pdb=" O PHE I 592 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'Q' and resid 52A through 54 Processing helix chain 'Q' and resid 100 through 101 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'M' and resid 40 through 43 Processing helix chain 'M' and resid 60 through 65 removed outlier: 4.410A pdb=" N SER M 65 " --> pdb=" O PRO M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 75 No H-bonds generated for 'chain 'M' and resid 73 through 75' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'O' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.886A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 69 removed outlier: 4.009A pdb=" N THR A 175 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A 109 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA A 177 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N ASN A 107 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 515 through 519 Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.526A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'H' and resid 16 through 18 removed outlier: 6.089A pdb=" N GLY H 16 " --> pdb=" O THR H 82B" (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR H 82B" --> pdb=" O GLY H 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.571A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB3, first strand: chain 'C' and resid 4 through 8 removed outlier: 5.344A pdb=" N GLY C 16 " --> pdb=" O ASN C 82B" (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 56 through 59 removed outlier: 5.452A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 56 through 59 removed outlier: 5.452A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.183A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.886A pdb=" N GLY E 36 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AC2, first strand: chain 'E' and resid 67 through 69 removed outlier: 4.009A pdb=" N THR E 175 " --> pdb=" O TYR E 109 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR E 109 " --> pdb=" O THR E 175 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA E 177 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N ASN E 107 " --> pdb=" O ALA E 177 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR E 220 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS E 140 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALA E 222 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER E 142 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG E 219 " --> pdb=" O GLU E 235 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 515 through 519 Processing sheet with id=AC4, first strand: chain 'P' and resid 5 through 7 Processing sheet with id=AC5, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.526A pdb=" N MET P 34 " --> pdb=" O GLU P 50 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 10 through 12 Processing sheet with id=AC7, first strand: chain 'P' and resid 16 through 18 removed outlier: 6.089A pdb=" N GLY P 16 " --> pdb=" O THR P 82B" (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR P 82B" --> pdb=" O GLY P 16 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 4 through 7 Processing sheet with id=AC9, first strand: chain 'T' and resid 10 through 13 removed outlier: 3.572A pdb=" N ALA T 34 " --> pdb=" O GLN T 89 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 10 through 13 Processing sheet with id=AD2, first strand: chain 'J' and resid 4 through 8 removed outlier: 5.344A pdb=" N GLY J 16 " --> pdb=" O ASN J 82B" (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 56 through 59 removed outlier: 5.452A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 56 through 59 removed outlier: 5.452A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AD7, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.183A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR N 49 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 42 through 45 removed outlier: 6.886A pdb=" N GLY F 36 " --> pdb=" O ILE F 185 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 67 through 69 Processing sheet with id=AE1, first strand: chain 'F' and resid 67 through 69 removed outlier: 4.009A pdb=" N THR F 175 " --> pdb=" O TYR F 109 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR F 109 " --> pdb=" O THR F 175 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA F 177 " --> pdb=" O ASN F 107 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N ASN F 107 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS F 108 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL F 141 " --> pdb=" O CYS F 108 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASN F 110 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLY F 143 " --> pdb=" O ASN F 110 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR F 220 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS F 140 " --> pdb=" O TYR F 220 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA F 222 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER F 142 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG F 219 " --> pdb=" O GLU F 235 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 515 through 519 Processing sheet with id=AE3, first strand: chain 'Q' and resid 5 through 7 Processing sheet with id=AE4, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.526A pdb=" N MET Q 34 " --> pdb=" O GLU Q 50 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'Q' and resid 16 through 18 removed outlier: 6.088A pdb=" N GLY Q 16 " --> pdb=" O THR Q 82B" (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR Q 82B" --> pdb=" O GLY Q 16 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'U' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'U' and resid 10 through 13 removed outlier: 3.572A pdb=" N ALA U 34 " --> pdb=" O GLN U 89 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'U' and resid 10 through 13 Processing sheet with id=AF1, first strand: chain 'M' and resid 4 through 8 removed outlier: 5.344A pdb=" N GLY M 16 " --> pdb=" O ASN M 82B" (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 56 through 59 removed outlier: 5.452A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 56 through 59 removed outlier: 5.452A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'O' and resid 10 through 13 Processing sheet with id=AF6, first strand: chain 'O' and resid 53 through 54 removed outlier: 6.183A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR O 49 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR O 97 " --> pdb=" O GLN O 90 " (cutoff:3.500A) 738 hydrogen bonds defined for protein. 1710 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: 3.99 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4182 1.32 - 1.45: 5621 1.45 - 1.57: 9790 1.57 - 1.70: 3 1.70 - 1.82: 114 Bond restraints: 19710 Sorted by residual: bond pdb=" N TYR H 99 " pdb=" CA TYR H 99 " ideal model delta sigma weight residual 1.458 1.429 0.029 6.30e-03 2.52e+04 2.16e+01 bond pdb=" CA HIS U 90 " pdb=" C HIS U 90 " ideal model delta sigma weight residual 1.525 1.466 0.059 1.28e-02 6.10e+03 2.12e+01 bond pdb=" CA HIS L 90 " pdb=" C HIS L 90 " ideal model delta sigma weight residual 1.525 1.466 0.059 1.28e-02 6.10e+03 2.12e+01 bond pdb=" CA HIS T 90 " pdb=" C HIS T 90 " ideal model delta sigma weight residual 1.525 1.466 0.059 1.28e-02 6.10e+03 2.10e+01 bond pdb=" CB HIS T 90 " pdb=" CG HIS T 90 " ideal model delta sigma weight residual 1.497 1.434 0.063 1.40e-02 5.10e+03 2.05e+01 ... (remaining 19705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 22587 2.36 - 4.72: 3428 4.72 - 7.08: 585 7.08 - 9.44: 116 9.44 - 11.80: 23 Bond angle restraints: 26739 Sorted by residual: angle pdb=" C VAL F 92 " pdb=" N PRO F 93 " pdb=" CA PRO F 93 " ideal model delta sigma weight residual 119.66 127.38 -7.72 7.20e-01 1.93e+00 1.15e+02 angle pdb=" C VAL E 92 " pdb=" N PRO E 93 " pdb=" CA PRO E 93 " ideal model delta sigma weight residual 119.66 127.35 -7.69 7.20e-01 1.93e+00 1.14e+02 angle pdb=" C VAL A 92 " pdb=" N PRO A 93 " pdb=" CA PRO A 93 " ideal model delta sigma weight residual 119.66 127.33 -7.67 7.20e-01 1.93e+00 1.14e+02 angle pdb=" C ALA A 125 " pdb=" N PRO A 126 " pdb=" CA PRO A 126 " ideal model delta sigma weight residual 120.03 130.33 -10.30 9.90e-01 1.02e+00 1.08e+02 angle pdb=" C ALA F 125 " pdb=" N PRO F 126 " pdb=" CA PRO F 126 " ideal model delta sigma weight residual 120.03 130.32 -10.29 9.90e-01 1.02e+00 1.08e+02 ... (remaining 26734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 11586 21.51 - 43.01: 366 43.01 - 64.52: 96 64.52 - 86.03: 87 86.03 - 107.54: 39 Dihedral angle restraints: 12174 sinusoidal: 5328 harmonic: 6846 Sorted by residual: dihedral pdb=" CB CYS G 601 " pdb=" SG CYS G 601 " pdb=" SG CYS G 608 " pdb=" CB CYS G 608 " ideal model delta sinusoidal sigma weight residual 93.00 151.16 -58.16 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS I 601 " pdb=" SG CYS I 601 " pdb=" SG CYS I 608 " pdb=" CB CYS I 608 " ideal model delta sinusoidal sigma weight residual 93.00 151.16 -58.16 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS B 601 " pdb=" SG CYS B 601 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual 93.00 151.14 -58.14 1 1.00e+01 1.00e-02 4.53e+01 ... (remaining 12171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 2940 0.206 - 0.413: 78 0.413 - 0.619: 15 0.619 - 0.825: 0 0.825 - 1.031: 6 Chirality restraints: 3039 Sorted by residual: chirality pdb=" C1 MAN Z 5 " pdb=" O6 BMA Z 3 " pdb=" C2 MAN Z 5 " pdb=" O5 MAN Z 5 " both_signs ideal model delta sigma weight residual False 2.40 1.41 0.99 2.00e-02 2.50e+03 2.44e+03 chirality pdb=" C1 MAN V 5 " pdb=" O6 BMA V 3 " pdb=" C2 MAN V 5 " pdb=" O5 MAN V 5 " both_signs ideal model delta sigma weight residual False 2.40 1.41 0.99 2.00e-02 2.50e+03 2.44e+03 chirality pdb=" C1 MAN d 5 " pdb=" O6 BMA d 3 " pdb=" C2 MAN d 5 " pdb=" O5 MAN d 5 " both_signs ideal model delta sigma weight residual False 2.40 1.41 0.99 2.00e-02 2.50e+03 2.43e+03 ... (remaining 3036 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " 0.284 2.00e-02 2.50e+03 2.44e-01 7.44e+02 pdb=" C7 NAG W 2 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " -0.014 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " -0.413 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " 0.284 2.00e-02 2.50e+03 2.44e-01 7.44e+02 pdb=" C7 NAG a 2 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.014 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " -0.413 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " -0.284 2.00e-02 2.50e+03 2.44e-01 7.42e+02 pdb=" C7 NAG K 2 " 0.062 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.014 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " 0.413 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.205 2.00e-02 2.50e+03 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 60 2.39 - 3.02: 12986 3.02 - 3.65: 28992 3.65 - 4.27: 46890 4.27 - 4.90: 74584 Nonbonded interactions: 163512 Sorted by model distance: nonbonded pdb=" OE1 GLN G 567 " pdb=" CE2 TRP I 531 " model vdw 1.763 3.260 nonbonded pdb=" CE2 TRP B 531 " pdb=" OE1 GLN I 567 " model vdw 1.763 3.260 nonbonded pdb=" OE1 GLN B 567 " pdb=" CE2 TRP G 531 " model vdw 1.764 3.260 nonbonded pdb=" CD2 TRP B 531 " pdb=" OE1 GLN I 567 " model vdw 1.809 3.260 nonbonded pdb=" OE1 GLN G 567 " pdb=" CD2 TRP I 531 " model vdw 1.809 3.260 ... (remaining 163507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'K' selection = chain 'W' selection = chain 'a' } ncs_group { reference = chain 'R' selection = chain 'X' selection = chain 'b' } ncs_group { reference = chain 'S' selection = chain 'Y' selection = chain 'c' } ncs_group { reference = chain 'V' selection = chain 'Z' selection = chain 'd' } 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 group one per residue 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: 1.320 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.590 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:2.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.015 0.177 19782 Z= 0.919 Angle : 1.882 20.155 26928 Z= 1.204 Chirality : 0.103 1.031 3039 Planarity : 0.015 0.244 3372 Dihedral : 14.922 107.536 7749 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 1.27 % Allowed : 3.43 % Favored : 95.30 % Rotamer: Outliers : 0.45 % Allowed : 0.60 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.17), residues: 2361 helix: -0.19 (0.36), residues: 171 sheet: 0.51 (0.19), residues: 642 loop : 1.76 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 61 TYR 0.062 0.010 TYR Q 79 PHE 0.038 0.006 PHE U 91 TRP 0.068 0.011 TRP B 597 HIS 0.007 0.002 HIS T 90 Details of bonding type rmsd covalent geometry : bond 0.01456 (19710) covalent geometry : angle 1.81858 (26739) SS BOND : bond 0.08726 ( 27) SS BOND : angle 3.83029 ( 54) hydrogen bonds : bond 0.16709 ( 660) hydrogen bonds : angle 10.74925 ( 1710) link_ALPHA1-3 : bond 0.00087 ( 6) link_ALPHA1-3 : angle 4.95574 ( 18) link_ALPHA1-6 : bond 0.03477 ( 3) link_ALPHA1-6 : angle 9.86899 ( 9) link_BETA1-4 : bond 0.00335 ( 21) link_BETA1-4 : angle 2.81358 ( 63) link_NAG-ASN : bond 0.02210 ( 15) link_NAG-ASN : angle 9.76404 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 758 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 VAL cc_start: 0.9404 (t) cc_final: 0.9126 (p) REVERT: A 251 GLN cc_start: 0.9285 (mp10) cc_final: 0.8884 (pm20) REVERT: B 555 ILE cc_start: 0.9566 (mm) cc_final: 0.9193 (tt) REVERT: B 564 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8721 (mp0) REVERT: H 50 GLU cc_start: 0.8137 (tt0) cc_final: 0.7643 (tm-30) REVERT: H 61 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8560 (mm-30) REVERT: H 68 THR cc_start: 0.8763 (p) cc_final: 0.8547 (t) REVERT: H 103 TRP cc_start: 0.5952 (p90) cc_final: 0.5511 (p90) REVERT: L 17 GLU cc_start: 0.8923 (tt0) cc_final: 0.8712 (tt0) REVERT: L 58 VAL cc_start: 0.8752 (t) cc_final: 0.8401 (p) REVERT: L 81 GLU cc_start: 0.8788 (pt0) cc_final: 0.8308 (tm-30) REVERT: L 91 PHE cc_start: 0.7769 (m-10) cc_final: 0.7554 (m-10) REVERT: L 105 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8086 (mt-10) REVERT: C 12 VAL cc_start: 0.7496 (m) cc_final: 0.6905 (p) REVERT: C 63 LEU cc_start: 0.8565 (mt) cc_final: 0.8292 (mp) REVERT: C 64 LYS cc_start: 0.8871 (tttt) cc_final: 0.8602 (tptp) REVERT: C 81 LYS cc_start: 0.9193 (tttt) cc_final: 0.8920 (ptmm) REVERT: C 82 ILE cc_start: 0.8011 (mt) cc_final: 0.7670 (mm) REVERT: D 1 ASP cc_start: 0.8103 (m-30) cc_final: 0.7435 (p0) REVERT: D 82 ASP cc_start: 0.8386 (m-30) cc_final: 0.8145 (m-30) REVERT: E 75 VAL cc_start: 0.9329 (t) cc_final: 0.9066 (p) REVERT: E 117 ASP cc_start: 0.8449 (p0) cc_final: 0.8209 (t0) REVERT: E 178 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: E 223 THR cc_start: 0.9113 (m) cc_final: 0.8912 (p) REVERT: E 251 GLN cc_start: 0.9311 (mp10) cc_final: 0.8954 (pm20) REVERT: E 253 LEU cc_start: 0.9593 (mt) cc_final: 0.9371 (tt) REVERT: E 275 TRP cc_start: 0.6975 (m-90) cc_final: 0.5850 (m-90) REVERT: G 555 ILE cc_start: 0.9584 (mm) cc_final: 0.9243 (tt) REVERT: G 564 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8775 (mp0) REVERT: G 588 LYS cc_start: 0.9202 (mmtt) cc_final: 0.8915 (mmmm) REVERT: P 12 MET cc_start: 0.8528 (mtm) cc_final: 0.8280 (mtt) REVERT: P 20 LEU cc_start: 0.9197 (tp) cc_final: 0.8826 (tp) REVERT: P 35 ASN cc_start: 0.8169 (m-40) cc_final: 0.5644 (t0) REVERT: P 43 LYS cc_start: 0.9291 (mmtt) cc_final: 0.8631 (pttm) REVERT: P 68 THR cc_start: 0.8699 (p) cc_final: 0.8480 (t) REVERT: P 80 LEU cc_start: 0.9228 (tp) cc_final: 0.8879 (tp) REVERT: T 17 GLU cc_start: 0.8710 (tt0) cc_final: 0.8414 (tt0) REVERT: T 58 VAL cc_start: 0.8676 (t) cc_final: 0.8423 (p) REVERT: T 73 LEU cc_start: 0.9428 (tp) cc_final: 0.9079 (tt) REVERT: T 81 GLU cc_start: 0.8758 (pt0) cc_final: 0.8417 (tp30) REVERT: T 91 PHE cc_start: 0.7641 (m-10) cc_final: 0.7298 (m-10) REVERT: T 105 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7762 (mt-10) REVERT: J 12 VAL cc_start: 0.7672 (m) cc_final: 0.7224 (p) REVERT: J 63 LEU cc_start: 0.8803 (mt) cc_final: 0.8437 (mp) REVERT: J 64 LYS cc_start: 0.9057 (tttt) cc_final: 0.8804 (tptp) REVERT: J 69 ILE cc_start: 0.7640 (mt) cc_final: 0.7404 (mt) REVERT: J 80 LEU cc_start: 0.8832 (mt) cc_final: 0.8629 (mt) REVERT: N 1 ASP cc_start: 0.8207 (m-30) cc_final: 0.7521 (p0) REVERT: N 38 GLN cc_start: 0.8555 (tt0) cc_final: 0.8209 (tt0) REVERT: N 82 ASP cc_start: 0.8752 (m-30) cc_final: 0.8469 (m-30) REVERT: N 103 LYS cc_start: 0.8308 (mttt) cc_final: 0.8051 (mmtm) REVERT: F 35 LEU cc_start: 0.9150 (mt) cc_final: 0.8874 (mp) REVERT: F 75 VAL cc_start: 0.9353 (t) cc_final: 0.9094 (p) REVERT: F 178 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: F 223 THR cc_start: 0.9132 (m) cc_final: 0.8864 (p) REVERT: F 251 GLN cc_start: 0.9250 (mp10) cc_final: 0.8856 (pm20) REVERT: F 275 TRP cc_start: 0.7245 (m-90) cc_final: 0.5824 (m-90) REVERT: I 555 ILE cc_start: 0.9546 (mm) cc_final: 0.9195 (tt) REVERT: I 564 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8761 (mp0) REVERT: I 588 LYS cc_start: 0.9305 (mmtt) cc_final: 0.9084 (mmmm) REVERT: I 608 CYS cc_start: 0.6560 (m) cc_final: 0.6266 (m) REVERT: Q 20 LEU cc_start: 0.9260 (tp) cc_final: 0.9053 (tp) REVERT: Q 35 ASN cc_start: 0.8306 (m-40) cc_final: 0.5719 (t0) REVERT: Q 43 LYS cc_start: 0.9382 (mmtt) cc_final: 0.8742 (pttm) REVERT: U 17 GLU cc_start: 0.8806 (tt0) cc_final: 0.8538 (tt0) REVERT: U 58 VAL cc_start: 0.8659 (t) cc_final: 0.8356 (p) REVERT: U 87 TYR cc_start: 0.8697 (m-80) cc_final: 0.8067 (m-80) REVERT: U 91 PHE cc_start: 0.7748 (m-10) cc_final: 0.7344 (m-10) REVERT: M 12 VAL cc_start: 0.7389 (m) cc_final: 0.6906 (p) REVERT: M 63 LEU cc_start: 0.8819 (mt) cc_final: 0.8411 (mp) REVERT: M 69 ILE cc_start: 0.7659 (mt) cc_final: 0.7377 (mt) REVERT: M 75 ARG cc_start: 0.9025 (mtm180) cc_final: 0.8546 (ttp-110) REVERT: M 81 LYS cc_start: 0.9226 (tttt) cc_final: 0.8957 (ptmm) REVERT: O 1 ASP cc_start: 0.8185 (m-30) cc_final: 0.7500 (p0) REVERT: O 23 CYS cc_start: 0.5829 (t) cc_final: 0.4962 (t) REVERT: O 38 GLN cc_start: 0.8463 (tt0) cc_final: 0.8156 (tt0) REVERT: O 82 ASP cc_start: 0.8409 (m-30) cc_final: 0.8138 (m-30) outliers start: 9 outliers final: 4 residues processed: 767 average time/residue: 0.1380 time to fit residues: 158.0851 Evaluate side-chains 425 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 416 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.1980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 602 HIS H 3 GLN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN E 39 HIS E 73 ASN P 3 GLN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN Q 3 GLN Q 53 ASN ** Q 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.068809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054029 restraints weight = 102875.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.055534 restraints weight = 59465.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.056502 restraints weight = 41218.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.057157 restraints weight = 32579.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.057525 restraints weight = 27916.428| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 19782 Z= 0.236 Angle : 0.958 13.611 26928 Z= 0.494 Chirality : 0.052 0.238 3039 Planarity : 0.008 0.118 3372 Dihedral : 13.502 90.824 3534 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.34 % Favored : 94.16 % Rotamer: Outliers : 0.10 % Allowed : 2.18 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.17), residues: 2361 helix: 0.52 (0.37), residues: 144 sheet: -0.16 (0.18), residues: 666 loop : 0.88 (0.17), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 94 TYR 0.036 0.003 TYR O 36 PHE 0.019 0.003 PHE F 88 TRP 0.028 0.003 TRP U 35 HIS 0.012 0.002 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00513 (19710) covalent geometry : angle 0.92934 (26739) SS BOND : bond 0.00522 ( 27) SS BOND : angle 1.82183 ( 54) hydrogen bonds : bond 0.05545 ( 660) hydrogen bonds : angle 8.28424 ( 1710) link_ALPHA1-3 : bond 0.01043 ( 6) link_ALPHA1-3 : angle 1.91532 ( 18) link_ALPHA1-6 : bond 0.02131 ( 3) link_ALPHA1-6 : angle 2.74442 ( 9) link_BETA1-4 : bond 0.00556 ( 21) link_BETA1-4 : angle 2.48894 ( 63) link_NAG-ASN : bond 0.00313 ( 15) link_NAG-ASN : angle 4.54199 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 579 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 VAL cc_start: 0.9503 (t) cc_final: 0.9182 (p) REVERT: A 117 ASP cc_start: 0.8639 (p0) cc_final: 0.8436 (p0) REVERT: A 251 GLN cc_start: 0.9276 (mp10) cc_final: 0.9038 (pm20) REVERT: H 2 VAL cc_start: 0.8134 (p) cc_final: 0.7631 (t) REVERT: H 18 MET cc_start: 0.8627 (tmm) cc_final: 0.8240 (tmm) REVERT: H 43 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8679 (pttm) REVERT: H 82 MET cc_start: 0.9181 (mtp) cc_final: 0.8965 (mtp) REVERT: H 86 ASP cc_start: 0.8133 (m-30) cc_final: 0.7930 (m-30) REVERT: L 5 THR cc_start: 0.8545 (p) cc_final: 0.8259 (p) REVERT: L 13 VAL cc_start: 0.9396 (m) cc_final: 0.9168 (p) REVERT: L 90 HIS cc_start: 0.5707 (m-70) cc_final: 0.5446 (m-70) REVERT: L 98 PHE cc_start: 0.8671 (m-80) cc_final: 0.8185 (m-80) REVERT: C 53 TRP cc_start: 0.5955 (t-100) cc_final: 0.5725 (t-100) REVERT: C 64 LYS cc_start: 0.8895 (tttt) cc_final: 0.8540 (tptp) REVERT: C 69 ILE cc_start: 0.7504 (mt) cc_final: 0.7247 (mt) REVERT: C 75 ARG cc_start: 0.8811 (ttp-110) cc_final: 0.8350 (mtm110) REVERT: C 82 ILE cc_start: 0.7839 (mt) cc_final: 0.7572 (mp) REVERT: C 100 MET cc_start: 0.8344 (ttp) cc_final: 0.8128 (ttp) REVERT: D 1 ASP cc_start: 0.8082 (m-30) cc_final: 0.7357 (p0) REVERT: D 44 PRO cc_start: 0.9011 (Cg_endo) cc_final: 0.8700 (Cg_exo) REVERT: D 54 ARG cc_start: 0.8371 (ptt90) cc_final: 0.8080 (ptt90) REVERT: E 35 LEU cc_start: 0.9192 (mp) cc_final: 0.8731 (mp) REVERT: E 75 VAL cc_start: 0.9399 (t) cc_final: 0.9125 (p) REVERT: E 223 THR cc_start: 0.9012 (m) cc_final: 0.8784 (m) REVERT: E 251 GLN cc_start: 0.9279 (mp10) cc_final: 0.8980 (pm20) REVERT: G 555 ILE cc_start: 0.9515 (mm) cc_final: 0.9160 (tp) REVERT: G 588 LYS cc_start: 0.9146 (mmtt) cc_final: 0.8827 (mmtm) REVERT: G 602 HIS cc_start: 0.7726 (t70) cc_final: 0.7438 (t-170) REVERT: P 2 VAL cc_start: 0.8087 (p) cc_final: 0.7574 (t) REVERT: P 20 LEU cc_start: 0.9352 (tp) cc_final: 0.9132 (tp) REVERT: P 43 LYS cc_start: 0.9168 (mmtt) cc_final: 0.8748 (pttm) REVERT: T 13 VAL cc_start: 0.9500 (m) cc_final: 0.9279 (p) REVERT: T 98 PHE cc_start: 0.8623 (m-80) cc_final: 0.8358 (m-80) REVERT: J 53 TRP cc_start: 0.5767 (t-100) cc_final: 0.5489 (t-100) REVERT: J 64 LYS cc_start: 0.8924 (tttt) cc_final: 0.8711 (tptt) REVERT: J 75 ARG cc_start: 0.8850 (ttp-110) cc_final: 0.8323 (mtm110) REVERT: J 100 TYR cc_start: 0.7905 (t80) cc_final: 0.7564 (t80) REVERT: N 1 ASP cc_start: 0.8260 (m-30) cc_final: 0.7381 (p0) REVERT: N 8 PRO cc_start: 0.8321 (Cg_endo) cc_final: 0.7749 (Cg_exo) REVERT: N 48 ILE cc_start: 0.8855 (mt) cc_final: 0.8578 (mt) REVERT: F 69 ASN cc_start: 0.8761 (t0) cc_final: 0.8492 (t0) REVERT: F 75 VAL cc_start: 0.9462 (t) cc_final: 0.9216 (p) REVERT: F 223 THR cc_start: 0.9132 (m) cc_final: 0.8918 (m) REVERT: F 251 GLN cc_start: 0.9347 (mp10) cc_final: 0.8952 (pm20) REVERT: I 555 ILE cc_start: 0.9507 (mm) cc_final: 0.9128 (tp) REVERT: I 588 LYS cc_start: 0.9356 (mmtt) cc_final: 0.9138 (mmmm) REVERT: I 602 HIS cc_start: 0.7909 (t70) cc_final: 0.7618 (t-170) REVERT: Q 5 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8630 (tp40) REVERT: Q 45 LEU cc_start: 0.8572 (tp) cc_final: 0.8349 (tp) REVERT: Q 46 GLU cc_start: 0.9102 (pt0) cc_final: 0.8810 (pm20) REVERT: U 87 TYR cc_start: 0.8799 (m-80) cc_final: 0.8569 (m-80) REVERT: M 20 LEU cc_start: 0.8901 (mp) cc_final: 0.8565 (mt) REVERT: M 27 PHE cc_start: 0.6334 (t80) cc_final: 0.5978 (t80) REVERT: M 53 TRP cc_start: 0.5874 (t-100) cc_final: 0.5655 (t-100) REVERT: M 77 GLN cc_start: 0.7583 (mt0) cc_final: 0.6608 (mt0) REVERT: O 1 ASP cc_start: 0.8374 (m-30) cc_final: 0.7500 (p0) REVERT: O 8 PRO cc_start: 0.8790 (Cg_endo) cc_final: 0.8224 (Cg_exo) REVERT: O 44 PRO cc_start: 0.8947 (Cg_endo) cc_final: 0.8699 (Cg_exo) REVERT: O 48 ILE cc_start: 0.8483 (mt) cc_final: 0.8116 (mt) REVERT: O 85 ASP cc_start: 0.8499 (t0) cc_final: 0.8289 (t0) outliers start: 2 outliers final: 0 residues processed: 579 average time/residue: 0.1372 time to fit residues: 119.2645 Evaluate side-chains 384 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 117 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 195 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 HIS P 53 ASN ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 GLN T 79 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** Q 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 GLN O 27 GLN O 38 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.067778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.052844 restraints weight = 105192.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.054348 restraints weight = 60205.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.055318 restraints weight = 41415.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.055957 restraints weight = 32642.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.056356 restraints weight = 28012.893| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19782 Z= 0.197 Angle : 0.839 9.784 26928 Z= 0.428 Chirality : 0.050 0.251 3039 Planarity : 0.006 0.088 3372 Dihedral : 11.783 86.607 3534 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.84 % Favored : 93.65 % Rotamer: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.17), residues: 2361 helix: 0.46 (0.37), residues: 156 sheet: -0.29 (0.18), residues: 672 loop : 0.24 (0.17), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 83 TYR 0.033 0.003 TYR P 99 PHE 0.030 0.002 PHE G 582 TRP 0.019 0.002 TRP Q 103 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00429 (19710) covalent geometry : angle 0.81583 (26739) SS BOND : bond 0.00535 ( 27) SS BOND : angle 1.41623 ( 54) hydrogen bonds : bond 0.04759 ( 660) hydrogen bonds : angle 7.37246 ( 1710) link_ALPHA1-3 : bond 0.01107 ( 6) link_ALPHA1-3 : angle 1.53259 ( 18) link_ALPHA1-6 : bond 0.02172 ( 3) link_ALPHA1-6 : angle 3.49039 ( 9) link_BETA1-4 : bond 0.00505 ( 21) link_BETA1-4 : angle 2.18871 ( 63) link_NAG-ASN : bond 0.00254 ( 15) link_NAG-ASN : angle 3.69156 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 496 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 VAL cc_start: 0.9495 (t) cc_final: 0.9260 (p) REVERT: A 117 ASP cc_start: 0.8716 (p0) cc_final: 0.8417 (p0) REVERT: A 251 GLN cc_start: 0.9400 (mp10) cc_final: 0.9085 (pm20) REVERT: H 18 MET cc_start: 0.8612 (tmm) cc_final: 0.7934 (tmm) REVERT: H 34 MET cc_start: 0.6913 (mmp) cc_final: 0.6251 (mmp) REVERT: L 13 VAL cc_start: 0.9400 (m) cc_final: 0.9117 (p) REVERT: L 39 LYS cc_start: 0.9188 (mttm) cc_final: 0.8919 (mmtt) REVERT: L 83 PHE cc_start: 0.8506 (m-10) cc_final: 0.8194 (m-10) REVERT: C 20 LEU cc_start: 0.8704 (mt) cc_final: 0.8496 (mt) REVERT: C 64 LYS cc_start: 0.8917 (tttt) cc_final: 0.8565 (tptp) REVERT: C 75 ARG cc_start: 0.8829 (ttp-110) cc_final: 0.8374 (mtm110) REVERT: C 81 LYS cc_start: 0.8968 (tmtt) cc_final: 0.8746 (tptp) REVERT: C 82 ILE cc_start: 0.8377 (mt) cc_final: 0.7911 (mp) REVERT: C 100 MET cc_start: 0.8482 (ttp) cc_final: 0.8173 (ttp) REVERT: D 1 ASP cc_start: 0.8168 (m-30) cc_final: 0.7306 (p0) REVERT: D 4 MET cc_start: 0.6900 (tpt) cc_final: 0.6687 (tpp) REVERT: D 17 ASP cc_start: 0.6412 (m-30) cc_final: 0.6167 (m-30) REVERT: D 44 PRO cc_start: 0.8988 (Cg_endo) cc_final: 0.8662 (Cg_exo) REVERT: D 54 ARG cc_start: 0.8371 (ptt90) cc_final: 0.8080 (ptm-80) REVERT: E 35 LEU cc_start: 0.9166 (mp) cc_final: 0.8895 (mm) REVERT: E 75 VAL cc_start: 0.9483 (t) cc_final: 0.9205 (p) REVERT: E 117 ASP cc_start: 0.8648 (p0) cc_final: 0.8446 (p0) REVERT: E 251 GLN cc_start: 0.9460 (mp10) cc_final: 0.9086 (pm20) REVERT: G 588 LYS cc_start: 0.9212 (mmtt) cc_final: 0.9010 (mmtm) REVERT: G 602 HIS cc_start: 0.7843 (t70) cc_final: 0.7523 (t-170) REVERT: P 5 GLN cc_start: 0.8894 (mm110) cc_final: 0.8659 (mm-40) REVERT: P 18 MET cc_start: 0.7957 (tmm) cc_final: 0.7719 (tmm) REVERT: P 34 MET cc_start: 0.6413 (mmp) cc_final: 0.5348 (mmp) REVERT: P 80 LEU cc_start: 0.8886 (tt) cc_final: 0.8634 (tt) REVERT: T 13 VAL cc_start: 0.9455 (m) cc_final: 0.9130 (p) REVERT: T 39 LYS cc_start: 0.9080 (mttm) cc_final: 0.8631 (mmtt) REVERT: T 83 PHE cc_start: 0.8583 (m-10) cc_final: 0.7842 (m-10) REVERT: J 64 LYS cc_start: 0.9068 (tttt) cc_final: 0.8804 (tptt) REVERT: J 75 ARG cc_start: 0.8861 (ttp-110) cc_final: 0.8300 (mtm110) REVERT: J 82 ASN cc_start: 0.8941 (t0) cc_final: 0.8682 (m110) REVERT: N 1 ASP cc_start: 0.8345 (m-30) cc_final: 0.7320 (p0) REVERT: N 44 PRO cc_start: 0.8757 (Cg_endo) cc_final: 0.8532 (Cg_exo) REVERT: N 47 LEU cc_start: 0.9276 (mt) cc_final: 0.9073 (mt) REVERT: F 251 GLN cc_start: 0.9478 (mp10) cc_final: 0.9029 (pm20) REVERT: I 602 HIS cc_start: 0.7984 (t70) cc_final: 0.7524 (t-170) REVERT: Q 64 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8677 (ttmt) REVERT: Q 82 MET cc_start: 0.9042 (mtp) cc_final: 0.8790 (mtp) REVERT: U 13 VAL cc_start: 0.9545 (m) cc_final: 0.9224 (p) REVERT: U 35 TRP cc_start: 0.8111 (m100) cc_final: 0.7758 (m100) REVERT: U 83 PHE cc_start: 0.8251 (m-80) cc_final: 0.7994 (m-80) REVERT: U 87 TYR cc_start: 0.8819 (m-80) cc_final: 0.8369 (m-80) REVERT: M 27 PHE cc_start: 0.6593 (t80) cc_final: 0.6195 (t80) REVERT: M 46 GLU cc_start: 0.8773 (tp30) cc_final: 0.8510 (tp30) REVERT: M 81 LYS cc_start: 0.8991 (tmtt) cc_final: 0.8700 (tptp) REVERT: O 1 ASP cc_start: 0.8399 (m-30) cc_final: 0.7375 (p0) REVERT: O 44 PRO cc_start: 0.8990 (Cg_endo) cc_final: 0.8666 (Cg_exo) REVERT: O 104 LEU cc_start: 0.8541 (mp) cc_final: 0.8248 (mt) outliers start: 2 outliers final: 0 residues processed: 498 average time/residue: 0.1273 time to fit residues: 95.9614 Evaluate side-chains 361 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 12 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN D 42 GLN E 39 HIS ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 ASN ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 ASN M 77 GLN O 37 GLN O 42 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.066827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.051383 restraints weight = 102408.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.052762 restraints weight = 60514.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.053673 restraints weight = 42859.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054252 restraints weight = 34269.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.054571 restraints weight = 29820.603| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 19782 Z= 0.231 Angle : 0.827 12.526 26928 Z= 0.422 Chirality : 0.048 0.237 3039 Planarity : 0.006 0.124 3372 Dihedral : 10.667 81.241 3534 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.73 % Favored : 92.88 % Rotamer: Outliers : 0.05 % Allowed : 4.86 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.17), residues: 2361 helix: 0.62 (0.37), residues: 162 sheet: -0.52 (0.18), residues: 729 loop : -0.11 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG P 94 TYR 0.030 0.003 TYR L 87 PHE 0.021 0.002 PHE B 582 TRP 0.027 0.002 TRP H 103 HIS 0.007 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00504 (19710) covalent geometry : angle 0.80792 (26739) SS BOND : bond 0.00661 ( 27) SS BOND : angle 1.62188 ( 54) hydrogen bonds : bond 0.04611 ( 660) hydrogen bonds : angle 7.08857 ( 1710) link_ALPHA1-3 : bond 0.00763 ( 6) link_ALPHA1-3 : angle 1.71880 ( 18) link_ALPHA1-6 : bond 0.00936 ( 3) link_ALPHA1-6 : angle 3.24236 ( 9) link_BETA1-4 : bond 0.00371 ( 21) link_BETA1-4 : angle 2.04001 ( 63) link_NAG-ASN : bond 0.00329 ( 15) link_NAG-ASN : angle 3.03169 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 454 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8741 (p0) cc_final: 0.8447 (p0) REVERT: A 243 GLN cc_start: 0.8648 (mp10) cc_final: 0.8270 (mp10) REVERT: A 251 GLN cc_start: 0.9450 (mp10) cc_final: 0.9145 (pm20) REVERT: H 27 PHE cc_start: 0.6808 (t80) cc_final: 0.6428 (t80) REVERT: H 46 GLU cc_start: 0.9094 (pt0) cc_final: 0.8878 (pm20) REVERT: L 83 PHE cc_start: 0.8504 (m-10) cc_final: 0.8144 (m-10) REVERT: C 20 LEU cc_start: 0.8744 (mt) cc_final: 0.8510 (mt) REVERT: C 64 LYS cc_start: 0.8935 (tttt) cc_final: 0.8569 (tptp) REVERT: C 75 ARG cc_start: 0.8906 (ttp-110) cc_final: 0.8354 (mtm110) REVERT: C 81 LYS cc_start: 0.8913 (tmtt) cc_final: 0.8684 (tptp) REVERT: C 82 ILE cc_start: 0.8419 (mt) cc_final: 0.7990 (mp) REVERT: C 100 MET cc_start: 0.8307 (ttp) cc_final: 0.7897 (ttp) REVERT: D 4 MET cc_start: 0.7343 (tpt) cc_final: 0.6823 (tpp) REVERT: D 17 ASP cc_start: 0.6551 (m-30) cc_final: 0.6085 (m-30) REVERT: D 36 TYR cc_start: 0.8582 (m-80) cc_final: 0.7904 (m-80) REVERT: D 44 PRO cc_start: 0.9041 (Cg_endo) cc_final: 0.8746 (Cg_exo) REVERT: D 54 ARG cc_start: 0.8270 (ptt90) cc_final: 0.7855 (ptm-80) REVERT: D 103 LYS cc_start: 0.8321 (mppt) cc_final: 0.8073 (mmtm) REVERT: E 117 ASP cc_start: 0.8841 (p0) cc_final: 0.8584 (p0) REVERT: E 251 GLN cc_start: 0.9507 (mp10) cc_final: 0.9134 (pm20) REVERT: G 602 HIS cc_start: 0.7811 (t70) cc_final: 0.7342 (t-170) REVERT: T 13 VAL cc_start: 0.9510 (m) cc_final: 0.9195 (p) REVERT: T 83 PHE cc_start: 0.8398 (m-10) cc_final: 0.7780 (m-10) REVERT: T 98 PHE cc_start: 0.8888 (m-80) cc_final: 0.8536 (m-10) REVERT: J 64 LYS cc_start: 0.9047 (tttt) cc_final: 0.8782 (tptp) REVERT: J 75 ARG cc_start: 0.8963 (ttp-110) cc_final: 0.8278 (mtm110) REVERT: J 79 PHE cc_start: 0.8315 (m-80) cc_final: 0.7307 (m-80) REVERT: J 82 ASN cc_start: 0.8980 (t0) cc_final: 0.8743 (m-40) REVERT: J 100 MET cc_start: 0.8275 (ttm) cc_final: 0.7942 (mtp) REVERT: N 1 ASP cc_start: 0.8289 (m-30) cc_final: 0.7230 (p0) REVERT: N 36 TYR cc_start: 0.8554 (m-80) cc_final: 0.7504 (m-80) REVERT: N 82 ASP cc_start: 0.8701 (m-30) cc_final: 0.8477 (m-30) REVERT: F 251 GLN cc_start: 0.9503 (mp10) cc_final: 0.9058 (pm20) REVERT: I 567 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8034 (tm-30) REVERT: I 602 HIS cc_start: 0.8164 (t70) cc_final: 0.7617 (t-170) REVERT: Q 3 GLN cc_start: 0.8964 (mm110) cc_final: 0.8673 (mm-40) REVERT: Q 32 TYR cc_start: 0.5962 (p90) cc_final: 0.5115 (p90) REVERT: Q 45 LEU cc_start: 0.8782 (tp) cc_final: 0.8440 (tp) REVERT: Q 46 GLU cc_start: 0.9075 (pt0) cc_final: 0.8663 (pm20) REVERT: Q 91 TYR cc_start: 0.8766 (m-80) cc_final: 0.8409 (m-80) REVERT: U 21 ILE cc_start: 0.9497 (mp) cc_final: 0.9285 (mp) REVERT: U 35 TRP cc_start: 0.8050 (m100) cc_final: 0.7666 (m100) REVERT: U 83 PHE cc_start: 0.8162 (m-80) cc_final: 0.7610 (m-80) REVERT: U 87 TYR cc_start: 0.8793 (m-80) cc_final: 0.8359 (m-80) REVERT: U 98 PHE cc_start: 0.8737 (m-80) cc_final: 0.8412 (m-10) REVERT: M 19 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8340 (mmmm) REVERT: M 27 PHE cc_start: 0.6697 (t80) cc_final: 0.6301 (t80) REVERT: M 75 ARG cc_start: 0.8913 (ttp-110) cc_final: 0.8638 (mtm110) REVERT: M 81 LYS cc_start: 0.8940 (tmtt) cc_final: 0.8532 (tptp) REVERT: O 38 GLN cc_start: 0.8012 (tt0) cc_final: 0.7458 (tt0) REVERT: O 85 ASP cc_start: 0.8379 (t0) cc_final: 0.8137 (t0) REVERT: O 104 LEU cc_start: 0.8515 (mp) cc_final: 0.8244 (mt) outliers start: 1 outliers final: 0 residues processed: 455 average time/residue: 0.1187 time to fit residues: 82.6191 Evaluate side-chains 329 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 219 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 44 GLN B 570 GLN B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN I 514 ASN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 ASN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.067061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.051587 restraints weight = 102113.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.053069 restraints weight = 59070.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054025 restraints weight = 40952.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.054642 restraints weight = 32367.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.055040 restraints weight = 27796.967| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19782 Z= 0.164 Angle : 0.775 10.707 26928 Z= 0.394 Chirality : 0.047 0.242 3039 Planarity : 0.005 0.106 3372 Dihedral : 9.910 75.459 3534 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.82 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.17), residues: 2361 helix: 0.64 (0.37), residues: 162 sheet: -0.47 (0.18), residues: 729 loop : -0.23 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 18 TYR 0.033 0.003 TYR Q 32 PHE 0.051 0.002 PHE L 91 TRP 0.045 0.002 TRP B 531 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00361 (19710) covalent geometry : angle 0.75844 (26739) SS BOND : bond 0.00584 ( 27) SS BOND : angle 1.73293 ( 54) hydrogen bonds : bond 0.04422 ( 660) hydrogen bonds : angle 6.80828 ( 1710) link_ALPHA1-3 : bond 0.00999 ( 6) link_ALPHA1-3 : angle 1.29320 ( 18) link_ALPHA1-6 : bond 0.01233 ( 3) link_ALPHA1-6 : angle 2.51284 ( 9) link_BETA1-4 : bond 0.00399 ( 21) link_BETA1-4 : angle 1.88627 ( 63) link_NAG-ASN : bond 0.00148 ( 15) link_NAG-ASN : angle 2.64684 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8729 (p0) cc_final: 0.8435 (p0) REVERT: A 251 GLN cc_start: 0.9377 (mp10) cc_final: 0.9099 (pm20) REVERT: H 12 MET cc_start: 0.8755 (ttt) cc_final: 0.8522 (ttt) REVERT: H 43 LYS cc_start: 0.9294 (mmtt) cc_final: 0.8816 (pttm) REVERT: H 46 GLU cc_start: 0.9079 (pt0) cc_final: 0.8709 (pm20) REVERT: H 85 GLU cc_start: 0.8621 (pm20) cc_final: 0.8122 (pm20) REVERT: L 83 PHE cc_start: 0.8375 (m-10) cc_final: 0.7988 (m-10) REVERT: C 64 LYS cc_start: 0.8911 (tttt) cc_final: 0.8519 (tptp) REVERT: C 75 ARG cc_start: 0.8883 (ttp-110) cc_final: 0.8389 (mtm110) REVERT: C 81 LYS cc_start: 0.9041 (tmtt) cc_final: 0.8794 (tptp) REVERT: D 4 MET cc_start: 0.7775 (tpt) cc_final: 0.7459 (tpp) REVERT: D 17 ASP cc_start: 0.6496 (m-30) cc_final: 0.6198 (m-30) REVERT: D 54 ARG cc_start: 0.8228 (ptt90) cc_final: 0.7865 (ptm-80) REVERT: D 71 PHE cc_start: 0.8427 (m-80) cc_final: 0.8147 (m-80) REVERT: D 83 LEU cc_start: 0.8848 (mt) cc_final: 0.8456 (pt) REVERT: D 103 LYS cc_start: 0.8284 (mppt) cc_final: 0.8009 (mmtm) REVERT: E 117 ASP cc_start: 0.8841 (p0) cc_final: 0.8546 (p0) REVERT: E 251 GLN cc_start: 0.9434 (mp10) cc_final: 0.9078 (pm20) REVERT: G 565 THR cc_start: 0.9328 (m) cc_final: 0.8988 (t) REVERT: G 588 LYS cc_start: 0.9400 (mmmt) cc_final: 0.9173 (mmtp) REVERT: G 602 HIS cc_start: 0.7769 (t70) cc_final: 0.7462 (t-170) REVERT: T 13 VAL cc_start: 0.9487 (m) cc_final: 0.9168 (p) REVERT: T 21 ILE cc_start: 0.9539 (mp) cc_final: 0.9334 (mp) REVERT: T 35 TRP cc_start: 0.7569 (m100) cc_final: 0.7170 (m100) REVERT: T 83 PHE cc_start: 0.8394 (m-10) cc_final: 0.7758 (m-10) REVERT: J 64 LYS cc_start: 0.9074 (tttt) cc_final: 0.8784 (tptt) REVERT: J 75 ARG cc_start: 0.8899 (ttp-110) cc_final: 0.8274 (mtm110) REVERT: J 82 ASN cc_start: 0.8995 (t0) cc_final: 0.8737 (m110) REVERT: N 83 LEU cc_start: 0.8737 (mt) cc_final: 0.8450 (pt) REVERT: F 251 GLN cc_start: 0.9491 (mp10) cc_final: 0.8995 (pm20) REVERT: I 582 PHE cc_start: 0.8353 (m-80) cc_final: 0.7879 (m-80) REVERT: I 602 HIS cc_start: 0.8251 (t70) cc_final: 0.7691 (t-170) REVERT: Q 45 LEU cc_start: 0.8712 (tp) cc_final: 0.8423 (tp) REVERT: Q 46 GLU cc_start: 0.9070 (pt0) cc_final: 0.8699 (pm20) REVERT: Q 91 TYR cc_start: 0.8614 (m-80) cc_final: 0.8285 (m-80) REVERT: Q 100 MET cc_start: 0.7574 (ttp) cc_final: 0.7278 (ttp) REVERT: U 13 VAL cc_start: 0.9231 (m) cc_final: 0.8949 (p) REVERT: U 21 ILE cc_start: 0.9498 (mp) cc_final: 0.9279 (mp) REVERT: U 35 TRP cc_start: 0.7877 (m100) cc_final: 0.7568 (m100) REVERT: U 83 PHE cc_start: 0.8138 (m-80) cc_final: 0.7671 (m-80) REVERT: U 87 TYR cc_start: 0.8762 (m-80) cc_final: 0.8371 (m-80) REVERT: U 98 PHE cc_start: 0.8707 (m-80) cc_final: 0.8425 (m-10) REVERT: M 19 LYS cc_start: 0.8525 (mmmt) cc_final: 0.8312 (mmmm) REVERT: M 27 PHE cc_start: 0.6956 (t80) cc_final: 0.6629 (t80) REVERT: M 46 GLU cc_start: 0.8929 (tp30) cc_final: 0.8438 (tp30) REVERT: M 75 ARG cc_start: 0.8941 (ttp-110) cc_final: 0.8663 (mtm110) REVERT: M 81 LYS cc_start: 0.9004 (tmtt) cc_final: 0.8681 (tptp) REVERT: O 38 GLN cc_start: 0.7952 (tt0) cc_final: 0.7488 (tt0) REVERT: O 44 PRO cc_start: 0.8883 (Cg_endo) cc_final: 0.8432 (Cg_exo) REVERT: O 85 ASP cc_start: 0.8411 (t0) cc_final: 0.8206 (t0) REVERT: O 104 LEU cc_start: 0.8578 (mp) cc_final: 0.8260 (mt) outliers start: 0 outliers final: 0 residues processed: 471 average time/residue: 0.1292 time to fit residues: 92.7180 Evaluate side-chains 335 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 208 optimal weight: 30.0000 chunk 23 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 195 optimal weight: 0.4980 chunk 94 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 44 GLN ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN O 42 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.068292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.052901 restraints weight = 100031.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.054380 restraints weight = 57769.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055363 restraints weight = 40114.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055994 restraints weight = 31547.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.056392 restraints weight = 27074.219| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.246 19782 Z= 0.176 Angle : 0.791 30.155 26928 Z= 0.395 Chirality : 0.047 0.260 3039 Planarity : 0.007 0.261 3372 Dihedral : 9.260 67.913 3534 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.12 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.17), residues: 2361 helix: 0.54 (0.37), residues: 162 sheet: -0.36 (0.18), residues: 714 loop : -0.35 (0.17), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 94 TYR 0.050 0.003 TYR H 55 PHE 0.058 0.002 PHE Q 27 TRP 0.052 0.002 TRP B 531 HIS 0.014 0.001 HIS U 90 Details of bonding type rmsd covalent geometry : bond 0.00401 (19710) covalent geometry : angle 0.77869 (26739) SS BOND : bond 0.00718 ( 27) SS BOND : angle 1.35761 ( 54) hydrogen bonds : bond 0.04350 ( 660) hydrogen bonds : angle 6.58635 ( 1710) link_ALPHA1-3 : bond 0.01114 ( 6) link_ALPHA1-3 : angle 1.28719 ( 18) link_ALPHA1-6 : bond 0.01134 ( 3) link_ALPHA1-6 : angle 2.04562 ( 9) link_BETA1-4 : bond 0.00431 ( 21) link_BETA1-4 : angle 1.79676 ( 63) link_NAG-ASN : bond 0.00178 ( 15) link_NAG-ASN : angle 2.40208 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 478 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8688 (p0) cc_final: 0.8327 (p0) REVERT: A 251 GLN cc_start: 0.9402 (mp10) cc_final: 0.9056 (pm20) REVERT: H 12 MET cc_start: 0.8588 (ttt) cc_final: 0.8383 (ttt) REVERT: H 100 MET cc_start: 0.7118 (ttp) cc_final: 0.6378 (ttp) REVERT: C 20 LEU cc_start: 0.8734 (mp) cc_final: 0.8395 (mt) REVERT: C 43 LYS cc_start: 0.8439 (ptpp) cc_final: 0.8184 (pttm) REVERT: C 64 LYS cc_start: 0.8925 (tttt) cc_final: 0.8537 (pttm) REVERT: C 75 ARG cc_start: 0.8834 (ttp-110) cc_final: 0.8508 (mtm110) REVERT: C 81 LYS cc_start: 0.8970 (tmtt) cc_final: 0.8758 (tptp) REVERT: C 82 ILE cc_start: 0.8436 (mt) cc_final: 0.8000 (mp) REVERT: C 100 MET cc_start: 0.8269 (ttm) cc_final: 0.8020 (ttm) REVERT: D 17 ASP cc_start: 0.6353 (m-30) cc_final: 0.6138 (m-30) REVERT: D 18 ARG cc_start: 0.8739 (mmt-90) cc_final: 0.8290 (mmt-90) REVERT: D 54 ARG cc_start: 0.8105 (ptt90) cc_final: 0.7902 (ptm-80) REVERT: D 71 PHE cc_start: 0.8328 (m-80) cc_final: 0.8111 (m-80) REVERT: D 83 LEU cc_start: 0.8842 (mt) cc_final: 0.8330 (pt) REVERT: D 103 LYS cc_start: 0.8289 (mppt) cc_final: 0.8016 (mmtm) REVERT: E 117 ASP cc_start: 0.8777 (p0) cc_final: 0.8430 (p0) REVERT: E 122 LEU cc_start: 0.8656 (mt) cc_final: 0.8382 (mt) REVERT: E 251 GLN cc_start: 0.9409 (mp10) cc_final: 0.9027 (pm20) REVERT: G 565 THR cc_start: 0.9302 (m) cc_final: 0.8992 (t) REVERT: G 588 LYS cc_start: 0.9335 (mmmt) cc_final: 0.9127 (mmtt) REVERT: G 602 HIS cc_start: 0.7499 (t70) cc_final: 0.7249 (t-170) REVERT: P 43 LYS cc_start: 0.9112 (mmmt) cc_final: 0.8714 (pttm) REVERT: P 80 LEU cc_start: 0.8797 (tt) cc_final: 0.8417 (tt) REVERT: P 91 TYR cc_start: 0.8381 (m-80) cc_final: 0.7780 (m-80) REVERT: T 13 VAL cc_start: 0.8842 (m) cc_final: 0.8388 (p) REVERT: T 50 SER cc_start: 0.8763 (m) cc_final: 0.8476 (t) REVERT: T 83 PHE cc_start: 0.8353 (m-10) cc_final: 0.8124 (m-10) REVERT: T 86 TYR cc_start: 0.9047 (m-80) cc_final: 0.8746 (m-80) REVERT: T 90 HIS cc_start: 0.5716 (m-70) cc_final: 0.5387 (m170) REVERT: J 63 LEU cc_start: 0.8769 (mt) cc_final: 0.8501 (mt) REVERT: J 64 LYS cc_start: 0.9131 (tttt) cc_final: 0.8917 (pttm) REVERT: J 75 ARG cc_start: 0.8848 (ttp-110) cc_final: 0.8416 (mtm110) REVERT: J 80 LEU cc_start: 0.9003 (mt) cc_final: 0.8798 (mt) REVERT: J 81 LYS cc_start: 0.9007 (tmtt) cc_final: 0.8806 (tptp) REVERT: J 82 ASN cc_start: 0.8890 (t0) cc_final: 0.8680 (m-40) REVERT: N 17 ASP cc_start: 0.6721 (m-30) cc_final: 0.6153 (m-30) REVERT: N 83 LEU cc_start: 0.8588 (mt) cc_final: 0.7828 (pt) REVERT: F 251 GLN cc_start: 0.9437 (mp10) cc_final: 0.8936 (pm20) REVERT: I 550 ASN cc_start: 0.8577 (t0) cc_final: 0.8158 (t0) REVERT: I 602 HIS cc_start: 0.8253 (t70) cc_final: 0.7554 (t-170) REVERT: Q 45 LEU cc_start: 0.8681 (tp) cc_final: 0.8444 (tp) REVERT: Q 46 GLU cc_start: 0.8966 (pt0) cc_final: 0.8655 (pm20) REVERT: Q 86 ASP cc_start: 0.8557 (m-30) cc_final: 0.8223 (m-30) REVERT: Q 91 TYR cc_start: 0.8524 (m-80) cc_final: 0.8123 (m-80) REVERT: Q 98 ASN cc_start: 0.8433 (p0) cc_final: 0.8111 (p0) REVERT: Q 100 MET cc_start: 0.7388 (ttp) cc_final: 0.7108 (ttp) REVERT: U 13 VAL cc_start: 0.9159 (m) cc_final: 0.8768 (p) REVERT: U 35 TRP cc_start: 0.7965 (m100) cc_final: 0.7585 (m100) REVERT: U 83 PHE cc_start: 0.7896 (m-80) cc_final: 0.7460 (m-80) REVERT: U 87 TYR cc_start: 0.8530 (m-80) cc_final: 0.8291 (m-80) REVERT: U 98 PHE cc_start: 0.8732 (m-80) cc_final: 0.8222 (m-80) REVERT: M 19 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8305 (mmmm) REVERT: M 46 GLU cc_start: 0.8867 (tp30) cc_final: 0.8493 (tp30) REVERT: M 75 ARG cc_start: 0.8995 (ttp-110) cc_final: 0.8718 (mtm110) REVERT: M 81 LYS cc_start: 0.8973 (tmtt) cc_final: 0.8656 (tptp) REVERT: O 17 ASP cc_start: 0.6871 (m-30) cc_final: 0.6323 (m-30) REVERT: O 38 GLN cc_start: 0.7955 (tt0) cc_final: 0.7129 (tt0) REVERT: O 44 PRO cc_start: 0.8824 (Cg_endo) cc_final: 0.8095 (Cg_exo) REVERT: O 78 MET cc_start: 0.7612 (ppp) cc_final: 0.7362 (ppp) REVERT: O 85 ASP cc_start: 0.8270 (t0) cc_final: 0.7947 (t0) REVERT: O 87 PHE cc_start: 0.7976 (m-80) cc_final: 0.7418 (m-80) REVERT: O 104 LEU cc_start: 0.8526 (mp) cc_final: 0.8183 (mt) outliers start: 0 outliers final: 0 residues processed: 478 average time/residue: 0.1388 time to fit residues: 101.5203 Evaluate side-chains 345 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 2 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 187 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 211 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN D 42 GLN E 39 HIS G 567 GLN ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.067238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.051987 restraints weight = 102731.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.053477 restraints weight = 58676.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.054461 restraints weight = 40362.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055090 restraints weight = 31535.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055474 restraints weight = 26962.172| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19782 Z= 0.156 Angle : 0.756 12.483 26928 Z= 0.380 Chirality : 0.047 0.304 3039 Planarity : 0.006 0.173 3372 Dihedral : 8.742 58.632 3534 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.12 % Favored : 92.50 % Rotamer: Outliers : 0.05 % Allowed : 2.13 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.17), residues: 2361 helix: 0.75 (0.38), residues: 162 sheet: -0.43 (0.18), residues: 735 loop : -0.47 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG P 94 TYR 0.040 0.003 TYR H 55 PHE 0.049 0.002 PHE L 91 TRP 0.055 0.002 TRP L 35 HIS 0.006 0.001 HIS U 90 Details of bonding type rmsd covalent geometry : bond 0.00342 (19710) covalent geometry : angle 0.74323 (26739) SS BOND : bond 0.00642 ( 27) SS BOND : angle 1.53157 ( 54) hydrogen bonds : bond 0.04307 ( 660) hydrogen bonds : angle 6.50097 ( 1710) link_ALPHA1-3 : bond 0.00968 ( 6) link_ALPHA1-3 : angle 1.29700 ( 18) link_ALPHA1-6 : bond 0.01071 ( 3) link_ALPHA1-6 : angle 1.72689 ( 9) link_BETA1-4 : bond 0.00446 ( 21) link_BETA1-4 : angle 1.73617 ( 63) link_NAG-ASN : bond 0.00095 ( 15) link_NAG-ASN : angle 2.26626 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 457 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8722 (p0) cc_final: 0.8342 (p0) REVERT: A 251 GLN cc_start: 0.9429 (mp10) cc_final: 0.9058 (pm20) REVERT: H 27 PHE cc_start: 0.6759 (t80) cc_final: 0.6343 (t80) REVERT: H 80 LEU cc_start: 0.9142 (tt) cc_final: 0.8889 (tt) REVERT: H 100 MET cc_start: 0.7040 (ttp) cc_final: 0.6546 (ttp) REVERT: L 104 LEU cc_start: 0.6468 (pp) cc_final: 0.6263 (pp) REVERT: C 64 LYS cc_start: 0.8825 (tttt) cc_final: 0.8524 (pttm) REVERT: C 75 ARG cc_start: 0.8850 (ttp-110) cc_final: 0.8541 (mtm110) REVERT: C 81 LYS cc_start: 0.8967 (tmtt) cc_final: 0.8762 (tptp) REVERT: C 82 ILE cc_start: 0.8478 (mt) cc_final: 0.8039 (mp) REVERT: C 100 MET cc_start: 0.8255 (ttm) cc_final: 0.7963 (ttm) REVERT: D 4 MET cc_start: 0.7901 (tpt) cc_final: 0.7589 (tpp) REVERT: D 18 ARG cc_start: 0.8776 (mmt-90) cc_final: 0.8258 (mmt-90) REVERT: D 71 PHE cc_start: 0.8230 (m-80) cc_final: 0.7880 (m-80) REVERT: D 78 MET cc_start: 0.7889 (ppp) cc_final: 0.7688 (ppp) REVERT: D 83 LEU cc_start: 0.8851 (mt) cc_final: 0.8338 (pt) REVERT: E 117 ASP cc_start: 0.8790 (p0) cc_final: 0.8408 (p0) REVERT: E 251 GLN cc_start: 0.9414 (mp10) cc_final: 0.9015 (pm20) REVERT: G 602 HIS cc_start: 0.7743 (t70) cc_final: 0.7324 (t-170) REVERT: P 61 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8678 (mm-30) REVERT: P 82 MET cc_start: 0.9074 (mmp) cc_final: 0.8054 (mmp) REVERT: P 86 ASP cc_start: 0.8617 (m-30) cc_final: 0.8390 (m-30) REVERT: P 91 TYR cc_start: 0.8471 (m-80) cc_final: 0.8259 (m-80) REVERT: P 98 ASN cc_start: 0.8414 (p0) cc_final: 0.8036 (p0) REVERT: T 13 VAL cc_start: 0.9064 (m) cc_final: 0.8665 (p) REVERT: T 21 ILE cc_start: 0.9485 (mp) cc_final: 0.9275 (mp) REVERT: T 83 PHE cc_start: 0.8341 (m-10) cc_final: 0.8109 (m-10) REVERT: T 87 TYR cc_start: 0.7797 (m-80) cc_final: 0.6986 (m-80) REVERT: J 64 LYS cc_start: 0.9149 (tttt) cc_final: 0.8830 (tptp) REVERT: J 75 ARG cc_start: 0.8826 (ttp-110) cc_final: 0.8266 (mtm110) REVERT: J 81 LYS cc_start: 0.8981 (tmtt) cc_final: 0.8736 (tptp) REVERT: J 82 ASN cc_start: 0.8896 (t0) cc_final: 0.8694 (m110) REVERT: N 38 GLN cc_start: 0.8185 (tt0) cc_final: 0.7772 (tt0) REVERT: N 78 MET cc_start: 0.8321 (ppp) cc_final: 0.8079 (ppp) REVERT: N 83 LEU cc_start: 0.8689 (mt) cc_final: 0.7908 (pt) REVERT: F 69 ASN cc_start: 0.9030 (t0) cc_final: 0.8813 (t0) REVERT: F 251 GLN cc_start: 0.9409 (mp10) cc_final: 0.8916 (pm20) REVERT: I 550 ASN cc_start: 0.8627 (t0) cc_final: 0.8240 (t0) REVERT: I 602 HIS cc_start: 0.8266 (t70) cc_final: 0.7779 (t-170) REVERT: Q 12 MET cc_start: 0.8109 (ptm) cc_final: 0.7842 (pmm) REVERT: Q 98 ASN cc_start: 0.8434 (p0) cc_final: 0.8081 (p0) REVERT: U 13 VAL cc_start: 0.9091 (m) cc_final: 0.8799 (p) REVERT: U 35 TRP cc_start: 0.8040 (m100) cc_final: 0.7736 (m100) REVERT: U 70 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8616 (pm20) REVERT: M 19 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8302 (mmmm) REVERT: M 46 GLU cc_start: 0.8854 (tp30) cc_final: 0.8492 (tp30) REVERT: M 75 ARG cc_start: 0.8996 (ttp-110) cc_final: 0.8697 (mtm110) REVERT: M 81 LYS cc_start: 0.9017 (tmtt) cc_final: 0.8706 (tptp) REVERT: O 17 ASP cc_start: 0.6863 (m-30) cc_final: 0.6315 (m-30) REVERT: O 44 PRO cc_start: 0.8897 (Cg_endo) cc_final: 0.8417 (Cg_exo) REVERT: O 85 ASP cc_start: 0.8353 (t0) cc_final: 0.8137 (t0) REVERT: O 87 PHE cc_start: 0.7964 (m-80) cc_final: 0.7255 (m-80) REVERT: O 103 LYS cc_start: 0.8381 (mppt) cc_final: 0.8119 (mmtt) REVERT: O 104 LEU cc_start: 0.8577 (mp) cc_final: 0.8207 (mt) outliers start: 1 outliers final: 0 residues processed: 457 average time/residue: 0.1383 time to fit residues: 96.2556 Evaluate side-chains 339 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 100 optimal weight: 0.0670 chunk 79 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 174 optimal weight: 0.6980 chunk 182 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 104 optimal weight: 0.0010 overall best weight: 0.5326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN P 81 GLN ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS F 44 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.068677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.053342 restraints weight = 101046.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.054860 restraints weight = 58028.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055848 restraints weight = 39901.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.056496 restraints weight = 31176.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.056837 restraints weight = 26644.604| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19782 Z= 0.139 Angle : 0.756 11.973 26928 Z= 0.379 Chirality : 0.047 0.263 3039 Planarity : 0.005 0.119 3372 Dihedral : 8.056 58.426 3534 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.45 % Favored : 92.16 % Rotamer: Outliers : 0.05 % Allowed : 1.19 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.17), residues: 2361 helix: 0.50 (0.36), residues: 162 sheet: -0.45 (0.18), residues: 789 loop : -0.48 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG Q 94 TYR 0.051 0.002 TYR F 232 PHE 0.052 0.002 PHE L 91 TRP 0.044 0.002 TRP T 35 HIS 0.005 0.001 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00295 (19710) covalent geometry : angle 0.74546 (26739) SS BOND : bond 0.00351 ( 27) SS BOND : angle 1.37049 ( 54) hydrogen bonds : bond 0.04309 ( 660) hydrogen bonds : angle 6.35606 ( 1710) link_ALPHA1-3 : bond 0.01069 ( 6) link_ALPHA1-3 : angle 1.07054 ( 18) link_ALPHA1-6 : bond 0.01290 ( 3) link_ALPHA1-6 : angle 0.90136 ( 9) link_BETA1-4 : bond 0.00475 ( 21) link_BETA1-4 : angle 1.72019 ( 63) link_NAG-ASN : bond 0.00280 ( 15) link_NAG-ASN : angle 2.18839 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 489 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8775 (p0) cc_final: 0.8480 (p0) REVERT: A 251 GLN cc_start: 0.9394 (mp10) cc_final: 0.9030 (pm20) REVERT: B 582 PHE cc_start: 0.8655 (m-80) cc_final: 0.8172 (m-10) REVERT: H 18 MET cc_start: 0.8659 (tmm) cc_final: 0.8436 (tmm) REVERT: H 61 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8707 (mm-30) REVERT: L 83 PHE cc_start: 0.7861 (m-80) cc_final: 0.7573 (m-10) REVERT: L 91 PHE cc_start: 0.6285 (m-80) cc_final: 0.5716 (m-10) REVERT: C 37 PHE cc_start: 0.6467 (p90) cc_final: 0.5568 (p90) REVERT: C 64 LYS cc_start: 0.8831 (tttt) cc_final: 0.8531 (pttm) REVERT: C 75 ARG cc_start: 0.8774 (ttp-110) cc_final: 0.8480 (mtm110) REVERT: C 81 LYS cc_start: 0.8943 (tmtt) cc_final: 0.8735 (tptp) REVERT: C 82 ILE cc_start: 0.8494 (mt) cc_final: 0.8046 (mp) REVERT: C 100 MET cc_start: 0.8115 (ttm) cc_final: 0.7537 (mtp) REVERT: D 4 MET cc_start: 0.7695 (tpt) cc_final: 0.7372 (tpp) REVERT: D 18 ARG cc_start: 0.8611 (mmt-90) cc_final: 0.8260 (mmt-90) REVERT: D 45 LYS cc_start: 0.9072 (ptpp) cc_final: 0.8836 (ptpp) REVERT: D 71 PHE cc_start: 0.8383 (m-80) cc_final: 0.8061 (m-80) REVERT: D 83 LEU cc_start: 0.8794 (mt) cc_final: 0.8357 (pt) REVERT: E 117 ASP cc_start: 0.8812 (p0) cc_final: 0.8415 (p0) REVERT: E 251 GLN cc_start: 0.9379 (mp10) cc_final: 0.9005 (pm20) REVERT: G 543 TYR cc_start: 0.8554 (m-80) cc_final: 0.8339 (m-80) REVERT: G 582 PHE cc_start: 0.8595 (m-80) cc_final: 0.7600 (m-80) REVERT: P 34 MET cc_start: 0.8748 (tpp) cc_final: 0.8398 (tpp) REVERT: P 98 ASN cc_start: 0.8178 (p0) cc_final: 0.7845 (p0) REVERT: T 13 VAL cc_start: 0.8861 (m) cc_final: 0.8471 (p) REVERT: J 46 GLU cc_start: 0.8659 (tp30) cc_final: 0.8264 (tp30) REVERT: J 64 LYS cc_start: 0.9095 (tttt) cc_final: 0.8727 (tptp) REVERT: J 75 ARG cc_start: 0.8805 (ttp-110) cc_final: 0.8505 (mtm110) REVERT: J 79 PHE cc_start: 0.8358 (m-80) cc_final: 0.7971 (m-80) REVERT: J 81 LYS cc_start: 0.9047 (tmtt) cc_final: 0.8806 (tptp) REVERT: N 83 LEU cc_start: 0.8532 (mt) cc_final: 0.7554 (pt) REVERT: N 105 GLU cc_start: 0.5896 (tt0) cc_final: 0.5689 (tt0) REVERT: F 117 ASP cc_start: 0.8714 (p0) cc_final: 0.8163 (p0) REVERT: F 251 GLN cc_start: 0.9379 (mp10) cc_final: 0.9102 (mm-40) REVERT: I 550 ASN cc_start: 0.8643 (t0) cc_final: 0.8178 (t0) REVERT: Q 43 LYS cc_start: 0.9166 (mmtt) cc_final: 0.8832 (pttt) REVERT: Q 98 ASN cc_start: 0.8171 (p0) cc_final: 0.7785 (p0) REVERT: Q 100 MET cc_start: 0.7495 (ttp) cc_final: 0.7289 (ttp) REVERT: U 13 VAL cc_start: 0.9038 (m) cc_final: 0.8726 (p) REVERT: U 39 LYS cc_start: 0.8957 (mttm) cc_final: 0.8574 (mttm) REVERT: U 83 PHE cc_start: 0.8292 (m-80) cc_final: 0.7894 (m-80) REVERT: M 19 LYS cc_start: 0.8478 (mmmt) cc_final: 0.8274 (mmmm) REVERT: M 43 LYS cc_start: 0.8412 (ptpp) cc_final: 0.8207 (mmmt) REVERT: M 46 GLU cc_start: 0.8871 (tp30) cc_final: 0.8475 (tp30) REVERT: M 75 ARG cc_start: 0.8955 (ttp-110) cc_final: 0.8651 (mtm110) REVERT: M 81 LYS cc_start: 0.8986 (tmtt) cc_final: 0.8679 (tptp) REVERT: O 11 LEU cc_start: 0.9485 (tt) cc_final: 0.9276 (tt) REVERT: O 17 ASP cc_start: 0.6786 (m-30) cc_final: 0.6346 (m-30) REVERT: O 44 PRO cc_start: 0.8799 (Cg_endo) cc_final: 0.8379 (Cg_exo) REVERT: O 78 MET cc_start: 0.7799 (ppp) cc_final: 0.7503 (ppp) REVERT: O 83 LEU cc_start: 0.8659 (mt) cc_final: 0.8094 (pt) REVERT: O 85 ASP cc_start: 0.8402 (t0) cc_final: 0.8150 (t0) REVERT: O 87 PHE cc_start: 0.8051 (m-80) cc_final: 0.7378 (m-80) outliers start: 1 outliers final: 1 residues processed: 489 average time/residue: 0.1288 time to fit residues: 96.4694 Evaluate side-chains 364 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 176 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 130 optimal weight: 30.0000 chunk 84 optimal weight: 0.0170 chunk 194 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 chunk 189 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN B 602 HIS B 613 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN E 44 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 HIS M 100BASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.068173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.053091 restraints weight = 102603.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.054639 restraints weight = 58425.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.055655 restraints weight = 39798.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.056316 restraints weight = 30869.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.056738 restraints weight = 26159.835| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19782 Z= 0.145 Angle : 0.760 11.901 26928 Z= 0.385 Chirality : 0.047 0.238 3039 Planarity : 0.005 0.070 3372 Dihedral : 7.581 58.037 3534 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.62 % Favored : 92.04 % Rotamer: Outliers : 0.05 % Allowed : 0.40 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.17), residues: 2361 helix: 0.57 (0.37), residues: 162 sheet: -0.51 (0.18), residues: 801 loop : -0.55 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 94 TYR 0.036 0.002 TYR U 87 PHE 0.056 0.003 PHE L 91 TRP 0.082 0.003 TRP L 35 HIS 0.005 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00316 (19710) covalent geometry : angle 0.74984 (26739) SS BOND : bond 0.00376 ( 27) SS BOND : angle 1.39008 ( 54) hydrogen bonds : bond 0.04321 ( 660) hydrogen bonds : angle 6.26796 ( 1710) link_ALPHA1-3 : bond 0.01082 ( 6) link_ALPHA1-3 : angle 1.08789 ( 18) link_ALPHA1-6 : bond 0.01428 ( 3) link_ALPHA1-6 : angle 1.47754 ( 9) link_BETA1-4 : bond 0.00517 ( 21) link_BETA1-4 : angle 1.69596 ( 63) link_NAG-ASN : bond 0.00208 ( 15) link_NAG-ASN : angle 2.10902 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 458 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8775 (p0) cc_final: 0.8468 (p0) REVERT: A 251 GLN cc_start: 0.9406 (mp10) cc_final: 0.9030 (pm20) REVERT: B 582 PHE cc_start: 0.8515 (m-80) cc_final: 0.7639 (m-80) REVERT: H 18 MET cc_start: 0.8713 (tmm) cc_final: 0.8482 (tmm) REVERT: H 61 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8728 (mm-30) REVERT: H 69 ILE cc_start: 0.9272 (mm) cc_final: 0.9003 (mm) REVERT: H 80 LEU cc_start: 0.8894 (tt) cc_final: 0.8051 (tp) REVERT: H 82 MET cc_start: 0.8846 (mmp) cc_final: 0.8308 (mmp) REVERT: H 94 ARG cc_start: 0.7217 (tpt-90) cc_final: 0.6717 (tpp80) REVERT: L 83 PHE cc_start: 0.7793 (m-80) cc_final: 0.7431 (m-10) REVERT: L 96 TYR cc_start: 0.8352 (m-80) cc_final: 0.7928 (m-10) REVERT: C 64 LYS cc_start: 0.8843 (tttt) cc_final: 0.8561 (pttm) REVERT: C 75 ARG cc_start: 0.8768 (ttp-110) cc_final: 0.8474 (mtm110) REVERT: C 81 LYS cc_start: 0.8993 (tmtt) cc_final: 0.8745 (tptp) REVERT: C 82 ILE cc_start: 0.8499 (mt) cc_final: 0.8067 (mp) REVERT: C 86 ASP cc_start: 0.7771 (m-30) cc_final: 0.7435 (m-30) REVERT: D 4 MET cc_start: 0.7576 (tpt) cc_final: 0.7291 (tpp) REVERT: D 18 ARG cc_start: 0.8652 (mmt-90) cc_final: 0.8319 (mmt-90) REVERT: D 71 PHE cc_start: 0.8319 (m-80) cc_final: 0.8007 (m-80) REVERT: D 83 LEU cc_start: 0.8796 (mt) cc_final: 0.8358 (pt) REVERT: E 117 ASP cc_start: 0.8803 (p0) cc_final: 0.8384 (p0) REVERT: E 251 GLN cc_start: 0.9409 (mp10) cc_final: 0.9018 (pm20) REVERT: G 582 PHE cc_start: 0.8451 (m-80) cc_final: 0.8037 (m-80) REVERT: G 602 HIS cc_start: 0.8080 (t-170) cc_final: 0.7799 (t-170) REVERT: P 34 MET cc_start: 0.8713 (tpp) cc_final: 0.8325 (tpp) REVERT: P 48 VAL cc_start: 0.9132 (t) cc_final: 0.8612 (t) REVERT: P 86 ASP cc_start: 0.8572 (m-30) cc_final: 0.8366 (m-30) REVERT: P 98 ASN cc_start: 0.8218 (p0) cc_final: 0.7932 (p0) REVERT: T 39 LYS cc_start: 0.9052 (mttm) cc_final: 0.8838 (mmtt) REVERT: T 83 PHE cc_start: 0.8250 (m-80) cc_final: 0.7865 (m-10) REVERT: J 37 PHE cc_start: 0.5126 (p90) cc_final: 0.4242 (p90) REVERT: J 64 LYS cc_start: 0.9113 (tttt) cc_final: 0.8759 (tptp) REVERT: J 75 ARG cc_start: 0.8808 (ttp-110) cc_final: 0.8524 (mtm110) REVERT: J 81 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8872 (tptp) REVERT: J 86 ASP cc_start: 0.8271 (m-30) cc_final: 0.7769 (m-30) REVERT: N 83 LEU cc_start: 0.8627 (mt) cc_final: 0.7821 (pt) REVERT: N 98 PHE cc_start: 0.6603 (p90) cc_final: 0.6162 (p90) REVERT: F 251 GLN cc_start: 0.9374 (mp10) cc_final: 0.9123 (mm-40) REVERT: I 534 TYR cc_start: 0.8530 (t80) cc_final: 0.8230 (t80) REVERT: I 550 ASN cc_start: 0.8625 (t0) cc_final: 0.8160 (t0) REVERT: Q 43 LYS cc_start: 0.9272 (mmtt) cc_final: 0.8772 (pttt) REVERT: Q 80 LEU cc_start: 0.9280 (tt) cc_final: 0.9027 (tt) REVERT: Q 98 ASN cc_start: 0.8079 (p0) cc_final: 0.7650 (p0) REVERT: U 13 VAL cc_start: 0.9171 (m) cc_final: 0.8865 (p) REVERT: U 35 TRP cc_start: 0.7475 (m100) cc_final: 0.7094 (m100) REVERT: U 39 LYS cc_start: 0.8560 (mttm) cc_final: 0.8294 (mmtp) REVERT: U 83 PHE cc_start: 0.8393 (m-80) cc_final: 0.7842 (m-10) REVERT: M 19 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8249 (mmmm) REVERT: M 46 GLU cc_start: 0.8768 (tp30) cc_final: 0.8234 (tp30) REVERT: M 75 ARG cc_start: 0.8945 (ttp-110) cc_final: 0.8659 (mtm110) REVERT: M 81 LYS cc_start: 0.8962 (tmtt) cc_final: 0.8664 (tptp) REVERT: O 17 ASP cc_start: 0.7111 (m-30) cc_final: 0.6676 (m-30) REVERT: O 44 PRO cc_start: 0.8709 (Cg_endo) cc_final: 0.8202 (Cg_exo) REVERT: O 78 MET cc_start: 0.7868 (ppp) cc_final: 0.7590 (ppp) REVERT: O 83 LEU cc_start: 0.8784 (mt) cc_final: 0.8206 (pt) REVERT: O 85 ASP cc_start: 0.8386 (t0) cc_final: 0.8139 (t0) REVERT: O 87 PHE cc_start: 0.8096 (m-80) cc_final: 0.7412 (m-80) outliers start: 1 outliers final: 0 residues processed: 459 average time/residue: 0.1355 time to fit residues: 95.0109 Evaluate side-chains 350 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 132 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 232 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100BASN N 37 GLN N 79 GLN F 73 ASN ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 613 HIS ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100BASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.065752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050560 restraints weight = 105329.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.051960 restraints weight = 62182.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052909 restraints weight = 43388.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.053518 restraints weight = 34168.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053903 restraints weight = 29312.200| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.6792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19782 Z= 0.218 Angle : 0.817 13.407 26928 Z= 0.415 Chirality : 0.047 0.235 3039 Planarity : 0.005 0.082 3372 Dihedral : 7.602 57.402 3534 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.67 % Favored : 91.95 % Rotamer: Outliers : 0.10 % Allowed : 0.50 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.17), residues: 2361 helix: 0.78 (0.39), residues: 162 sheet: -0.47 (0.18), residues: 792 loop : -0.63 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG Q 94 TYR 0.024 0.003 TYR T 36 PHE 0.044 0.002 PHE P 27 TRP 0.057 0.004 TRP P 47 HIS 0.009 0.001 HIS U 90 Details of bonding type rmsd covalent geometry : bond 0.00482 (19710) covalent geometry : angle 0.80554 (26739) SS BOND : bond 0.00533 ( 27) SS BOND : angle 1.66568 ( 54) hydrogen bonds : bond 0.04497 ( 660) hydrogen bonds : angle 6.41261 ( 1710) link_ALPHA1-3 : bond 0.01154 ( 6) link_ALPHA1-3 : angle 1.32642 ( 18) link_ALPHA1-6 : bond 0.01403 ( 3) link_ALPHA1-6 : angle 1.96336 ( 9) link_BETA1-4 : bond 0.00487 ( 21) link_BETA1-4 : angle 1.66660 ( 63) link_NAG-ASN : bond 0.00249 ( 15) link_NAG-ASN : angle 2.27422 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 411 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8938 (p0) cc_final: 0.8699 (p0) REVERT: A 251 GLN cc_start: 0.9451 (mp10) cc_final: 0.9113 (pm20) REVERT: B 565 THR cc_start: 0.9353 (m) cc_final: 0.9050 (p) REVERT: H 61 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8708 (mm-30) REVERT: H 80 LEU cc_start: 0.8818 (tt) cc_final: 0.8557 (tp) REVERT: H 91 TYR cc_start: 0.8536 (m-80) cc_final: 0.8016 (m-80) REVERT: L 70 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8507 (pm20) REVERT: L 83 PHE cc_start: 0.8210 (m-80) cc_final: 0.7966 (m-10) REVERT: C 64 LYS cc_start: 0.8962 (tttt) cc_final: 0.8673 (pttm) REVERT: C 75 ARG cc_start: 0.8833 (ttp-110) cc_final: 0.8511 (mtm110) REVERT: C 81 LYS cc_start: 0.8974 (tmtt) cc_final: 0.8761 (tptp) REVERT: C 82 ILE cc_start: 0.8442 (mt) cc_final: 0.8003 (mp) REVERT: D 17 ASP cc_start: 0.6952 (m-30) cc_final: 0.6750 (m-30) REVERT: D 83 LEU cc_start: 0.8879 (mt) cc_final: 0.8471 (pt) REVERT: E 117 ASP cc_start: 0.8999 (p0) cc_final: 0.8589 (p0) REVERT: E 251 GLN cc_start: 0.9524 (mp10) cc_final: 0.9137 (pm20) REVERT: P 82 MET cc_start: 0.8969 (mmp) cc_final: 0.8724 (mmm) REVERT: P 91 TYR cc_start: 0.8618 (m-80) cc_final: 0.8186 (m-80) REVERT: P 98 ASN cc_start: 0.8362 (p0) cc_final: 0.8010 (p0) REVERT: T 39 LYS cc_start: 0.9052 (mttm) cc_final: 0.8615 (mmtt) REVERT: T 83 PHE cc_start: 0.8172 (m-80) cc_final: 0.7819 (m-10) REVERT: J 46 GLU cc_start: 0.8712 (tp30) cc_final: 0.8367 (tp30) REVERT: J 64 LYS cc_start: 0.9127 (tttt) cc_final: 0.8732 (tptp) REVERT: J 75 ARG cc_start: 0.8810 (ttp-110) cc_final: 0.8266 (mtm110) REVERT: J 81 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8811 (tptp) REVERT: N 105 GLU cc_start: 0.5889 (tt0) cc_final: 0.5556 (tt0) REVERT: F 69 ASN cc_start: 0.9078 (t0) cc_final: 0.8877 (t0) REVERT: F 251 GLN cc_start: 0.9427 (mp10) cc_final: 0.9166 (mm-40) REVERT: Q 43 LYS cc_start: 0.9314 (mmtt) cc_final: 0.8769 (pttt) REVERT: Q 80 LEU cc_start: 0.9311 (tt) cc_final: 0.9044 (tt) REVERT: Q 98 ASN cc_start: 0.8356 (p0) cc_final: 0.8038 (p0) REVERT: U 83 PHE cc_start: 0.8434 (m-80) cc_final: 0.8042 (m-10) REVERT: M 19 LYS cc_start: 0.8585 (mmmt) cc_final: 0.8323 (mmmm) REVERT: M 46 GLU cc_start: 0.8845 (tp30) cc_final: 0.8396 (tp30) REVERT: M 75 ARG cc_start: 0.9039 (ttp-110) cc_final: 0.8724 (mtm110) REVERT: M 81 LYS cc_start: 0.8976 (tmtt) cc_final: 0.8671 (tptp) REVERT: O 17 ASP cc_start: 0.6798 (m-30) cc_final: 0.6371 (m-30) REVERT: O 38 GLN cc_start: 0.7936 (tt0) cc_final: 0.7436 (tt0) REVERT: O 78 MET cc_start: 0.7911 (ppp) cc_final: 0.7567 (ppp) REVERT: O 83 LEU cc_start: 0.8766 (mt) cc_final: 0.8291 (pt) REVERT: O 85 ASP cc_start: 0.8557 (t0) cc_final: 0.8350 (t0) REVERT: O 87 PHE cc_start: 0.8085 (m-80) cc_final: 0.7491 (m-80) REVERT: O 103 LYS cc_start: 0.8257 (mppt) cc_final: 0.8010 (mmtt) outliers start: 2 outliers final: 0 residues processed: 412 average time/residue: 0.1351 time to fit residues: 86.0175 Evaluate side-chains 319 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 50 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 232 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN J 100BASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 516 HIS ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.065160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.049569 restraints weight = 101373.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.050955 restraints weight = 59802.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.051859 restraints weight = 42048.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.052432 restraints weight = 33287.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.052826 restraints weight = 28772.160| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19782 Z= 0.245 Angle : 0.833 10.830 26928 Z= 0.427 Chirality : 0.048 0.239 3039 Planarity : 0.006 0.101 3372 Dihedral : 7.848 56.614 3534 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.60 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.17), residues: 2361 helix: 0.74 (0.40), residues: 162 sheet: -0.61 (0.18), residues: 777 loop : -0.72 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 94 TYR 0.035 0.003 TYR O 36 PHE 0.051 0.003 PHE Q 27 TRP 0.050 0.003 TRP L 35 HIS 0.007 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00546 (19710) covalent geometry : angle 0.82029 (26739) SS BOND : bond 0.00608 ( 27) SS BOND : angle 1.80980 ( 54) hydrogen bonds : bond 0.04696 ( 660) hydrogen bonds : angle 6.55167 ( 1710) link_ALPHA1-3 : bond 0.00587 ( 6) link_ALPHA1-3 : angle 1.28414 ( 18) link_ALPHA1-6 : bond 0.00519 ( 3) link_ALPHA1-6 : angle 1.58420 ( 9) link_BETA1-4 : bond 0.00407 ( 21) link_BETA1-4 : angle 1.66186 ( 63) link_NAG-ASN : bond 0.00390 ( 15) link_NAG-ASN : angle 2.48392 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3199.09 seconds wall clock time: 56 minutes 21.70 seconds (3381.70 seconds total)