Starting phenix.real_space_refine on Sun Sep 13 00:02:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5kel_8240/09_2026/5kel_8240.cif Found real_map, /net/cci-nas-00/data/ceres_data/5kel_8240/09_2026/5kel_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_8240/09_2026/5kel_8240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5kel_8240/09_2026/5kel_8240.map" model { file = "/net/cci-nas-00/data/ceres_data/5kel_8240/09_2026/5kel_8240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5kel_8240/09_2026/5kel_8240.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5kel_8240/09_2026/5kel_8240.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5kel_8240/09_2026/5kel_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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: 3.86, per 1000 atoms: 0.20 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: 2.27 Conformation dependent library (CDL) restraints added in 860.4 milliseconds 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: 4.01 Time building geometry restraints manager: 2.79 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 - 17.39: 10727 17.39 - 34.77: 361 34.77 - 52.16: 102 52.16 - 69.55: 48 69.55 - 86.93: 27 Dihedral angle restraints: 11265 sinusoidal: 4419 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 11262 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: 1.500 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 19.730 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 11.368 86.932 6840 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 are 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/Z covalent geometry : bond 0.01456 / 0.91 (19710) covalent geometry : angle 1.81858 / 1.19 (26739) SS BOND : bond 0.08726 / 4.58 ( 27) SS BOND : angle 3.83029 / 2.66 ( 54) hydrogen bonds : bond 0.16709 / 10.90 ( 660) hydrogen bonds : angle 10.74925 / 7.45 ( 1710) link_ALPHA1-3 : bond 0.00087 / 0.04 ( 6) link_ALPHA1-3 : angle 4.95574 / 3.66 ( 18) link_ALPHA1-6 : bond 0.03477 / 1.61 ( 3) link_ALPHA1-6 : angle 9.86899 / 5.16 ( 9) link_BETA1-4 : bond 0.00335 / 0.24 ( 21) link_BETA1-4 : angle 2.81358 / 1.53 ( 63) link_NAG-ASN : bond 0.02210 / 1.36 ( 15) link_NAG-ASN : angle 9.76404 / 6.53 ( 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 : 0.745 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: 0.8762 (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: 0.7405 (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: 0.5825 (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: 0.8820 (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: 0.1549 time to fit residues: 178.2738 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 : 0.740 ------------------------------------------------------------------------------- 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... 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 = 0.3546 r_free = 0.3546 target = 0.069002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054168 restraints weight = 102432.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.055677 restraints weight = 59441.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.056654 restraints weight = 41241.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.057300 restraints weight = 32612.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.057686 restraints weight = 27961.692| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 19782 Z= 0.241 Angle : 0.951 14.159 26928 Z= 0.493 Chirality : 0.051 0.290 3039 Planarity : 0.008 0.106 3372 Dihedral : 6.702 57.015 2625 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.25 % Favored : 94.24 % Rotamer: Outliers : 0.05 % Allowed : 2.03 % Favored : 97.92 % 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 are not related in a simple way. whole: 0.69 (0.17), residues: 2361 helix: 0.56 (0.37), residues: 144 sheet: -0.13 (0.18), residues: 666 loop : 0.91 (0.17), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Q 94 TYR 0.037 0.003 TYR O 36 PHE 0.020 0.003 PHE F 88 TRP 0.026 0.003 TRP U 35 HIS 0.011 0.002 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.24 (19710) covalent geometry : angle 0.92864 / 0.49 (26739) SS BOND : bond 0.00720 / 0.42 ( 27) SS BOND : angle 1.88791 / 1.27 ( 54) hydrogen bonds : bond 0.05594 / 3.73 ( 660) hydrogen bonds : angle 8.29973 / 5.91 ( 1710) link_ALPHA1-3 : bond 0.00858 / 0.44 ( 6) link_ALPHA1-3 : angle 1.57130 / 1.12 ( 18) link_ALPHA1-6 : bond 0.02058 / 1.00 ( 3) link_ALPHA1-6 : angle 2.39297 / 1.28 ( 9) link_BETA1-4 : bond 0.00456 / 0.26 ( 21) link_BETA1-4 : angle 2.15719 / 1.52 ( 63) link_NAG-ASN : bond 0.00194 / 0.12 ( 15) link_NAG-ASN : angle 3.92534 / 2.52 ( 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 574 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 573 time to evaluate : 0.777 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: A 75 VAL cc_start: 0.9502 (t) cc_final: 0.9177 (p) REVERT: A 251 GLN cc_start: 0.9277 (mp10) cc_final: 0.9036 (pm20) REVERT: B 582 PHE cc_start: 0.7973 (m-80) cc_final: 0.7702 (m-80) REVERT: H 2 VAL cc_start: 0.8145 (p) cc_final: 0.7717 (t) REVERT: H 18 MET cc_start: 0.8624 (tmm) cc_final: 0.8245 (tmm) REVERT: H 43 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8680 (pttm) REVERT: H 82 MET cc_start: 0.9172 (mtp) cc_final: 0.8877 (mtp) REVERT: L 13 VAL cc_start: 0.9390 (m) cc_final: 0.9170 (p) REVERT: L 98 PHE cc_start: 0.8678 (m-80) cc_final: 0.8094 (m-80) REVERT: C 53 TRP cc_start: 0.5956 (t-100) cc_final: 0.5752 (t-100) REVERT: C 64 LYS cc_start: 0.8898 (tttt) cc_final: 0.8546 (tptp) REVERT: C 69 ILE cc_start: 0.7509 (mt) cc_final: 0.7251 (mt) REVERT: C 75 ARG cc_start: 0.8806 (ttp-110) cc_final: 0.8386 (mtm110) REVERT: C 82 ILE cc_start: 0.7855 (mt) cc_final: 0.7582 (mp) REVERT: D 1 ASP cc_start: 0.8086 (m-30) cc_final: 0.7363 (p0) REVERT: D 44 PRO cc_start: 0.9068 (Cg_endo) cc_final: 0.8790 (Cg_exo) REVERT: D 54 ARG cc_start: 0.8322 (ptt90) cc_final: 0.7926 (ptt90) REVERT: E 35 LEU cc_start: 0.9188 (mp) cc_final: 0.8728 (mp) REVERT: E 75 VAL cc_start: 0.9398 (t) cc_final: 0.9125 (p) REVERT: E 251 GLN cc_start: 0.9282 (mp10) cc_final: 0.8980 (pm20) REVERT: G 555 ILE cc_start: 0.9522 (mm) cc_final: 0.9172 (tp) REVERT: G 588 LYS cc_start: 0.9148 (mmtt) cc_final: 0.8836 (mmtm) REVERT: G 602 HIS cc_start: 0.7718 (t70) cc_final: 0.7442 (t-170) REVERT: P 20 LEU cc_start: 0.9350 (tp) cc_final: 0.9126 (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: 0.9287 (p) REVERT: T 98 PHE cc_start: 0.8651 (m-80) cc_final: 0.8406 (m-80) REVERT: J 53 TRP cc_start: 0.5769 (t-100) cc_final: 0.5542 (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: 0.8325 (mtm110) REVERT: J 100 TYR cc_start: 0.7933 (t80) cc_final: 0.7496 (t80) REVERT: N 1 ASP cc_start: 0.8261 (m-30) cc_final: 0.7383 (p0) REVERT: N 8 PRO cc_start: 0.8322 (Cg_endo) cc_final: 0.7749 (Cg_exo) REVERT: N 48 ILE cc_start: 0.8849 (mt) cc_final: 0.8574 (mt) REVERT: F 69 ASN cc_start: 0.8758 (t0) cc_final: 0.8490 (t0) REVERT: F 75 VAL cc_start: 0.9460 (t) cc_final: 0.9217 (p) REVERT: F 223 THR cc_start: 0.9134 (m) cc_final: 0.8928 (m) REVERT: F 251 GLN cc_start: 0.9349 (mp10) cc_final: 0.8953 (pm20) REVERT: I 555 ILE cc_start: 0.9509 (mm) cc_final: 0.9133 (tp) REVERT: I 588 LYS cc_start: 0.9358 (mmtt) cc_final: 0.9133 (mmmm) REVERT: I 602 HIS cc_start: 0.7901 (t70) cc_final: 0.7614 (t-170) REVERT: Q 5 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8614 (tp40) REVERT: Q 32 TYR cc_start: 0.5155 (p90) cc_final: 0.4705 (p90) REVERT: Q 45 LEU cc_start: 0.8569 (tp) cc_final: 0.8343 (tp) REVERT: Q 46 GLU cc_start: 0.9104 (pt0) cc_final: 0.8809 (pm20) REVERT: U 87 TYR cc_start: 0.8800 (m-80) cc_final: 0.8566 (m-80) REVERT: M 20 LEU cc_start: 0.8826 (mp) cc_final: 0.8538 (mt) REVERT: M 27 PHE cc_start: 0.6341 (t80) cc_final: 0.5985 (t80) REVERT: M 53 TRP cc_start: 0.5888 (t-100) cc_final: 0.5665 (t-100) REVERT: M 77 GLN cc_start: 0.7591 (mt0) cc_final: 0.6549 (mt0) REVERT: O 1 ASP cc_start: 0.8379 (m-30) cc_final: 0.7503 (p0) REVERT: O 8 PRO cc_start: 0.8791 (Cg_endo) cc_final: 0.8218 (Cg_exo) REVERT: O 44 PRO cc_start: 0.8950 (Cg_endo) cc_final: 0.8708 (Cg_exo) REVERT: O 48 ILE cc_start: 0.8480 (mt) cc_final: 0.8121 (mt) outliers start: 1 outliers final: 0 residues processed: 574 average time/residue: 0.1496 time to fit residues: 129.9141 Evaluate side-chains 382 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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: 0.8980 chunk 134 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 144 optimal weight: 0.0060 chunk 96 optimal weight: 1.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 570 GLN B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN L 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.067972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053240 restraints weight = 105879.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.054833 restraints weight = 58475.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.055879 restraints weight = 39300.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056565 restraints weight = 30337.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.056977 restraints weight = 25639.341| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 19782 Z= 0.177 Angle : 0.829 12.572 26928 Z= 0.423 Chirality : 0.049 0.306 3039 Planarity : 0.006 0.141 3372 Dihedral : 6.323 52.464 2625 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.59 % Favored : 93.90 % Rotamer: Outliers : 0.15 % Allowed : 2.63 % Favored : 97.22 % 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 are not related in a simple way. whole: 0.11 (0.17), residues: 2361 helix: 0.67 (0.36), residues: 150 sheet: -0.29 (0.18), residues: 678 loop : 0.31 (0.17), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 94 TYR 0.029 0.003 TYR Q 32 PHE 0.027 0.002 PHE G 582 TRP 0.022 0.002 TRP H 103 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (19710) covalent geometry : angle 0.81297 / 0.42 (26739) SS BOND : bond 0.00499 / 0.31 ( 27) SS BOND : angle 1.39971 / 0.90 ( 54) hydrogen bonds : bond 0.04764 / 3.18 ( 660) hydrogen bonds : angle 7.39536 / 5.25 ( 1710) link_ALPHA1-3 : bond 0.00506 / 0.28 ( 6) link_ALPHA1-3 : angle 1.43561 / 1.03 ( 18) link_ALPHA1-6 : bond 0.01285 / 0.60 ( 3) link_ALPHA1-6 : angle 2.30966 / 1.22 ( 9) link_BETA1-4 : bond 0.00403 / 0.25 ( 21) link_BETA1-4 : angle 1.92346 / 1.34 ( 63) link_NAG-ASN : bond 0.00313 / 0.21 ( 15) link_NAG-ASN : angle 2.94798 / 1.91 ( 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 511 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 508 time to evaluate : 0.747 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: A 75 VAL cc_start: 0.9483 (t) cc_final: 0.9234 (p) REVERT: A 117 ASP cc_start: 0.8684 (p0) cc_final: 0.8430 (p0) REVERT: A 251 GLN cc_start: 0.9388 (mp10) cc_final: 0.9067 (pm20) REVERT: H 18 MET cc_start: 0.8512 (tmm) cc_final: 0.8096 (tmm) REVERT: H 43 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8613 (pttm) REVERT: H 46 GLU cc_start: 0.9090 (pt0) cc_final: 0.8704 (pt0) REVERT: H 51 ILE cc_start: 0.9139 (tp) cc_final: 0.8860 (tt) REVERT: H 82 MET cc_start: 0.9255 (mtp) cc_final: 0.9017 (mtp) REVERT: L 13 VAL cc_start: 0.9394 (m) cc_final: 0.9172 (p) REVERT: L 39 LYS cc_start: 0.9176 (mttm) cc_final: 0.8905 (mmtt) REVERT: L 83 PHE cc_start: 0.8455 (m-10) cc_final: 0.8153 (m-10) REVERT: C 64 LYS cc_start: 0.8916 (tttt) cc_final: 0.8567 (tptp) REVERT: C 75 ARG cc_start: 0.8844 (ttp-110) cc_final: 0.8400 (mtm110) REVERT: C 81 LYS cc_start: 0.8963 (tmtt) cc_final: 0.8744 (tptp) REVERT: C 82 ILE cc_start: 0.8248 (mt) cc_final: 0.7815 (mp) REVERT: C 100 MET cc_start: 0.8621 (ttm) cc_final: 0.8274 (ttm) REVERT: D 1 ASP cc_start: 0.8124 (m-30) cc_final: 0.7384 (p0) REVERT: D 36 TYR cc_start: 0.8458 (m-80) cc_final: 0.7257 (m-80) REVERT: D 44 PRO cc_start: 0.8984 (Cg_endo) cc_final: 0.8668 (Cg_exo) REVERT: D 54 ARG cc_start: 0.8360 (ptt90) cc_final: 0.8074 (ptm-80) REVERT: E 35 LEU cc_start: 0.9145 (mp) cc_final: 0.8868 (mm) REVERT: E 75 VAL cc_start: 0.9477 (t) cc_final: 0.9215 (p) REVERT: E 99 TYR cc_start: 0.8866 (p90) cc_final: 0.8570 (p90) REVERT: E 117 ASP cc_start: 0.8636 (p0) cc_final: 0.8402 (p0) REVERT: E 251 GLN cc_start: 0.9439 (mp10) cc_final: 0.9074 (pm20) REVERT: G 588 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8976 (mmtm) REVERT: G 602 HIS cc_start: 0.7862 (t70) cc_final: 0.7494 (t-170) REVERT: P 34 MET cc_start: 0.6788 (mmp) cc_final: 0.6518 (mmp) REVERT: P 80 LEU cc_start: 0.8831 (tt) cc_final: 0.8217 (tt) REVERT: T 13 VAL cc_start: 0.9414 (m) cc_final: 0.9085 (p) REVERT: T 39 LYS cc_start: 0.9072 (mttm) cc_final: 0.8600 (mmtt) REVERT: T 83 PHE cc_start: 0.8533 (m-10) cc_final: 0.7805 (m-10) REVERT: J 64 LYS cc_start: 0.8975 (tttt) cc_final: 0.8754 (tptt) REVERT: J 75 ARG cc_start: 0.8873 (ttp-110) cc_final: 0.8279 (mtm110) REVERT: J 82 ASN cc_start: 0.8934 (t0) cc_final: 0.8673 (m110) REVERT: J 100 TYR cc_start: 0.8139 (t80) cc_final: 0.7924 (t80) REVERT: J 100 MET cc_start: 0.8152 (ttm) cc_final: 0.7923 (ttm) REVERT: N 1 ASP cc_start: 0.8289 (m-30) cc_final: 0.7334 (p0) REVERT: N 44 PRO cc_start: 0.8748 (Cg_endo) cc_final: 0.8522 (Cg_exo) REVERT: N 47 LEU cc_start: 0.9259 (mt) cc_final: 0.9054 (mt) REVERT: F 251 GLN cc_start: 0.9458 (mp10) cc_final: 0.8986 (pm20) REVERT: I 555 ILE cc_start: 0.9419 (mm) cc_final: 0.8926 (tt) REVERT: I 602 HIS cc_start: 0.7921 (t70) cc_final: 0.7439 (t-170) REVERT: Q 5 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8571 (tp40) REVERT: Q 64 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8659 (ttmt) REVERT: Q 82 MET cc_start: 0.9004 (mtp) cc_final: 0.8697 (mtp) REVERT: U 35 TRP cc_start: 0.7985 (m100) cc_final: 0.7702 (m100) REVERT: U 83 PHE cc_start: 0.8195 (m-80) cc_final: 0.7961 (m-80) REVERT: U 87 TYR cc_start: 0.8737 (m-80) cc_final: 0.8318 (m-80) REVERT: M 27 PHE cc_start: 0.6563 (t80) cc_final: 0.6139 (t80) REVERT: M 46 GLU cc_start: 0.8713 (tp30) cc_final: 0.8437 (tp30) REVERT: M 81 LYS cc_start: 0.8985 (tmtt) cc_final: 0.8696 (tptp) REVERT: O 1 ASP cc_start: 0.8347 (m-30) cc_final: 0.7372 (p0) REVERT: O 44 PRO cc_start: 0.8982 (Cg_endo) cc_final: 0.8670 (Cg_exo) REVERT: O 85 ASP cc_start: 0.8461 (t0) cc_final: 0.8235 (t0) REVERT: O 104 LEU cc_start: 0.8517 (mp) cc_final: 0.8215 (mt) outliers start: 3 outliers final: 0 residues processed: 510 average time/residue: 0.1514 time to fit residues: 117.1826 Evaluate side-chains 364 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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: 9.9990 chunk 208 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 GLN B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS G 613 HIS ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 ASN T 37 GLN T 45 GLN I 567 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** M 77 GLN O 37 GLN O 42 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.066962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.051252 restraints weight = 100733.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.052609 restraints weight = 60587.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053459 restraints weight = 43443.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.054034 restraints weight = 35383.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.054344 restraints weight = 30957.763| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 19782 Z= 0.284 Angle : 0.887 12.260 26928 Z= 0.450 Chirality : 0.049 0.396 3039 Planarity : 0.006 0.090 3372 Dihedral : 6.204 37.696 2625 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.03 % Favored : 92.59 % Rotamer: Outliers : 0.15 % Allowed : 4.27 % Favored : 95.59 % 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 are not related in a simple way. whole: -0.45 (0.17), residues: 2361 helix: 0.54 (0.37), residues: 162 sheet: -0.55 (0.18), residues: 726 loop : -0.17 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 299 TYR 0.034 0.003 TYR H 99 PHE 0.058 0.003 PHE Q 27 TRP 0.025 0.003 TRP H 103 HIS 0.007 0.002 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.28 (19710) covalent geometry : angle 0.87247 / 0.45 (26739) SS BOND : bond 0.00727 / 0.49 ( 27) SS BOND : angle 1.68575 / 1.05 ( 54) hydrogen bonds : bond 0.04858 / 3.24 ( 660) hydrogen bonds : angle 7.26936 / 5.17 ( 1710) link_ALPHA1-3 : bond 0.00268 / 0.15 ( 6) link_ALPHA1-3 : angle 1.47947 / 0.90 ( 18) link_ALPHA1-6 : bond 0.00843 / 0.38 ( 3) link_ALPHA1-6 : angle 2.68992 / 1.41 ( 9) link_BETA1-4 : bond 0.00439 / 0.24 ( 21) link_BETA1-4 : angle 1.77019 / 1.26 ( 63) link_NAG-ASN : bond 0.00516 / 0.31 ( 15) link_NAG-ASN : angle 2.96911 / 1.86 ( 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 448 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 445 time to evaluate : 0.768 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 75 VAL cc_start: 0.9493 (t) cc_final: 0.9293 (p) REVERT: A 117 ASP cc_start: 0.8763 (p0) cc_final: 0.8496 (p0) REVERT: A 243 GLN cc_start: 0.8745 (mp10) cc_final: 0.8509 (mp10) REVERT: A 251 GLN cc_start: 0.9447 (mp10) cc_final: 0.9133 (pm20) REVERT: B 543 TYR cc_start: 0.8860 (m-80) cc_final: 0.8659 (m-80) REVERT: H 12 MET cc_start: 0.8708 (ttt) cc_final: 0.8433 (ttt) REVERT: H 18 MET cc_start: 0.8351 (tmm) cc_final: 0.8142 (tmm) REVERT: H 34 MET cc_start: 0.7114 (mmp) cc_final: 0.6720 (mmp) REVERT: H 100 MET cc_start: 0.7342 (ttp) cc_final: 0.6898 (ttp) REVERT: L 83 PHE cc_start: 0.8483 (m-10) cc_final: 0.8119 (m-10) REVERT: L 87 TYR cc_start: 0.8623 (m-80) cc_final: 0.8410 (m-80) REVERT: C 20 LEU cc_start: 0.8748 (mt) cc_final: 0.8537 (mt) REVERT: C 50 LEU cc_start: 0.9114 (tp) cc_final: 0.8885 (tp) REVERT: C 64 LYS cc_start: 0.8940 (tttt) cc_final: 0.8585 (tptp) REVERT: C 69 ILE cc_start: 0.7647 (mt) cc_final: 0.7442 (mt) REVERT: C 75 ARG cc_start: 0.8916 (ttp-110) cc_final: 0.8354 (mtm110) REVERT: C 81 LYS cc_start: 0.8935 (tmtt) cc_final: 0.8707 (tptp) REVERT: C 82 ILE cc_start: 0.8448 (mt) cc_final: 0.7984 (mp) REVERT: C 100 MET cc_start: 0.8456 (ttm) cc_final: 0.8179 (mtp) REVERT: D 17 ASP cc_start: 0.6639 (m-30) cc_final: 0.6226 (m-30) REVERT: D 36 TYR cc_start: 0.8816 (m-80) cc_final: 0.8004 (m-80) REVERT: D 44 PRO cc_start: 0.9033 (Cg_endo) cc_final: 0.8697 (Cg_exo) REVERT: D 83 LEU cc_start: 0.8796 (mt) cc_final: 0.8429 (pt) REVERT: D 103 LYS cc_start: 0.8280 (mppt) cc_final: 0.8008 (mmtm) REVERT: E 75 VAL cc_start: 0.9485 (t) cc_final: 0.9280 (p) REVERT: E 117 ASP cc_start: 0.8789 (p0) cc_final: 0.8502 (p0) REVERT: E 251 GLN cc_start: 0.9516 (mp10) cc_final: 0.9147 (pm20) REVERT: G 602 HIS cc_start: 0.7896 (t70) cc_final: 0.7418 (t-170) REVERT: P 5 GLN cc_start: 0.8843 (tp40) cc_final: 0.8374 (tp40) REVERT: P 100 MET cc_start: 0.7916 (ttp) cc_final: 0.7654 (ttt) REVERT: T 13 VAL cc_start: 0.9534 (m) cc_final: 0.9210 (p) REVERT: T 83 PHE cc_start: 0.8405 (m-10) cc_final: 0.7761 (m-10) REVERT: J 64 LYS cc_start: 0.9055 (tttt) cc_final: 0.8799 (tptp) REVERT: J 75 ARG cc_start: 0.8962 (ttp-110) cc_final: 0.8276 (mtm110) REVERT: J 82 ASN cc_start: 0.9022 (t0) cc_final: 0.8761 (m-40) REVERT: J 100 MET cc_start: 0.8252 (ttm) cc_final: 0.7884 (mtp) REVERT: N 36 TYR cc_start: 0.8380 (m-80) cc_final: 0.8116 (m-80) REVERT: N 44 PRO cc_start: 0.9012 (Cg_endo) cc_final: 0.8781 (Cg_exo) REVERT: N 82 ASP cc_start: 0.8636 (m-30) cc_final: 0.8415 (m-30) REVERT: F 251 GLN cc_start: 0.9495 (mp10) cc_final: 0.9068 (pm20) REVERT: I 602 HIS cc_start: 0.8039 (t70) cc_final: 0.7445 (t-170) REVERT: Q 45 LEU cc_start: 0.8771 (tp) cc_final: 0.8490 (tp) REVERT: Q 46 GLU cc_start: 0.9134 (pt0) cc_final: 0.8719 (pm20) REVERT: Q 64 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8663 (ttmt) REVERT: U 35 TRP cc_start: 0.8043 (m100) cc_final: 0.7657 (m100) REVERT: U 83 PHE cc_start: 0.8282 (m-80) cc_final: 0.7772 (m-80) REVERT: U 87 TYR cc_start: 0.8868 (m-80) cc_final: 0.8367 (m-80) REVERT: U 98 PHE cc_start: 0.8759 (m-80) cc_final: 0.8402 (m-80) REVERT: M 19 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8331 (mmmm) REVERT: M 27 PHE cc_start: 0.6749 (t80) cc_final: 0.6403 (t80) REVERT: M 46 GLU cc_start: 0.8909 (tp30) cc_final: 0.8597 (tp30) REVERT: M 75 ARG cc_start: 0.8924 (ttp-110) cc_final: 0.8668 (mtm110) REVERT: M 81 LYS cc_start: 0.8926 (tmtt) cc_final: 0.8521 (tptp) REVERT: O 44 PRO cc_start: 0.8890 (Cg_endo) cc_final: 0.8607 (Cg_exo) REVERT: O 85 ASP cc_start: 0.8385 (t0) cc_final: 0.8136 (t0) REVERT: O 104 LEU cc_start: 0.8546 (mp) cc_final: 0.8263 (mt) outliers start: 3 outliers final: 0 residues processed: 448 average time/residue: 0.1384 time to fit residues: 95.3349 Evaluate side-chains 325 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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: 0.9990 chunk 112 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 570 GLN B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN E 44 GLN P 81 GLN ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 514 ASN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 ASN U 45 GLN O 42 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.068229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.052279 restraints weight = 97888.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053673 restraints weight = 58677.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054584 restraints weight = 42047.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.055174 restraints weight = 33805.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.055507 restraints weight = 29449.975| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19782 Z= 0.190 Angle : 0.802 11.122 26928 Z= 0.408 Chirality : 0.048 0.383 3039 Planarity : 0.005 0.067 3372 Dihedral : 5.908 31.025 2625 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.03 % Favored : 92.59 % Rotamer: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % 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 are not related in a simple way. whole: -0.55 (0.17), residues: 2361 helix: 0.70 (0.37), residues: 162 sheet: -0.57 (0.18), residues: 741 loop : -0.29 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 94 TYR 0.030 0.003 TYR O 36 PHE 0.067 0.002 PHE H 27 TRP 0.024 0.002 TRP Q 103 HIS 0.006 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (19710) covalent geometry : angle 0.78841 / 0.41 (26739) SS BOND : bond 0.00515 / 0.34 ( 27) SS BOND : angle 1.73404 / 1.12 ( 54) hydrogen bonds : bond 0.04566 / 3.02 ( 660) hydrogen bonds : angle 6.87211 / 4.91 ( 1710) link_ALPHA1-3 : bond 0.00432 / 0.24 ( 6) link_ALPHA1-3 : angle 1.33807 / 0.94 ( 18) link_ALPHA1-6 : bond 0.00541 / 0.24 ( 3) link_ALPHA1-6 : angle 1.83733 / 0.97 ( 9) link_BETA1-4 : bond 0.00337 / 0.21 ( 21) link_BETA1-4 : angle 1.76768 / 1.24 ( 63) link_NAG-ASN : bond 0.00269 / 0.17 ( 15) link_NAG-ASN : angle 2.48788 / 1.54 ( 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 463 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 462 time to evaluate : 0.761 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: 0.8726 (p0) cc_final: 0.8405 (p0) REVERT: A 251 GLN cc_start: 0.9414 (mp10) cc_final: 0.9095 (pm20) REVERT: B 531 TRP cc_start: 0.6982 (m-10) cc_final: 0.6504 (m-10) REVERT: H 5 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8737 (mm-40) REVERT: H 18 MET cc_start: 0.8333 (tmm) cc_final: 0.8019 (tmm) REVERT: H 73 ASP cc_start: 0.8375 (m-30) cc_final: 0.7992 (m-30) REVERT: H 102 TYR cc_start: 0.7906 (m-80) cc_final: 0.7687 (m-80) REVERT: L 83 PHE cc_start: 0.8352 (m-10) cc_final: 0.7911 (m-10) REVERT: L 87 TYR cc_start: 0.8415 (m-80) cc_final: 0.8203 (m-80) REVERT: C 64 LYS cc_start: 0.8944 (tttt) cc_final: 0.8574 (tptp) REVERT: C 75 ARG cc_start: 0.8880 (ttp-110) cc_final: 0.8344 (mtm110) REVERT: C 81 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8764 (tptp) REVERT: D 4 MET cc_start: 0.7542 (tpt) cc_final: 0.7277 (tpp) REVERT: D 8 PRO cc_start: 0.8832 (Cg_exo) cc_final: 0.8483 (Cg_endo) REVERT: D 11 LEU cc_start: 0.9194 (mt) cc_final: 0.8964 (mt) REVERT: D 17 ASP cc_start: 0.6397 (m-30) cc_final: 0.6021 (m-30) REVERT: D 36 TYR cc_start: 0.8757 (m-80) cc_final: 0.7881 (m-80) REVERT: D 44 PRO cc_start: 0.9016 (Cg_endo) cc_final: 0.8597 (Cg_exo) REVERT: D 83 LEU cc_start: 0.8850 (mt) cc_final: 0.8377 (pt) REVERT: D 103 LYS cc_start: 0.8289 (mppt) cc_final: 0.7998 (mmtm) REVERT: E 75 VAL cc_start: 0.9475 (t) cc_final: 0.9254 (p) REVERT: E 117 ASP cc_start: 0.8856 (p0) cc_final: 0.8481 (p0) REVERT: E 251 GLN cc_start: 0.9465 (mp10) cc_final: 0.9090 (pm20) REVERT: G 543 TYR cc_start: 0.8732 (m-80) cc_final: 0.8426 (m-80) REVERT: G 588 LYS cc_start: 0.9353 (mmmt) cc_final: 0.9145 (mmtm) REVERT: G 602 HIS cc_start: 0.7879 (t70) cc_final: 0.7417 (t-170) REVERT: P 5 GLN cc_start: 0.8981 (tp40) cc_final: 0.8633 (tp40) REVERT: T 13 VAL cc_start: 0.9449 (m) cc_final: 0.9081 (p) REVERT: T 35 TRP cc_start: 0.7624 (m100) cc_final: 0.7411 (m100) REVERT: T 83 PHE cc_start: 0.8411 (m-10) cc_final: 0.8196 (m-10) REVERT: T 87 TYR cc_start: 0.8204 (m-80) cc_final: 0.7417 (m-80) REVERT: J 64 LYS cc_start: 0.9074 (tttt) cc_final: 0.8808 (tptp) REVERT: J 75 ARG cc_start: 0.9002 (ttp-110) cc_final: 0.8470 (mtm110) REVERT: J 79 PHE cc_start: 0.8462 (m-10) cc_final: 0.6389 (m-10) REVERT: J 82 ASN cc_start: 0.8993 (t0) cc_final: 0.8727 (m110) REVERT: N 36 TYR cc_start: 0.8269 (m-80) cc_final: 0.8016 (m-80) REVERT: N 44 PRO cc_start: 0.9048 (Cg_endo) cc_final: 0.8811 (Cg_exo) REVERT: N 82 ASP cc_start: 0.8565 (m-30) cc_final: 0.8322 (m-30) REVERT: N 83 LEU cc_start: 0.8801 (mt) cc_final: 0.8388 (pt) REVERT: N 87 PHE cc_start: 0.7919 (m-10) cc_final: 0.7702 (m-80) REVERT: F 251 GLN cc_start: 0.9400 (mp10) cc_final: 0.8969 (pm20) REVERT: I 567 GLN cc_start: 0.8234 (pp30) cc_final: 0.7629 (pp30) REVERT: I 602 HIS cc_start: 0.8047 (t70) cc_final: 0.7447 (t-170) REVERT: Q 5 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8476 (mp10) REVERT: Q 12 MET cc_start: 0.8186 (ptt) cc_final: 0.7439 (pmm) REVERT: Q 18 MET cc_start: 0.8191 (tmm) cc_final: 0.7577 (tmm) REVERT: Q 45 LEU cc_start: 0.8746 (tp) cc_final: 0.8422 (tp) REVERT: Q 46 GLU cc_start: 0.9012 (pt0) cc_final: 0.8701 (pm20) REVERT: Q 82 MET cc_start: 0.8845 (mtp) cc_final: 0.8641 (mtp) REVERT: Q 91 TYR cc_start: 0.8563 (m-80) cc_final: 0.8160 (m-80) REVERT: Q 100 MET cc_start: 0.7267 (ttp) cc_final: 0.6690 (tmm) REVERT: U 21 ILE cc_start: 0.9444 (mp) cc_final: 0.9226 (mp) REVERT: U 35 TRP cc_start: 0.7869 (m100) cc_final: 0.7529 (m100) REVERT: U 83 PHE cc_start: 0.8195 (m-80) cc_final: 0.7605 (m-80) REVERT: U 87 TYR cc_start: 0.8760 (m-80) cc_final: 0.8358 (m-80) REVERT: U 98 PHE cc_start: 0.8718 (m-80) cc_final: 0.8341 (m-10) REVERT: M 19 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8296 (mmmm) REVERT: M 27 PHE cc_start: 0.7145 (t80) cc_final: 0.6865 (t80) REVERT: M 75 ARG cc_start: 0.8879 (ttp-110) cc_final: 0.8479 (mtm110) REVERT: M 81 LYS cc_start: 0.8933 (tmtt) cc_final: 0.8639 (tptp) REVERT: M 82 ILE cc_start: 0.8425 (mm) cc_final: 0.7858 (mm) REVERT: O 44 PRO cc_start: 0.8781 (Cg_endo) cc_final: 0.8323 (Cg_exo) REVERT: O 85 ASP cc_start: 0.8343 (t0) cc_final: 0.8093 (t0) REVERT: O 87 PHE cc_start: 0.8007 (m-80) cc_final: 0.7454 (m-80) REVERT: O 104 LEU cc_start: 0.8529 (mp) cc_final: 0.8222 (mt) outliers start: 1 outliers final: 0 residues processed: 462 average time/residue: 0.1493 time to fit residues: 106.4057 Evaluate side-chains 340 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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: 0.2980 chunk 97 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 195 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN E 44 GLN ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS F 73 ASN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.066929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.051599 restraints weight = 102883.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.053138 restraints weight = 57667.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.054154 restraints weight = 39146.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054822 restraints weight = 30287.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055220 restraints weight = 25612.610| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19782 Z= 0.150 Angle : 0.757 9.570 26928 Z= 0.385 Chirality : 0.047 0.340 3039 Planarity : 0.005 0.069 3372 Dihedral : 5.684 37.878 2625 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.84 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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 are not related in a simple way. whole: -0.57 (0.17), residues: 2361 helix: 0.72 (0.37), residues: 162 sheet: -0.54 (0.18), residues: 747 loop : -0.34 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 89 TYR 0.034 0.003 TYR A 232 PHE 0.073 0.002 PHE H 27 TRP 0.021 0.002 TRP Q 103 HIS 0.005 0.001 HIS F 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (19710) covalent geometry : angle 0.74527 / 0.38 (26739) SS BOND : bond 0.00403 / 0.26 ( 27) SS BOND : angle 1.51819 / 0.92 ( 54) hydrogen bonds : bond 0.04325 / 2.87 ( 660) hydrogen bonds : angle 6.62022 / 4.73 ( 1710) link_ALPHA1-3 : bond 0.00477 / 0.26 ( 6) link_ALPHA1-3 : angle 1.31178 / 0.92 ( 18) link_ALPHA1-6 : bond 0.00520 / 0.24 ( 3) link_ALPHA1-6 : angle 1.65020 / 0.88 ( 9) link_BETA1-4 : bond 0.00351 / 0.22 ( 21) link_BETA1-4 : angle 1.67409 / 1.15 ( 63) link_NAG-ASN : bond 0.00256 / 0.16 ( 15) link_NAG-ASN : angle 2.16646 / 1.38 ( 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 470 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 0.800 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: A 117 ASP cc_start: 0.8785 (p0) cc_final: 0.8525 (p0) REVERT: A 251 GLN cc_start: 0.9392 (mp10) cc_final: 0.9017 (pm20) REVERT: B 531 TRP cc_start: 0.7000 (m-10) cc_final: 0.6700 (m-10) REVERT: B 570 GLN cc_start: 0.9224 (tp-100) cc_final: 0.9011 (tp-100) REVERT: C 20 LEU cc_start: 0.8724 (mp) cc_final: 0.8358 (mt) REVERT: C 64 LYS cc_start: 0.8899 (tttt) cc_final: 0.8487 (tptp) REVERT: C 75 ARG cc_start: 0.8897 (ttp-110) cc_final: 0.8582 (mtm110) REVERT: C 81 LYS cc_start: 0.9024 (tmtt) cc_final: 0.8785 (tptp) REVERT: C 82 ILE cc_start: 0.8412 (mt) cc_final: 0.7995 (mp) REVERT: D 4 MET cc_start: 0.7797 (tpt) cc_final: 0.7331 (tpp) REVERT: D 18 ARG cc_start: 0.8399 (mmt-90) cc_final: 0.8129 (mmp80) REVERT: D 36 TYR cc_start: 0.8660 (m-80) cc_final: 0.8416 (m-80) REVERT: D 71 PHE cc_start: 0.8387 (m-80) cc_final: 0.8002 (m-80) REVERT: D 83 LEU cc_start: 0.8703 (mt) cc_final: 0.8383 (pt) REVERT: D 103 LYS cc_start: 0.8347 (mppt) cc_final: 0.8047 (mmtm) REVERT: E 75 VAL cc_start: 0.9423 (t) cc_final: 0.9211 (p) REVERT: E 117 ASP cc_start: 0.8887 (p0) cc_final: 0.8547 (p0) REVERT: E 251 GLN cc_start: 0.9450 (mp10) cc_final: 0.9035 (pm20) REVERT: G 534 TYR cc_start: 0.8659 (t80) cc_final: 0.8429 (t80) REVERT: G 543 TYR cc_start: 0.8663 (m-80) cc_final: 0.8399 (m-80) REVERT: G 602 HIS cc_start: 0.7880 (t70) cc_final: 0.7419 (t-170) REVERT: P 5 GLN cc_start: 0.9005 (tp40) cc_final: 0.8741 (tp40) REVERT: P 12 MET cc_start: 0.8291 (ttp) cc_final: 0.8065 (ptm) REVERT: P 43 LYS cc_start: 0.9299 (mmtt) cc_final: 0.8818 (pttm) REVERT: P 61 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8757 (mm-30) REVERT: T 13 VAL cc_start: 0.8922 (m) cc_final: 0.8443 (p) REVERT: T 50 SER cc_start: 0.8706 (m) cc_final: 0.8415 (t) REVERT: T 83 PHE cc_start: 0.8387 (m-10) cc_final: 0.8120 (m-10) REVERT: J 64 LYS cc_start: 0.9147 (tttt) cc_final: 0.8816 (tptt) REVERT: J 75 ARG cc_start: 0.8881 (ttp-110) cc_final: 0.8550 (mtm110) REVERT: J 82 ASN cc_start: 0.8938 (t0) cc_final: 0.8703 (m-40) REVERT: N 44 PRO cc_start: 0.8899 (Cg_endo) cc_final: 0.8289 (Cg_exo) REVERT: F 117 ASP cc_start: 0.8846 (p0) cc_final: 0.8289 (p0) REVERT: F 251 GLN cc_start: 0.9482 (mp10) cc_final: 0.8960 (pm20) REVERT: I 550 ASN cc_start: 0.8613 (t0) cc_final: 0.8201 (t0) REVERT: I 567 GLN cc_start: 0.8171 (pp30) cc_final: 0.7608 (pp30) REVERT: I 602 HIS cc_start: 0.8014 (t70) cc_final: 0.7370 (t-170) REVERT: Q 5 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8501 (mp10) REVERT: Q 18 MET cc_start: 0.8288 (tmm) cc_final: 0.7985 (tmm) REVERT: Q 27 PHE cc_start: 0.6287 (t80) cc_final: 0.6018 (t80) REVERT: Q 45 LEU cc_start: 0.8684 (tp) cc_final: 0.8378 (tp) REVERT: Q 46 GLU cc_start: 0.9035 (pt0) cc_final: 0.8722 (pm20) REVERT: Q 91 TYR cc_start: 0.8571 (m-80) cc_final: 0.8203 (m-80) REVERT: U 13 VAL cc_start: 0.9265 (m) cc_final: 0.8963 (p) REVERT: U 35 TRP cc_start: 0.7791 (m100) cc_final: 0.7319 (m100) REVERT: U 83 PHE cc_start: 0.8245 (m-80) cc_final: 0.7941 (m-10) REVERT: U 87 TYR cc_start: 0.8586 (m-80) cc_final: 0.8307 (m-80) REVERT: U 98 PHE cc_start: 0.8723 (m-80) cc_final: 0.8327 (m-10) REVERT: M 19 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8293 (mmmm) REVERT: M 27 PHE cc_start: 0.7160 (t80) cc_final: 0.6960 (t80) REVERT: M 46 GLU cc_start: 0.8897 (tp30) cc_final: 0.8446 (tp30) REVERT: M 75 ARG cc_start: 0.9023 (ttp-110) cc_final: 0.8581 (mtm110) REVERT: M 81 LYS cc_start: 0.9028 (tmtt) cc_final: 0.8683 (tptp) REVERT: O 44 PRO cc_start: 0.8819 (Cg_endo) cc_final: 0.8372 (Cg_exo) REVERT: O 78 MET cc_start: 0.7579 (ppp) cc_final: 0.7371 (ppp) REVERT: O 85 ASP cc_start: 0.8492 (t0) cc_final: 0.8171 (t0) REVERT: O 87 PHE cc_start: 0.8055 (m-80) cc_final: 0.7488 (m-80) REVERT: O 104 LEU cc_start: 0.8659 (mp) cc_final: 0.8322 (mt) outliers start: 0 outliers final: 0 residues processed: 470 average time/residue: 0.1470 time to fit residues: 106.2691 Evaluate side-chains 344 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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: 0.6980 chunk 178 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 214 optimal weight: 9.9990 chunk 233 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 211 optimal weight: 0.3980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 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** O 42 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.068020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052441 restraints weight = 100863.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.053904 restraints weight = 58660.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054849 restraints weight = 40821.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055493 restraints weight = 32295.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055900 restraints weight = 27670.474| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19782 Z= 0.146 Angle : 0.742 9.510 26928 Z= 0.376 Chirality : 0.047 0.317 3039 Planarity : 0.005 0.072 3372 Dihedral : 5.561 42.035 2625 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.24 % Favored : 92.38 % Rotamer: Outliers : 0.10 % Allowed : 1.49 % Favored : 98.41 % 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 are not related in a simple way. whole: -0.56 (0.17), residues: 2361 helix: 0.71 (0.38), residues: 162 sheet: -0.42 (0.18), residues: 741 loop : -0.40 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 76 TYR 0.029 0.002 TYR H 32 PHE 0.068 0.002 PHE H 27 TRP 0.018 0.002 TRP Q 103 HIS 0.015 0.001 HIS U 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (19710) covalent geometry : angle 0.73048 / 0.37 (26739) SS BOND : bond 0.00423 / 0.26 ( 27) SS BOND : angle 1.45624 / 0.97 ( 54) hydrogen bonds : bond 0.04228 / 2.82 ( 660) hydrogen bonds : angle 6.48478 / 4.67 ( 1710) link_ALPHA1-3 : bond 0.00602 / 0.32 ( 6) link_ALPHA1-3 : angle 1.38442 / 0.95 ( 18) link_ALPHA1-6 : bond 0.00664 / 0.33 ( 3) link_ALPHA1-6 : angle 1.75035 / 0.94 ( 9) link_BETA1-4 : bond 0.00368 / 0.23 ( 21) link_BETA1-4 : angle 1.67096 / 1.13 ( 63) link_NAG-ASN : bond 0.00232 / 0.14 ( 15) link_NAG-ASN : angle 2.03744 / 1.32 ( 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 464 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 462 time to evaluate : 0.718 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: 0.8825 (p0) cc_final: 0.8605 (p0) REVERT: A 251 GLN cc_start: 0.9403 (mp10) cc_final: 0.9037 (pm20) REVERT: B 531 TRP cc_start: 0.7053 (m-10) cc_final: 0.6818 (m-10) REVERT: B 570 GLN cc_start: 0.9218 (tp-100) cc_final: 0.8964 (tp-100) REVERT: H 50 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7077 (mm-30) REVERT: H 73 ASP cc_start: 0.8399 (m-30) cc_final: 0.8088 (m-30) REVERT: C 20 LEU cc_start: 0.8719 (mp) cc_final: 0.8369 (mt) REVERT: C 64 LYS cc_start: 0.8813 (tttt) cc_final: 0.8450 (tptp) REVERT: C 75 ARG cc_start: 0.8867 (ttp-110) cc_final: 0.8546 (mtm110) REVERT: C 81 LYS cc_start: 0.9016 (tmtt) cc_final: 0.8737 (tptp) REVERT: C 82 ILE cc_start: 0.8485 (mt) cc_final: 0.8049 (mp) REVERT: D 4 MET cc_start: 0.7832 (tpt) cc_final: 0.7338 (tpp) REVERT: D 17 ASP cc_start: 0.6694 (m-30) cc_final: 0.6343 (m-30) REVERT: D 71 PHE cc_start: 0.8358 (m-80) cc_final: 0.7956 (m-80) REVERT: D 78 MET cc_start: 0.7940 (ppp) cc_final: 0.7726 (ppp) REVERT: D 83 LEU cc_start: 0.8700 (mt) cc_final: 0.8327 (pt) REVERT: D 85 ASP cc_start: 0.8386 (t0) cc_final: 0.8160 (t0) REVERT: E 75 VAL cc_start: 0.9410 (t) cc_final: 0.9200 (p) REVERT: E 117 ASP cc_start: 0.8896 (p0) cc_final: 0.8554 (p0) REVERT: E 251 GLN cc_start: 0.9478 (mp10) cc_final: 0.9080 (pm20) REVERT: G 543 TYR cc_start: 0.8696 (m-80) cc_final: 0.8465 (m-80) REVERT: G 565 THR cc_start: 0.9383 (m) cc_final: 0.9058 (t) REVERT: G 602 HIS cc_start: 0.7992 (t70) cc_final: 0.7699 (t-170) REVERT: P 5 GLN cc_start: 0.9087 (tp40) cc_final: 0.8818 (tp40) REVERT: P 61 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8708 (mm-30) REVERT: P 98 ASN cc_start: 0.8284 (p0) cc_final: 0.7866 (p0) REVERT: T 13 VAL cc_start: 0.8991 (m) cc_final: 0.8607 (p) REVERT: T 21 ILE cc_start: 0.9491 (mp) cc_final: 0.9253 (mp) REVERT: T 35 TRP cc_start: 0.7533 (m100) cc_final: 0.7195 (m100) REVERT: T 87 TYR cc_start: 0.8016 (m-80) cc_final: 0.7361 (m-80) REVERT: J 64 LYS cc_start: 0.9083 (tttt) cc_final: 0.8702 (tptp) REVERT: J 75 ARG cc_start: 0.8847 (ttp-110) cc_final: 0.8327 (mtm110) REVERT: N 44 PRO cc_start: 0.8864 (Cg_endo) cc_final: 0.8351 (Cg_exo) REVERT: F 117 ASP cc_start: 0.8821 (p0) cc_final: 0.8299 (p0) REVERT: F 251 GLN cc_start: 0.9468 (mp10) cc_final: 0.8940 (pm20) REVERT: I 550 ASN cc_start: 0.8647 (t0) cc_final: 0.8217 (t0) REVERT: I 567 GLN cc_start: 0.8177 (pp30) cc_final: 0.7616 (pp30) REVERT: I 602 HIS cc_start: 0.8266 (t70) cc_final: 0.7975 (t-170) REVERT: Q 5 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8539 (mp10) REVERT: Q 45 LEU cc_start: 0.8812 (tp) cc_final: 0.8466 (tp) REVERT: Q 46 GLU cc_start: 0.9021 (pt0) cc_final: 0.8756 (pm20) REVERT: Q 82 MET cc_start: 0.8539 (mtp) cc_final: 0.8262 (mtp) REVERT: Q 91 TYR cc_start: 0.8622 (m-80) cc_final: 0.8185 (m-80) REVERT: Q 98 ASN cc_start: 0.8832 (p0) cc_final: 0.8451 (p0) REVERT: U 13 VAL cc_start: 0.9219 (m) cc_final: 0.8943 (p) REVERT: U 35 TRP cc_start: 0.8194 (m100) cc_final: 0.7826 (m100) REVERT: U 70 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8609 (pm20) REVERT: U 87 TYR cc_start: 0.8561 (m-80) cc_final: 0.8177 (m-80) REVERT: U 98 PHE cc_start: 0.8788 (m-80) cc_final: 0.8231 (m-80) REVERT: M 19 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8255 (mmmm) REVERT: M 46 GLU cc_start: 0.8885 (tp30) cc_final: 0.8491 (tp30) REVERT: M 75 ARG cc_start: 0.8972 (ttp-110) cc_final: 0.8552 (mtm110) REVERT: M 81 LYS cc_start: 0.9033 (tmtt) cc_final: 0.8691 (tptp) REVERT: O 36 TYR cc_start: 0.8517 (m-80) cc_final: 0.8164 (m-80) REVERT: O 44 PRO cc_start: 0.8792 (Cg_endo) cc_final: 0.8400 (Cg_exo) REVERT: O 83 LEU cc_start: 0.8538 (mt) cc_final: 0.8076 (pt) REVERT: O 85 ASP cc_start: 0.8361 (t0) cc_final: 0.8052 (t0) REVERT: O 87 PHE cc_start: 0.8010 (m-80) cc_final: 0.7283 (m-80) outliers start: 2 outliers final: 0 residues processed: 462 average time/residue: 0.1426 time to fit residues: 101.9686 Evaluate side-chains 351 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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: 2.9990 chunk 79 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 174 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN E 44 GLN G 567 GLN ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS F 44 GLN I 613 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.067755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.052094 restraints weight = 100637.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.053514 restraints weight = 59332.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054444 restraints weight = 41789.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055054 restraints weight = 33196.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.055448 restraints weight = 28602.655| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19782 Z= 0.157 Angle : 0.747 9.507 26928 Z= 0.379 Chirality : 0.046 0.292 3039 Planarity : 0.005 0.075 3372 Dihedral : 5.545 35.448 2625 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.84 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % 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 are not related in a simple way. whole: -0.64 (0.17), residues: 2361 helix: 0.63 (0.38), residues: 162 sheet: -0.47 (0.18), residues: 783 loop : -0.45 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 94 TYR 0.039 0.003 TYR H 32 PHE 0.056 0.002 PHE H 27 TRP 0.022 0.002 TRP Q 103 HIS 0.005 0.001 HIS F 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (19710) covalent geometry : angle 0.73712 / 0.38 (26739) SS BOND : bond 0.00515 / 0.34 ( 27) SS BOND : angle 1.43665 / 0.92 ( 54) hydrogen bonds : bond 0.04319 / 2.90 ( 660) hydrogen bonds : angle 6.46861 / 4.65 ( 1710) link_ALPHA1-3 : bond 0.00440 / 0.24 ( 6) link_ALPHA1-3 : angle 1.33330 / 0.88 ( 18) link_ALPHA1-6 : bond 0.00408 / 0.20 ( 3) link_ALPHA1-6 : angle 1.56018 / 0.84 ( 9) link_BETA1-4 : bond 0.00337 / 0.21 ( 21) link_BETA1-4 : angle 1.62361 / 1.09 ( 63) link_NAG-ASN : bond 0.00182 / 0.11 ( 15) link_NAG-ASN : angle 2.01308 / 1.33 ( 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 448 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 0.772 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: A 117 ASP cc_start: 0.8929 (p0) cc_final: 0.8721 (p0) REVERT: A 251 GLN cc_start: 0.9418 (mp10) cc_final: 0.9039 (pm20) REVERT: B 531 TRP cc_start: 0.7057 (m-10) cc_final: 0.6709 (m-10) REVERT: B 570 GLN cc_start: 0.9208 (tp-100) cc_final: 0.8936 (tp-100) REVERT: H 80 LEU cc_start: 0.9262 (tt) cc_final: 0.9008 (tt) REVERT: L 49 TYR cc_start: 0.6911 (m-80) cc_final: 0.5224 (m-80) REVERT: L 83 PHE cc_start: 0.8040 (m-80) cc_final: 0.7832 (m-10) REVERT: C 20 LEU cc_start: 0.8753 (mp) cc_final: 0.8383 (mt) REVERT: C 64 LYS cc_start: 0.8832 (tttt) cc_final: 0.8474 (tptp) REVERT: C 75 ARG cc_start: 0.8846 (ttp-110) cc_final: 0.8537 (mtm110) REVERT: C 81 LYS cc_start: 0.9037 (tmtt) cc_final: 0.8766 (tptp) REVERT: C 82 ILE cc_start: 0.8498 (mt) cc_final: 0.8072 (mp) REVERT: D 4 MET cc_start: 0.7759 (tpt) cc_final: 0.7300 (tpp) REVERT: D 18 ARG cc_start: 0.8444 (mmt-90) cc_final: 0.8155 (mmp80) REVERT: D 45 LYS cc_start: 0.9144 (ptpp) cc_final: 0.8927 (ptpp) REVERT: D 83 LEU cc_start: 0.8709 (mt) cc_final: 0.8305 (pt) REVERT: D 85 ASP cc_start: 0.8299 (t0) cc_final: 0.8088 (t0) REVERT: E 117 ASP cc_start: 0.8921 (p0) cc_final: 0.8555 (p0) REVERT: E 251 GLN cc_start: 0.9466 (mp10) cc_final: 0.9081 (pm20) REVERT: P 5 GLN cc_start: 0.9123 (tp40) cc_final: 0.8869 (tp40) REVERT: P 91 TYR cc_start: 0.8494 (m-80) cc_final: 0.7910 (m-80) REVERT: P 98 ASN cc_start: 0.8345 (p0) cc_final: 0.7915 (p0) REVERT: T 21 ILE cc_start: 0.9484 (mp) cc_final: 0.9277 (mp) REVERT: T 35 TRP cc_start: 0.7528 (m100) cc_final: 0.7215 (m100) REVERT: T 86 TYR cc_start: 0.9167 (m-80) cc_final: 0.8855 (m-80) REVERT: T 87 TYR cc_start: 0.8009 (m-80) cc_final: 0.7137 (m-80) REVERT: J 64 LYS cc_start: 0.9102 (tttt) cc_final: 0.8716 (tptp) REVERT: J 75 ARG cc_start: 0.8809 (ttp-110) cc_final: 0.8228 (mtm110) REVERT: J 86 ASP cc_start: 0.8309 (m-30) cc_final: 0.7788 (m-30) REVERT: N 44 PRO cc_start: 0.8799 (Cg_endo) cc_final: 0.8414 (Cg_exo) REVERT: N 105 GLU cc_start: 0.6031 (tt0) cc_final: 0.5760 (tm-30) REVERT: F 69 ASN cc_start: 0.9144 (t0) cc_final: 0.8921 (t0) REVERT: F 117 ASP cc_start: 0.8774 (p0) cc_final: 0.8291 (p0) REVERT: F 251 GLN cc_start: 0.9456 (mp10) cc_final: 0.9165 (mm-40) REVERT: I 550 ASN cc_start: 0.8677 (t0) cc_final: 0.8257 (t0) REVERT: I 602 HIS cc_start: 0.8405 (t70) cc_final: 0.7845 (t-170) REVERT: Q 5 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8562 (mp10) REVERT: Q 33 TRP cc_start: 0.8007 (p90) cc_final: 0.7740 (p90) REVERT: Q 82 MET cc_start: 0.8601 (mtp) cc_final: 0.8280 (mtp) REVERT: Q 91 TYR cc_start: 0.8629 (m-80) cc_final: 0.8206 (m-80) REVERT: Q 98 ASN cc_start: 0.8813 (p0) cc_final: 0.8408 (p0) REVERT: U 13 VAL cc_start: 0.9292 (m) cc_final: 0.8983 (p) REVERT: U 35 TRP cc_start: 0.8174 (m100) cc_final: 0.7864 (m100) REVERT: U 70 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8664 (pm20) REVERT: U 83 PHE cc_start: 0.8432 (m-80) cc_final: 0.8083 (m-10) REVERT: U 87 TYR cc_start: 0.8532 (m-80) cc_final: 0.8225 (m-80) REVERT: U 91 PHE cc_start: 0.4967 (m-10) cc_final: 0.4710 (m-10) REVERT: M 46 GLU cc_start: 0.8927 (tp30) cc_final: 0.8561 (tp30) REVERT: M 75 ARG cc_start: 0.8968 (ttp-110) cc_final: 0.8671 (mtm110) REVERT: M 81 LYS cc_start: 0.9007 (tmtt) cc_final: 0.8623 (tptp) REVERT: O 17 ASP cc_start: 0.6825 (m-30) cc_final: 0.6361 (m-30) REVERT: O 36 TYR cc_start: 0.8431 (m-80) cc_final: 0.8031 (m-80) REVERT: O 44 PRO cc_start: 0.8814 (Cg_endo) cc_final: 0.8349 (Cg_exo) REVERT: O 78 MET cc_start: 0.7746 (ppp) cc_final: 0.7455 (ppp) REVERT: O 83 LEU cc_start: 0.8640 (mt) cc_final: 0.8068 (pt) REVERT: O 85 ASP cc_start: 0.8433 (t0) cc_final: 0.8127 (t0) REVERT: O 87 PHE cc_start: 0.8056 (m-80) cc_final: 0.7303 (m-80) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.1513 time to fit residues: 104.1356 Evaluate side-chains 334 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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: 3.9990 chunk 201 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 84 optimal weight: 0.0970 chunk 194 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 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** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN I 514 ASN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82AASN U 90 HIS ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.066139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.051088 restraints weight = 102391.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052619 restraints weight = 57346.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.053614 restraints weight = 38701.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054273 restraints weight = 29864.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.054692 restraints weight = 25186.078| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.6449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19782 Z= 0.160 Angle : 0.753 10.778 26928 Z= 0.382 Chirality : 0.047 0.272 3039 Planarity : 0.005 0.067 3372 Dihedral : 5.487 34.021 2625 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.62 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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 are not related in a simple way. whole: -0.59 (0.17), residues: 2361 helix: 0.70 (0.39), residues: 162 sheet: -0.28 (0.19), residues: 711 loop : -0.53 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 94 TYR 0.042 0.002 TYR H 32 PHE 0.048 0.002 PHE H 27 TRP 0.057 0.002 TRP L 35 HIS 0.007 0.001 HIS G 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (19710) covalent geometry : angle 0.74305 / 0.38 (26739) SS BOND : bond 0.00428 / 0.25 ( 27) SS BOND : angle 1.49878 / 0.95 ( 54) hydrogen bonds : bond 0.04372 / 2.90 ( 660) hydrogen bonds : angle 6.37076 / 4.61 ( 1710) link_ALPHA1-3 : bond 0.00431 / 0.23 ( 6) link_ALPHA1-3 : angle 1.33553 / 0.88 ( 18) link_ALPHA1-6 : bond 0.00286 / 0.13 ( 3) link_ALPHA1-6 : angle 1.59563 / 0.86 ( 9) link_BETA1-4 : bond 0.00304 / 0.18 ( 21) link_BETA1-4 : angle 1.61443 / 1.06 ( 63) link_NAG-ASN : bond 0.00189 / 0.12 ( 15) link_NAG-ASN : angle 1.93032 / 1.28 ( 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 451 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.811 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: A 117 ASP cc_start: 0.8896 (p0) cc_final: 0.8676 (p0) REVERT: A 251 GLN cc_start: 0.9418 (mp10) cc_final: 0.9050 (pm20) REVERT: B 570 GLN cc_start: 0.9144 (tp-100) cc_final: 0.8886 (tp-100) REVERT: B 602 HIS cc_start: 0.7838 (t-170) cc_final: 0.7627 (t-170) REVERT: H 73 ASP cc_start: 0.8481 (m-30) cc_final: 0.8133 (m-30) REVERT: H 80 LEU cc_start: 0.9263 (tt) cc_final: 0.9013 (tt) REVERT: L 49 TYR cc_start: 0.6958 (m-80) cc_final: 0.5247 (m-80) REVERT: L 83 PHE cc_start: 0.7990 (m-80) cc_final: 0.7573 (m-10) REVERT: C 20 LEU cc_start: 0.8751 (mp) cc_final: 0.8396 (mt) REVERT: C 64 LYS cc_start: 0.8915 (tttt) cc_final: 0.8648 (pttm) REVERT: C 75 ARG cc_start: 0.8783 (ttp-110) cc_final: 0.8466 (mtm110) REVERT: C 81 LYS cc_start: 0.9021 (tmtt) cc_final: 0.8752 (tptp) REVERT: C 82 ILE cc_start: 0.8575 (mt) cc_final: 0.8113 (mp) REVERT: D 18 ARG cc_start: 0.8425 (mmt-90) cc_final: 0.8127 (mmp80) REVERT: D 83 LEU cc_start: 0.8694 (mt) cc_final: 0.8296 (pt) REVERT: D 85 ASP cc_start: 0.8511 (t0) cc_final: 0.8273 (t0) REVERT: E 99 TYR cc_start: 0.9179 (p90) cc_final: 0.8772 (p90) REVERT: E 117 ASP cc_start: 0.8860 (p0) cc_final: 0.8496 (p0) REVERT: E 251 GLN cc_start: 0.9462 (mp10) cc_final: 0.9074 (pm20) REVERT: P 5 GLN cc_start: 0.9088 (tp40) cc_final: 0.8830 (tp40) REVERT: P 27 PHE cc_start: 0.6488 (t80) cc_final: 0.6015 (t80) REVERT: P 61 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8778 (mm-30) REVERT: P 91 TYR cc_start: 0.8526 (m-80) cc_final: 0.7955 (m-80) REVERT: P 98 ASN cc_start: 0.8422 (p0) cc_final: 0.7990 (p0) REVERT: T 35 TRP cc_start: 0.7489 (m100) cc_final: 0.7190 (m100) REVERT: T 87 TYR cc_start: 0.7928 (m-80) cc_final: 0.7150 (m-80) REVERT: J 37 PHE cc_start: 0.7061 (p90) cc_final: 0.6474 (p90) REVERT: J 64 LYS cc_start: 0.9116 (tttt) cc_final: 0.8745 (tptp) REVERT: J 75 ARG cc_start: 0.8761 (ttp-110) cc_final: 0.8257 (mtm110) REVERT: J 79 PHE cc_start: 0.8400 (m-80) cc_final: 0.8027 (m-10) REVERT: J 86 ASP cc_start: 0.8073 (m-30) cc_final: 0.7863 (m-30) REVERT: N 44 PRO cc_start: 0.8795 (Cg_endo) cc_final: 0.8383 (Cg_exo) REVERT: N 105 GLU cc_start: 0.6054 (tt0) cc_final: 0.5799 (tm-30) REVERT: F 117 ASP cc_start: 0.8752 (p0) cc_final: 0.8280 (p0) REVERT: F 251 GLN cc_start: 0.9443 (mp10) cc_final: 0.9175 (mm-40) REVERT: I 534 TYR cc_start: 0.8587 (t80) cc_final: 0.8337 (t80) REVERT: I 550 ASN cc_start: 0.8717 (t0) cc_final: 0.8272 (t0) REVERT: I 602 HIS cc_start: 0.8430 (t70) cc_final: 0.7922 (t-170) REVERT: Q 5 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8504 (mp10) REVERT: Q 82 MET cc_start: 0.8822 (mtp) cc_final: 0.8425 (mtp) REVERT: Q 98 ASN cc_start: 0.8712 (p0) cc_final: 0.8228 (p0) REVERT: U 13 VAL cc_start: 0.9321 (m) cc_final: 0.9037 (p) REVERT: U 21 ILE cc_start: 0.9384 (mp) cc_final: 0.9154 (mp) REVERT: U 35 TRP cc_start: 0.8107 (m100) cc_final: 0.7825 (m100) REVERT: U 83 PHE cc_start: 0.8349 (m-80) cc_final: 0.7995 (m-10) REVERT: U 87 TYR cc_start: 0.8327 (m-80) cc_final: 0.8096 (m-80) REVERT: M 46 GLU cc_start: 0.8842 (tp30) cc_final: 0.8542 (tp30) REVERT: M 75 ARG cc_start: 0.8942 (ttp-110) cc_final: 0.8534 (mtm110) REVERT: M 81 LYS cc_start: 0.9023 (tmtt) cc_final: 0.8814 (tptt) REVERT: O 17 ASP cc_start: 0.6803 (m-30) cc_final: 0.6357 (m-30) REVERT: O 36 TYR cc_start: 0.8565 (m-80) cc_final: 0.8146 (m-80) REVERT: O 44 PRO cc_start: 0.8797 (Cg_endo) cc_final: 0.8322 (Cg_exo) REVERT: O 78 MET cc_start: 0.7761 (ppp) cc_final: 0.7492 (ppp) REVERT: O 83 LEU cc_start: 0.8593 (mt) cc_final: 0.8094 (pt) REVERT: O 85 ASP cc_start: 0.8563 (t0) cc_final: 0.8332 (t0) REVERT: O 87 PHE cc_start: 0.8103 (m-80) cc_final: 0.7312 (m-80) REVERT: O 103 LYS cc_start: 0.8234 (mppt) cc_final: 0.7942 (mmtm) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.1477 time to fit residues: 102.2163 Evaluate side-chains 337 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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: 4.9990 chunk 148 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 232 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN B 613 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN C 100BASN D 42 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS J 82BASN N 37 GLN N 38 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82AASN U 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.065912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050358 restraints weight = 100710.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.051726 restraints weight = 59348.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.052607 restraints weight = 41731.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.053217 restraints weight = 33275.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.053596 restraints weight = 28611.137| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19782 Z= 0.225 Angle : 0.817 12.309 26928 Z= 0.414 Chirality : 0.048 0.282 3039 Planarity : 0.005 0.068 3372 Dihedral : 5.744 40.782 2625 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.51 % Favored : 91.11 % Rotamer: Outliers : 0.10 % Allowed : 0.40 % Favored : 99.50 % 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 are not related in a simple way. whole: -0.79 (0.17), residues: 2361 helix: 0.80 (0.40), residues: 162 sheet: -0.49 (0.19), residues: 738 loop : -0.66 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 76 TYR 0.048 0.003 TYR H 32 PHE 0.060 0.003 PHE L 91 TRP 0.049 0.003 TRP C 103 HIS 0.003 0.001 HIS I 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (19710) covalent geometry : angle 0.80637 / 0.41 (26739) SS BOND : bond 0.00501 / 0.29 ( 27) SS BOND : angle 1.72321 / 1.12 ( 54) hydrogen bonds : bond 0.04550 / 3.05 ( 660) hydrogen bonds : angle 6.58345 / 4.75 ( 1710) link_ALPHA1-3 : bond 0.00299 / 0.16 ( 6) link_ALPHA1-3 : angle 1.39983 / 0.84 ( 18) link_ALPHA1-6 : bond 0.00114 / 0.05 ( 3) link_ALPHA1-6 : angle 1.82611 / 0.98 ( 9) link_BETA1-4 : bond 0.00302 / 0.19 ( 21) link_BETA1-4 : angle 1.60095 / 1.08 ( 63) link_NAG-ASN : bond 0.00336 / 0.21 ( 15) link_NAG-ASN : angle 2.11544 / 1.45 ( 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 417 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 415 time to evaluate : 0.687 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: A 117 ASP cc_start: 0.8996 (p0) cc_final: 0.8719 (p0) REVERT: A 251 GLN cc_start: 0.9429 (mp10) cc_final: 0.9088 (pm20) REVERT: H 73 ASP cc_start: 0.8558 (m-30) cc_final: 0.8179 (m-30) REVERT: H 80 LEU cc_start: 0.9271 (tt) cc_final: 0.9057 (tt) REVERT: L 83 PHE cc_start: 0.8313 (m-80) cc_final: 0.7891 (m-10) REVERT: L 91 PHE cc_start: 0.6653 (m-80) cc_final: 0.6325 (m-10) REVERT: C 50 LEU cc_start: 0.9015 (tp) cc_final: 0.8802 (tp) REVERT: C 64 LYS cc_start: 0.8896 (tttt) cc_final: 0.8626 (tptp) REVERT: C 75 ARG cc_start: 0.8828 (ttp-110) cc_final: 0.8503 (mtm110) REVERT: C 81 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8719 (tptp) REVERT: C 82 ILE cc_start: 0.8445 (mt) cc_final: 0.8021 (mp) REVERT: D 18 ARG cc_start: 0.8460 (mmt-90) cc_final: 0.8191 (mmp80) REVERT: D 105 GLU cc_start: 0.6399 (tt0) cc_final: 0.6176 (tt0) REVERT: E 99 TYR cc_start: 0.9348 (p90) cc_final: 0.9078 (p90) REVERT: E 117 ASP cc_start: 0.8924 (p0) cc_final: 0.8537 (p0) REVERT: E 251 GLN cc_start: 0.9499 (mp10) cc_final: 0.9128 (pm20) REVERT: P 5 GLN cc_start: 0.9123 (tp40) cc_final: 0.8917 (mp10) REVERT: P 12 MET cc_start: 0.8534 (ttp) cc_final: 0.8138 (ptm) REVERT: P 61 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8786 (mm-30) REVERT: P 73 ASP cc_start: 0.8302 (m-30) cc_final: 0.8024 (m-30) REVERT: T 35 TRP cc_start: 0.7868 (m100) cc_final: 0.7401 (m100) REVERT: T 83 PHE cc_start: 0.8692 (m-10) cc_final: 0.8367 (m-10) REVERT: J 64 LYS cc_start: 0.9121 (tttt) cc_final: 0.8725 (tptp) REVERT: J 75 ARG cc_start: 0.8847 (ttp-110) cc_final: 0.8395 (mtm110) REVERT: J 79 PHE cc_start: 0.8374 (m-80) cc_final: 0.8106 (m-10) REVERT: N 105 GLU cc_start: 0.6318 (tt0) cc_final: 0.5919 (tm-30) REVERT: F 69 ASN cc_start: 0.9202 (t0) cc_final: 0.8980 (t0) REVERT: F 117 ASP cc_start: 0.8883 (p0) cc_final: 0.8371 (p0) REVERT: F 251 GLN cc_start: 0.9453 (mp10) cc_final: 0.9160 (mm-40) REVERT: I 567 GLN cc_start: 0.8111 (pp30) cc_final: 0.7676 (pp30) REVERT: I 602 HIS cc_start: 0.8634 (t70) cc_final: 0.8359 (t-170) REVERT: Q 50 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6519 (mm-30) REVERT: Q 82 MET cc_start: 0.8869 (mtp) cc_final: 0.8541 (mtp) REVERT: Q 98 ASN cc_start: 0.8861 (p0) cc_final: 0.8397 (p0) REVERT: U 35 TRP cc_start: 0.8313 (m100) cc_final: 0.8022 (m100) REVERT: U 70 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8648 (pm20) REVERT: U 83 PHE cc_start: 0.8448 (m-80) cc_final: 0.8081 (m-10) REVERT: U 87 TYR cc_start: 0.8512 (m-80) cc_final: 0.8239 (m-80) REVERT: M 46 GLU cc_start: 0.8894 (tp30) cc_final: 0.8616 (tp30) REVERT: M 75 ARG cc_start: 0.8981 (ttp-110) cc_final: 0.8697 (mtm110) REVERT: M 81 LYS cc_start: 0.8960 (tmtt) cc_final: 0.8664 (tptp) REVERT: O 17 ASP cc_start: 0.6758 (m-30) cc_final: 0.6254 (m-30) REVERT: O 36 TYR cc_start: 0.8484 (m-80) cc_final: 0.8030 (m-80) REVERT: O 44 PRO cc_start: 0.8820 (Cg_endo) cc_final: 0.8386 (Cg_exo) REVERT: O 78 MET cc_start: 0.7788 (ppp) cc_final: 0.7489 (ppp) REVERT: O 83 LEU cc_start: 0.8514 (mt) cc_final: 0.7974 (pt) REVERT: O 85 ASP cc_start: 0.8627 (t0) cc_final: 0.8318 (t0) REVERT: O 87 PHE cc_start: 0.7949 (m-80) cc_final: 0.7189 (m-80) REVERT: O 107 ARG cc_start: 0.0619 (mtm180) cc_final: 0.0216 (mtm180) outliers start: 2 outliers final: 0 residues processed: 416 average time/residue: 0.1462 time to fit residues: 93.1602 Evaluate side-chains 315 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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: 7.9990 chunk 161 optimal weight: 0.4980 chunk 218 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 232 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100BASN D 42 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN J 100BASN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82AASN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.065569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.050601 restraints weight = 103571.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.052043 restraints weight = 60097.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.052977 restraints weight = 41502.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.053585 restraints weight = 32584.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.053998 restraints weight = 27801.141| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19782 Z= 0.157 Angle : 0.774 10.691 26928 Z= 0.393 Chirality : 0.047 0.273 3039 Planarity : 0.005 0.069 3372 Dihedral : 5.599 39.451 2625 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.09 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % 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 are not related in a simple way. whole: -0.78 (0.17), residues: 2361 helix: 0.83 (0.40), residues: 162 sheet: -0.41 (0.19), residues: 729 loop : -0.71 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 94 TYR 0.041 0.003 TYR H 32 PHE 0.036 0.002 PHE L 91 TRP 0.062 0.003 TRP B 531 HIS 0.003 0.001 HIS U 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (19710) covalent geometry : angle 0.76438 / 0.39 (26739) SS BOND : bond 0.00425 / 0.25 ( 27) SS BOND : angle 1.49149 / 0.98 ( 54) hydrogen bonds : bond 0.04386 / 2.92 ( 660) hydrogen bonds : angle 6.48907 / 4.69 ( 1710) link_ALPHA1-3 : bond 0.00442 / 0.24 ( 6) link_ALPHA1-3 : angle 1.35353 / 0.90 ( 18) link_ALPHA1-6 : bond 0.00233 / 0.11 ( 3) link_ALPHA1-6 : angle 1.60578 / 0.87 ( 9) link_BETA1-4 : bond 0.00307 / 0.20 ( 21) link_BETA1-4 : angle 1.65043 / 1.08 ( 63) link_NAG-ASN : bond 0.00199 / 0.13 ( 15) link_NAG-ASN : angle 1.90895 / 1.28 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3565.33 seconds wall clock time: 62 minutes 40.42 seconds (3760.42 seconds total)