Starting phenix.real_space_refine on Fri Jul 3 15:55:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqo_62509/07_2026/9kqo_62509.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqo_62509/07_2026/9kqo_62509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kqo_62509/07_2026/9kqo_62509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqo_62509/07_2026/9kqo_62509.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqo_62509/07_2026/9kqo_62509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqo_62509/07_2026/9kqo_62509.cif" } resolution = 3.48 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 Anisotropic ADP refinement not supported. Converting 14 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 294 5.49 5 S 33 5.16 5 C 8312 2.51 5 N 2739 2.21 5 O 3305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14687 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 476 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "L" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "M" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "R" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1060 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 14, 'TRANS': 135} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 8, 'ASP:plan': 3, 'ASN:plan1': 4, 'PHE:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 63 SG CYS A 948 45.627 41.176 19.516 1.00326.94 S ATOM 214 SG CYS A 968 45.760 43.297 18.918 1.00341.64 S ATOM 240 SG CYS A 971 41.508 42.574 20.339 1.00327.14 S ATOM 169 SG CYS A 963 42.826 39.803 34.681 1.00315.88 S ATOM 341 SG CYS A 983 41.027 38.743 30.577 1.00316.79 S ATOM 13181 SG CYS M 922 62.304 52.113 32.394 1.00220.59 S ATOM 13200 SG CYS M 925 65.908 51.426 33.034 1.00227.44 S ATOM 13340 SG CYS M 942 62.921 50.044 35.506 1.00214.52 S ATOM 13366 SG CYS M 945 64.156 53.067 35.876 1.00213.85 S ATOM 13295 SG CYS M 937 52.196 58.737 31.696 1.00230.65 S ATOM 13473 SG CYS M 957 55.486 60.248 32.826 1.00217.26 S ATOM 13495 SG CYS M 960 52.604 62.525 31.512 1.00244.30 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU B 73 " occ=0.53 ... (6 atoms not shown) pdb=" CD2 LEU B 73 " occ=0.53 residue: pdb=" N GLY B 75 " occ=0.56 ... (2 atoms not shown) pdb=" O GLY B 75 " occ=0.56 Time building chain proxies: 2.85, per 1000 atoms: 0.19 Number of scatterers: 14687 At special positions: 0 Unit cell: (119.214, 119.214, 120.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 33 16.00 P 294 15.00 O 3305 8.00 N 2739 7.00 C 8312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 NAG-SER " NAG D 201 " - " SER D 112 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 477.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 948 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 968 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 971 " pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 965 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 983 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 963 " pdb=" ZN M1001 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 945 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 942 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 922 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 925 " pdb=" ZN M1002 " pdb="ZN ZN M1002 " - pdb=" ND1 HIS M 939 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 937 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 957 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 960 " Number of angles added : 9 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 13 sheets defined 60.2% alpha, 5.9% beta 145 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 941 through 947 Processing helix chain 'A' and resid 969 through 978 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.476A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.588A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.643A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.332A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.600A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 55 Processing helix chain 'K' and resid 63 through 76 Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 42 Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.138A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'M' and resid 916 through 920 Processing helix chain 'M' and resid 942 through 952 Processing helix chain 'R' and resid 3 through 19 Processing helix chain 'R' and resid 89 through 94 Processing helix chain 'R' and resid 101 through 115 Processing helix chain 'R' and resid 123 through 132 Processing helix chain 'R' and resid 133 through 149 removed outlier: 3.698A pdb=" N TRP R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 966 through 967 removed outlier: 4.114A pdb=" N VAL A 959 " --> pdb=" O HIS A 996 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS A 996 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 16 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.739A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.670A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.794A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.740A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.253A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'G' and resid 101 through 102 removed outlier: 6.564A pdb=" N THR G 101 " --> pdb=" O TYR L 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB3, first strand: chain 'M' and resid 939 through 941 Processing sheet with id=AB4, first strand: chain 'R' and resid 24 through 28 removed outlier: 3.542A pdb=" N PHE R 53 " --> pdb=" O ILE R 40 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3550 1.33 - 1.45: 4200 1.45 - 1.57: 7170 1.57 - 1.69: 586 1.69 - 1.81: 47 Bond restraints: 15553 Sorted by residual: bond pdb=" N PRO R 64 " pdb=" CD PRO R 64 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.84e+01 bond pdb=" C3' DC I 52 " pdb=" C2' DC I 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C1' DC J 70 " pdb=" N1 DC J 70 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.08e+00 bond pdb=" C1' DC I 68 " pdb=" N1 DC I 68 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.07e+00 bond pdb=" C1' DT J -17 " pdb=" N1 DT J -17 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.48e+00 ... (remaining 15548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 21892 2.65 - 5.31: 386 5.31 - 7.96: 2 7.96 - 10.61: 0 10.61 - 13.26: 1 Bond angle restraints: 22281 Sorted by residual: angle pdb=" O4' DG I -35 " pdb=" C4' DG I -35 " pdb=" C3' DG I -35 " ideal model delta sigma weight residual 106.00 103.03 2.97 6.00e-01 2.78e+00 2.45e+01 angle pdb=" C TYR R 63 " pdb=" N PRO R 64 " pdb=" CA PRO R 64 " ideal model delta sigma weight residual 119.84 113.89 5.95 1.25e+00 6.40e-01 2.26e+01 angle pdb=" O4' DG I 20 " pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " ideal model delta sigma weight residual 106.00 103.28 2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT J 71 " pdb=" C4 DT J 71 " pdb=" O4 DT J 71 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT J 38 " pdb=" C4 DT J 38 " pdb=" O4 DT J 38 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 ... (remaining 22276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.74: 7239 33.74 - 67.49: 1360 67.49 - 101.23: 26 101.23 - 134.97: 0 134.97 - 168.72: 4 Dihedral angle restraints: 8629 sinusoidal: 5413 harmonic: 3216 Sorted by residual: dihedral pdb=" CA ARG B 72 " pdb=" C ARG B 72 " pdb=" N LEU B 73 " pdb=" CA LEU B 73 " ideal model delta harmonic sigma weight residual -180.00 -149.12 -30.88 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA ARG M 928 " pdb=" C ARG M 928 " pdb=" N LYS M 929 " pdb=" CA LYS M 929 " ideal model delta harmonic sigma weight residual -180.00 -159.33 -20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ILE L 29 " pdb=" C ILE L 29 " pdb=" N THR L 30 " pdb=" CA THR L 30 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 8626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1763 0.040 - 0.079: 374 0.079 - 0.119: 127 0.119 - 0.159: 209 0.159 - 0.198: 60 Chirality restraints: 2533 Sorted by residual: chirality pdb=" CB THR M 948 " pdb=" CA THR M 948 " pdb=" OG1 THR M 948 " pdb=" CG2 THR M 948 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CB THR D 119 " pdb=" CA THR D 119 " pdb=" OG1 THR D 119 " pdb=" CG2 THR D 119 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" C3' DA J 57 " pdb=" C4' DA J 57 " pdb=" O3' DA J 57 " pdb=" C2' DA J 57 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 2530 not shown) Planarity restraints: 1814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 201 " 0.054 2.00e-02 2.50e+03 4.53e-02 2.57e+01 pdb=" C7 NAG D 201 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG D 201 " -0.014 2.00e-02 2.50e+03 pdb=" N2 NAG D 201 " -0.072 2.00e-02 2.50e+03 pdb=" O7 NAG D 201 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 928 " -0.215 9.50e-02 1.11e+02 9.66e-02 5.74e+00 pdb=" NE ARG M 928 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG M 928 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG M 928 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG M 928 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 67 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO R 68 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 68 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 68 " -0.029 5.00e-02 4.00e+02 ... (remaining 1811 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 81 2.52 - 3.12: 10910 3.12 - 3.71: 26266 3.71 - 4.31: 35117 4.31 - 4.90: 52216 Nonbonded interactions: 124590 Sorted by model distance: nonbonded pdb=" OG1 THR M 952 " pdb=" OE1 GLN M 954 " model vdw 1.930 3.040 nonbonded pdb=" OH TYR C 50 " pdb=" OE1 GLN D 95 " model vdw 1.952 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 1.998 3.040 nonbonded pdb=" O TYR R 63 " pdb=" N ASN R 65 " model vdw 2.000 3.120 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.068 3.040 ... (remaining 124585 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 942 through 952 or resid 954 through 972 or resid 975 thro \ ugh 976 or resid 979 through 992 or resid 994 through 1102)) selection = (chain 'M' and (resid 916 through 925 or (resid 926 and (name N or name CA or na \ me C or name O or name CB )) or resid 928 through 929 or (resid 930 and (name N \ or name CA or name C or name O or name CB )) or resid 931 through 946 or resid 9 \ 49 through 950 or resid 953 through 966 or resid 968 through 973 or (resid 974 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1001 through 10 \ 02)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 31 through 124) selection = chain 'H' } ncs_group { reference = chain 'E' selection = (chain 'K' and resid 38 through 134) } ncs_group { reference = chain 'F' selection = (chain 'L' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) } 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=0.53 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.350 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.006 0.060 15568 Z= 0.479 Angle : 0.785 19.314 22292 Z= 0.621 Chirality : 0.059 0.198 2533 Planarity : 0.006 0.097 1814 Dihedral : 25.739 168.716 6547 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.74 % Rotamer: Outliers : 0.11 % Allowed : 0.11 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.32 (0.26), residues: 1081 helix: 2.03 (0.20), residues: 655 sheet: -0.60 (0.63), residues: 65 loop : -1.02 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 20 TYR 0.021 0.001 TYR C 57 PHE 0.016 0.001 PHE E 67 TRP 0.010 0.002 TRP R 36 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.48 (15553) covalent geometry : angle 0.76219 / 0.62 (22281) hydrogen bonds : bond 0.08203 / 5.76 ( 884) hydrogen bonds : angle 4.28457 / 2.99 ( 2231) metal coordination : bond 0.00878 / 0.58 ( 14) metal coordination : angle 9.28993 / 5.59 ( 9) link_NAG-SER : bond 0.04184 / 2.20 ( 1) link_NAG-SER : angle 3.89361 / 2.28 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.330 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: A 960 LEU cc_start: 0.9041 (mt) cc_final: 0.8464 (tt) REVERT: A 986 CYS cc_start: 0.8916 (t) cc_final: 0.8563 (p) REVERT: D 51 ASP cc_start: 0.9097 (p0) cc_final: 0.8653 (p0) REVERT: D 68 ASP cc_start: 0.8943 (t70) cc_final: 0.8380 (t0) REVERT: D 113 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8662 (mt-10) REVERT: E 41 TYR cc_start: 0.8622 (m-80) cc_final: 0.8353 (m-80) REVERT: E 56 LYS cc_start: 0.9264 (ttmm) cc_final: 0.8999 (ttpt) REVERT: F 25 ASN cc_start: 0.9152 (m110) cc_final: 0.8752 (m-40) REVERT: F 53 GLU cc_start: 0.8569 (tp30) cc_final: 0.8307 (tp30) REVERT: F 98 TYR cc_start: 0.9346 (m-10) cc_final: 0.9099 (m-10) REVERT: G 35 ARG cc_start: 0.9450 (ttm110) cc_final: 0.9039 (ttm-80) REVERT: G 71 ARG cc_start: 0.9084 (ttp80) cc_final: 0.8435 (ttp80) REVERT: G 72 ASP cc_start: 0.8867 (m-30) cc_final: 0.8455 (m-30) REVERT: G 91 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7619 (tm-30) REVERT: G 92 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8568 (mm-30) REVERT: H 42 TYR cc_start: 0.8774 (t80) cc_final: 0.8567 (t80) REVERT: H 88 THR cc_start: 0.9357 (m) cc_final: 0.9125 (p) REVERT: H 101 LEU cc_start: 0.9072 (mm) cc_final: 0.8819 (mm) REVERT: K 59 GLU cc_start: 0.8535 (pm20) cc_final: 0.8013 (pm20) REVERT: K 60 LEU cc_start: 0.9328 (mt) cc_final: 0.9017 (mt) REVERT: K 79 LYS cc_start: 0.8347 (tptt) cc_final: 0.7964 (tptp) REVERT: K 80 THR cc_start: 0.9183 (p) cc_final: 0.8750 (p) REVERT: K 81 ASP cc_start: 0.9114 (m-30) cc_final: 0.8761 (m-30) REVERT: K 123 ASP cc_start: 0.9050 (m-30) cc_final: 0.8777 (m-30) REVERT: M 929 LYS cc_start: 0.9407 (mmmt) cc_final: 0.9206 (tppt) REVERT: R 11 ARG cc_start: 0.9489 (ptm160) cc_final: 0.9274 (ptt-90) outliers start: 1 outliers final: 1 residues processed: 358 average time/residue: 0.1240 time to fit residues: 62.4286 Evaluate side-chains 332 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 2 GLN C 73 ASN E 125 GLN F 25 ASN G 68 ASN G 73 ASN H 63 ASN H 95 GLN K 68 GLN K 113 HIS ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** 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 = 0.3993 r_free = 0.3993 target = 0.133235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.076834 restraints weight = 30369.583| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.88 r_work: 0.2718 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15568 Z= 0.198 Angle : 0.688 16.780 22292 Z= 0.387 Chirality : 0.045 0.250 2533 Planarity : 0.005 0.048 1814 Dihedral : 29.160 168.067 4455 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.45 % Allowed : 11.23 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.40 (0.26), residues: 1081 helix: 2.10 (0.20), residues: 654 sheet: -0.48 (0.66), residues: 65 loop : -1.03 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 72 TYR 0.018 0.002 TYR D 121 PHE 0.018 0.002 PHE M 943 TRP 0.004 0.001 TRP R 36 HIS 0.008 0.001 HIS A 965 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 (15553) covalent geometry : angle 0.66515 / 0.39 (22281) hydrogen bonds : bond 0.05124 / 3.51 ( 884) hydrogen bonds : angle 3.66102 / 2.57 ( 2231) metal coordination : bond 0.01291 / 0.94 ( 14) metal coordination : angle 8.69888 / 5.22 ( 9) link_NAG-SER : bond 0.00394 / 0.21 ( 1) link_NAG-SER : angle 0.55917 / 0.30 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 343 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 LEU cc_start: 0.8942 (mt) cc_final: 0.8386 (tt) REVERT: A 965 HIS cc_start: 0.1765 (m-70) cc_final: 0.1351 (m-70) REVERT: A 985 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8568 (mmtm) REVERT: A 986 CYS cc_start: 0.8816 (t) cc_final: 0.8616 (p) REVERT: C 38 ASN cc_start: 0.9171 (t0) cc_final: 0.8967 (t0) REVERT: D 51 ASP cc_start: 0.9213 (p0) cc_final: 0.8872 (p0) REVERT: D 68 ASP cc_start: 0.9056 (t70) cc_final: 0.8507 (t0) REVERT: D 113 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8594 (mt-10) REVERT: E 56 LYS cc_start: 0.9271 (ttmm) cc_final: 0.9023 (ttpt) REVERT: F 25 ASN cc_start: 0.9219 (m-40) cc_final: 0.8908 (m110) REVERT: F 88 TYR cc_start: 0.9134 (m-10) cc_final: 0.8920 (m-10) REVERT: G 24 GLN cc_start: 0.9302 (mm-40) cc_final: 0.9074 (mm-40) REVERT: G 68 ASN cc_start: 0.8937 (m-40) cc_final: 0.8396 (m110) REVERT: G 71 ARG cc_start: 0.9111 (ttp80) cc_final: 0.8459 (ttp80) REVERT: G 72 ASP cc_start: 0.8820 (m-30) cc_final: 0.8457 (m-30) REVERT: G 91 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7851 (tm-30) REVERT: H 42 TYR cc_start: 0.8890 (t80) cc_final: 0.8599 (t80) REVERT: H 88 THR cc_start: 0.9433 (m) cc_final: 0.9173 (p) REVERT: H 101 LEU cc_start: 0.9142 (mm) cc_final: 0.8851 (mm) REVERT: K 59 GLU cc_start: 0.8942 (pm20) cc_final: 0.8489 (pm20) REVERT: K 79 LYS cc_start: 0.8471 (tptt) cc_final: 0.8144 (tptp) REVERT: K 80 THR cc_start: 0.9266 (p) cc_final: 0.8944 (p) REVERT: K 81 ASP cc_start: 0.9190 (m-30) cc_final: 0.8863 (m-30) REVERT: M 926 ASN cc_start: 0.9652 (m-40) cc_final: 0.9311 (m-40) REVERT: M 929 LYS cc_start: 0.9390 (mmmt) cc_final: 0.9160 (tppt) REVERT: M 949 ARG cc_start: 0.9185 (mtp85) cc_final: 0.8976 (tpp80) REVERT: M 952 THR cc_start: 0.9382 (p) cc_final: 0.8967 (p) REVERT: M 954 GLN cc_start: 0.8827 (mp10) cc_final: 0.8365 (mp10) REVERT: M 956 LYS cc_start: 0.9444 (mmmt) cc_final: 0.9204 (mmmt) outliers start: 22 outliers final: 15 residues processed: 349 average time/residue: 0.1308 time to fit residues: 63.6359 Evaluate side-chains 345 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 330 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 37 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 60 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 12 optimal weight: 50.0000 chunk 103 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 68 GLN E 93 GLN E 125 GLN G 73 ASN G 84 GLN H 63 ASN K 68 GLN L 25 ASN L 75 HIS ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 961 ASN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.134859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.077701 restraints weight = 30748.327| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.94 r_work: 0.2739 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15568 Z= 0.146 Angle : 0.627 13.285 22292 Z= 0.362 Chirality : 0.042 0.237 2533 Planarity : 0.005 0.046 1814 Dihedral : 29.218 166.166 4455 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.78 % Allowed : 13.46 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.50 (0.26), residues: 1081 helix: 2.20 (0.20), residues: 656 sheet: -0.37 (0.67), residues: 65 loop : -1.07 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 20 TYR 0.020 0.001 TYR H 83 PHE 0.014 0.001 PHE K 67 TRP 0.002 0.001 TRP R 36 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (15553) covalent geometry : angle 0.60623 / 0.36 (22281) hydrogen bonds : bond 0.04584 / 3.17 ( 884) hydrogen bonds : angle 3.42834 / 2.40 ( 2231) metal coordination : bond 0.00414 / 0.29 ( 14) metal coordination : angle 7.91316 / 4.88 ( 9) link_NAG-SER : bond 0.00149 / 0.08 ( 1) link_NAG-SER : angle 0.24853 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 338 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 LEU cc_start: 0.8927 (mt) cc_final: 0.8323 (tt) REVERT: A 965 HIS cc_start: 0.2029 (m-70) cc_final: 0.1541 (m-70) REVERT: A 986 CYS cc_start: 0.8890 (t) cc_final: 0.8639 (p) REVERT: C 38 ASN cc_start: 0.9181 (t0) cc_final: 0.8966 (t0) REVERT: D 68 ASP cc_start: 0.9069 (t70) cc_final: 0.8598 (t0) REVERT: D 113 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8630 (mt-10) REVERT: E 41 TYR cc_start: 0.8479 (m-80) cc_final: 0.7987 (m-80) REVERT: E 56 LYS cc_start: 0.9208 (ttmm) cc_final: 0.8973 (ttpt) REVERT: F 25 ASN cc_start: 0.9193 (m-40) cc_final: 0.8730 (m110) REVERT: F 98 TYR cc_start: 0.9439 (m-10) cc_final: 0.9218 (m-10) REVERT: G 68 ASN cc_start: 0.8936 (m-40) cc_final: 0.8379 (m110) REVERT: G 71 ARG cc_start: 0.9112 (ttp80) cc_final: 0.8518 (ttp80) REVERT: G 72 ASP cc_start: 0.8805 (m-30) cc_final: 0.8332 (m-30) REVERT: G 91 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7768 (tm-30) REVERT: G 92 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8415 (mm-30) REVERT: H 42 TYR cc_start: 0.8847 (t80) cc_final: 0.8575 (t80) REVERT: H 88 THR cc_start: 0.9443 (m) cc_final: 0.9198 (p) REVERT: H 92 ARG cc_start: 0.8794 (mtp85) cc_final: 0.8559 (mtp85) REVERT: H 101 LEU cc_start: 0.9132 (mm) cc_final: 0.8883 (mm) REVERT: K 42 ARG cc_start: 0.7844 (mmm160) cc_final: 0.7450 (mtp85) REVERT: K 59 GLU cc_start: 0.8911 (pm20) cc_final: 0.8440 (pm20) REVERT: K 79 LYS cc_start: 0.8380 (tptt) cc_final: 0.7859 (tttm) REVERT: K 80 THR cc_start: 0.9261 (p) cc_final: 0.8935 (p) REVERT: K 81 ASP cc_start: 0.9175 (m-30) cc_final: 0.8842 (m-30) REVERT: L 25 ASN cc_start: 0.9026 (m-40) cc_final: 0.8476 (m-40) REVERT: L 43 VAL cc_start: 0.9336 (t) cc_final: 0.9083 (m) REVERT: L 44 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.9025 (mtpt) REVERT: M 929 LYS cc_start: 0.9382 (mmmt) cc_final: 0.9090 (tppt) REVERT: M 949 ARG cc_start: 0.9179 (mtp85) cc_final: 0.8843 (tpp80) REVERT: M 952 THR cc_start: 0.9365 (p) cc_final: 0.8845 (p) REVERT: M 953 ARG cc_start: 0.9326 (mtp85) cc_final: 0.9092 (mtp85) REVERT: M 954 GLN cc_start: 0.8795 (mp10) cc_final: 0.8310 (mp10) REVERT: M 956 LYS cc_start: 0.9395 (mmmt) cc_final: 0.9021 (mmmt) REVERT: M 961 ASN cc_start: 0.8549 (t0) cc_final: 0.8319 (t0) REVERT: R 7 ARG cc_start: 0.8563 (ppt170) cc_final: 0.8150 (ppt170) REVERT: R 11 ARG cc_start: 0.9135 (ptt180) cc_final: 0.8836 (ptt-90) outliers start: 16 outliers final: 11 residues processed: 339 average time/residue: 0.1280 time to fit residues: 60.6036 Evaluate side-chains 335 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 323 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 37 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 120 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 68 GLN E 125 GLN G 73 ASN G 84 GLN H 63 ASN K 68 GLN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 926 ASN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.134262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.077265 restraints weight = 31080.868| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.98 r_work: 0.2734 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15568 Z= 0.149 Angle : 0.630 14.923 22292 Z= 0.357 Chirality : 0.042 0.231 2533 Planarity : 0.005 0.046 1814 Dihedral : 29.289 169.979 4455 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.11 % Allowed : 16.24 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.52 (0.26), residues: 1081 helix: 2.21 (0.20), residues: 656 sheet: -0.34 (0.62), residues: 75 loop : -1.08 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 20 TYR 0.022 0.001 TYR H 83 PHE 0.016 0.001 PHE M 941 TRP 0.003 0.000 TRP R 96 HIS 0.002 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (15553) covalent geometry : angle 0.60620 / 0.36 (22281) hydrogen bonds : bond 0.04545 / 3.14 ( 884) hydrogen bonds : angle 3.32862 / 2.34 ( 2231) metal coordination : bond 0.00348 / 0.23 ( 14) metal coordination : angle 8.59351 / 5.23 ( 9) link_NAG-SER : bond 0.00300 / 0.16 ( 1) link_NAG-SER : angle 0.84070 / 0.44 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 335 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 LEU cc_start: 0.8952 (mt) cc_final: 0.8392 (tt) REVERT: A 965 HIS cc_start: 0.1796 (m-70) cc_final: 0.1339 (m-70) REVERT: A 986 CYS cc_start: 0.8916 (t) cc_final: 0.8661 (p) REVERT: C 38 ASN cc_start: 0.9199 (t0) cc_final: 0.8961 (t0) REVERT: D 68 ASP cc_start: 0.9076 (t70) cc_final: 0.8615 (t0) REVERT: D 113 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8599 (mt-10) REVERT: E 41 TYR cc_start: 0.8499 (m-80) cc_final: 0.8027 (m-80) REVERT: E 56 LYS cc_start: 0.9213 (ttmm) cc_final: 0.8987 (ttpt) REVERT: F 25 ASN cc_start: 0.9194 (m-40) cc_final: 0.8859 (m110) REVERT: F 98 TYR cc_start: 0.9442 (m-10) cc_final: 0.9229 (m-10) REVERT: G 71 ARG cc_start: 0.9100 (ttp80) cc_final: 0.8598 (ttp80) REVERT: G 72 ASP cc_start: 0.8821 (m-30) cc_final: 0.8472 (m-30) REVERT: H 42 TYR cc_start: 0.8864 (t80) cc_final: 0.8594 (t80) REVERT: H 68 ASP cc_start: 0.8954 (t70) cc_final: 0.8730 (t0) REVERT: H 78 SER cc_start: 0.9536 (t) cc_final: 0.9251 (t) REVERT: H 88 THR cc_start: 0.9441 (m) cc_final: 0.9209 (p) REVERT: H 92 ARG cc_start: 0.8777 (mtp85) cc_final: 0.8571 (mtp85) REVERT: H 101 LEU cc_start: 0.9130 (mm) cc_final: 0.8868 (mm) REVERT: K 59 GLU cc_start: 0.8871 (pm20) cc_final: 0.8316 (pm20) REVERT: K 79 LYS cc_start: 0.8404 (tptt) cc_final: 0.7907 (tttm) REVERT: K 80 THR cc_start: 0.9265 (p) cc_final: 0.8956 (p) REVERT: K 81 ASP cc_start: 0.9159 (m-30) cc_final: 0.8826 (m-30) REVERT: L 43 VAL cc_start: 0.9350 (t) cc_final: 0.9094 (m) REVERT: M 927 MET cc_start: 0.9425 (ppp) cc_final: 0.9094 (pmm) REVERT: M 949 ARG cc_start: 0.9204 (mtp85) cc_final: 0.8825 (tpp80) REVERT: M 952 THR cc_start: 0.9389 (p) cc_final: 0.8779 (p) REVERT: M 953 ARG cc_start: 0.9304 (mtp85) cc_final: 0.9084 (mtp85) REVERT: M 954 GLN cc_start: 0.8748 (mp10) cc_final: 0.8280 (mp10) REVERT: M 956 LYS cc_start: 0.9385 (mmmt) cc_final: 0.9062 (mmmm) REVERT: R 76 MET cc_start: 0.4852 (pmm) cc_final: 0.3855 (tmm) outliers start: 19 outliers final: 12 residues processed: 338 average time/residue: 0.1323 time to fit residues: 62.5120 Evaluate side-chains 344 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 332 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 73 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN C 73 ASN E 68 GLN E 125 GLN G 73 ASN G 84 GLN H 63 ASN K 68 GLN L 25 ASN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 926 ASN ** R 80 ASN ** 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 = 0.3994 r_free = 0.3994 target = 0.133309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.076216 restraints weight = 31080.874| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.97 r_work: 0.2711 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15568 Z= 0.180 Angle : 0.642 18.310 22292 Z= 0.359 Chirality : 0.042 0.221 2533 Planarity : 0.006 0.143 1814 Dihedral : 29.405 179.721 4455 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.67 % Allowed : 17.58 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.51 (0.26), residues: 1081 helix: 2.19 (0.20), residues: 656 sheet: -0.35 (0.62), residues: 75 loop : -1.04 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 7 TYR 0.020 0.002 TYR H 83 PHE 0.022 0.001 PHE M 943 TRP 0.003 0.001 TRP R 96 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (15553) covalent geometry : angle 0.61616 / 0.36 (22281) hydrogen bonds : bond 0.04621 / 3.19 ( 884) hydrogen bonds : angle 3.35899 / 2.36 ( 2231) metal coordination : bond 0.00720 / 0.47 ( 14) metal coordination : angle 8.93784 / 5.37 ( 9) link_NAG-SER : bond 0.00314 / 0.17 ( 1) link_NAG-SER : angle 0.87754 / 0.47 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 334 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 LEU cc_start: 0.8985 (mt) cc_final: 0.8432 (tt) REVERT: A 965 HIS cc_start: 0.1903 (m-70) cc_final: 0.1432 (m-70) REVERT: A 986 CYS cc_start: 0.8956 (t) cc_final: 0.8685 (p) REVERT: C 38 ASN cc_start: 0.9241 (t0) cc_final: 0.9032 (t0) REVERT: D 68 ASP cc_start: 0.9106 (t70) cc_final: 0.8656 (t0) REVERT: D 113 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8702 (mt-10) REVERT: E 56 LYS cc_start: 0.9240 (ttmm) cc_final: 0.9024 (ttpt) REVERT: F 25 ASN cc_start: 0.9186 (m-40) cc_final: 0.8837 (m110) REVERT: F 77 LYS cc_start: 0.9290 (mmtm) cc_final: 0.8994 (mmtm) REVERT: F 88 TYR cc_start: 0.9212 (m-80) cc_final: 0.8943 (m-80) REVERT: G 68 ASN cc_start: 0.8950 (m-40) cc_final: 0.8421 (m110) REVERT: G 71 ARG cc_start: 0.9127 (ttp80) cc_final: 0.8619 (ttp80) REVERT: G 72 ASP cc_start: 0.8852 (m-30) cc_final: 0.8481 (m-30) REVERT: G 91 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7740 (tm-30) REVERT: H 42 TYR cc_start: 0.8948 (t80) cc_final: 0.8620 (t80) REVERT: H 47 GLN cc_start: 0.9339 (tt0) cc_final: 0.9103 (tm-30) REVERT: H 88 THR cc_start: 0.9442 (m) cc_final: 0.9204 (p) REVERT: H 101 LEU cc_start: 0.9144 (mm) cc_final: 0.8886 (mm) REVERT: K 59 GLU cc_start: 0.8852 (pm20) cc_final: 0.8448 (pm20) REVERT: K 79 LYS cc_start: 0.8471 (tptt) cc_final: 0.7972 (tttp) REVERT: K 80 THR cc_start: 0.9256 (p) cc_final: 0.8937 (p) REVERT: K 81 ASP cc_start: 0.9173 (m-30) cc_final: 0.8841 (m-30) REVERT: L 43 VAL cc_start: 0.9343 (t) cc_final: 0.9067 (m) REVERT: M 949 ARG cc_start: 0.9203 (mtp85) cc_final: 0.8786 (tpp80) REVERT: M 952 THR cc_start: 0.9341 (p) cc_final: 0.8785 (p) REVERT: M 953 ARG cc_start: 0.9270 (mtp85) cc_final: 0.9022 (mtp85) REVERT: M 954 GLN cc_start: 0.8736 (mp10) cc_final: 0.8323 (mp10) REVERT: M 956 LYS cc_start: 0.9368 (mmmt) cc_final: 0.9011 (mmmm) REVERT: R 11 ARG cc_start: 0.8960 (ptt-90) cc_final: 0.8639 (ptp-170) outliers start: 24 outliers final: 20 residues processed: 338 average time/residue: 0.1292 time to fit residues: 60.8529 Evaluate side-chains 345 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 325 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 933 VAL Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 37 ASN Chi-restraints excluded: chain R residue 89 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 81 optimal weight: 40.0000 chunk 112 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 125 optimal weight: 30.0000 chunk 62 optimal weight: 1.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 93 GLN E 125 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN L 25 ASN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.130680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.073827 restraints weight = 30917.810| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.93 r_work: 0.2651 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 15568 Z= 0.307 Angle : 0.720 17.716 22292 Z= 0.396 Chirality : 0.045 0.213 2533 Planarity : 0.005 0.057 1814 Dihedral : 29.607 173.489 4455 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.78 % Allowed : 17.35 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.27 (0.26), residues: 1081 helix: 1.99 (0.20), residues: 654 sheet: -0.41 (0.63), residues: 75 loop : -1.09 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 20 TYR 0.019 0.002 TYR H 83 PHE 0.014 0.002 PHE C 25 TRP 0.006 0.001 TRP R 96 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.31 (15553) covalent geometry : angle 0.69893 / 0.39 (22281) hydrogen bonds : bond 0.05411 / 3.72 ( 884) hydrogen bonds : angle 3.63104 / 2.54 ( 2231) metal coordination : bond 0.01184 / 0.79 ( 14) metal coordination : angle 8.69890 / 5.25 ( 9) link_NAG-SER : bond 0.00601 / 0.32 ( 1) link_NAG-SER : angle 1.60874 / 0.85 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 329 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 LEU cc_start: 0.8977 (mt) cc_final: 0.8410 (tt) REVERT: A 965 HIS cc_start: 0.2078 (m-70) cc_final: 0.1634 (m-70) REVERT: A 986 CYS cc_start: 0.8971 (t) cc_final: 0.8711 (p) REVERT: C 38 ASN cc_start: 0.9311 (t0) cc_final: 0.8960 (t0) REVERT: C 57 TYR cc_start: 0.9488 (t80) cc_final: 0.9029 (t80) REVERT: D 68 ASP cc_start: 0.9125 (t70) cc_final: 0.8604 (t0) REVERT: D 113 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8698 (mt-10) REVERT: E 56 LYS cc_start: 0.9329 (ttmm) cc_final: 0.9094 (ttpt) REVERT: G 68 ASN cc_start: 0.8968 (m-40) cc_final: 0.8404 (m110) REVERT: G 71 ARG cc_start: 0.9128 (ttp80) cc_final: 0.8630 (ttp80) REVERT: G 72 ASP cc_start: 0.8914 (m-30) cc_final: 0.8561 (m-30) REVERT: H 42 TYR cc_start: 0.8948 (t80) cc_final: 0.8587 (t80) REVERT: H 47 GLN cc_start: 0.9361 (tt0) cc_final: 0.9107 (tm-30) REVERT: H 86 ARG cc_start: 0.8858 (tpp80) cc_final: 0.8379 (tpp80) REVERT: H 88 THR cc_start: 0.9459 (m) cc_final: 0.9112 (p) REVERT: H 101 LEU cc_start: 0.9147 (mm) cc_final: 0.8858 (mm) REVERT: K 59 GLU cc_start: 0.8807 (pm20) cc_final: 0.8395 (pm20) REVERT: K 79 LYS cc_start: 0.8626 (tptt) cc_final: 0.8111 (tttp) REVERT: K 80 THR cc_start: 0.9218 (p) cc_final: 0.8856 (p) REVERT: K 81 ASP cc_start: 0.9178 (m-30) cc_final: 0.8846 (m-30) REVERT: M 949 ARG cc_start: 0.9209 (mtp85) cc_final: 0.8898 (tpp80) REVERT: M 952 THR cc_start: 0.9303 (p) cc_final: 0.8697 (p) REVERT: M 953 ARG cc_start: 0.9286 (mtp85) cc_final: 0.9057 (mtp85) REVERT: M 954 GLN cc_start: 0.8702 (mp10) cc_final: 0.8205 (mp10) REVERT: M 956 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9004 (mmmt) REVERT: M 961 ASN cc_start: 0.8987 (t0) cc_final: 0.8657 (t0) outliers start: 34 outliers final: 27 residues processed: 338 average time/residue: 0.1227 time to fit residues: 58.1468 Evaluate side-chains 349 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 322 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 120 CYS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 933 VAL Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 89 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.1980 chunk 91 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 68 GLN E 125 GLN F 25 ASN F 75 HIS G 73 ASN G 84 GLN H 63 ASN K 68 GLN L 25 ASN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 926 ASN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.133830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.077658 restraints weight = 30448.825| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.88 r_work: 0.2723 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15568 Z= 0.143 Angle : 0.634 14.384 22292 Z= 0.359 Chirality : 0.042 0.227 2533 Planarity : 0.005 0.090 1814 Dihedral : 29.493 172.779 4455 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.89 % Allowed : 20.24 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.50 (0.26), residues: 1081 helix: 2.17 (0.20), residues: 656 sheet: -0.34 (0.63), residues: 75 loop : -1.00 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 7 TYR 0.017 0.001 TYR H 83 PHE 0.024 0.001 PHE M 943 TRP 0.003 0.001 TRP R 36 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (15553) covalent geometry : angle 0.61378 / 0.36 (22281) hydrogen bonds : bond 0.04450 / 3.07 ( 884) hydrogen bonds : angle 3.28529 / 2.31 ( 2231) metal coordination : bond 0.00412 / 0.26 ( 14) metal coordination : angle 7.90402 / 4.84 ( 9) link_NAG-SER : bond 0.00241 / 0.13 ( 1) link_NAG-SER : angle 0.71842 / 0.39 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 344 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 LEU cc_start: 0.8907 (mt) cc_final: 0.8269 (tt) REVERT: A 965 HIS cc_start: 0.1953 (m-70) cc_final: 0.1483 (m-70) REVERT: A 986 CYS cc_start: 0.8995 (t) cc_final: 0.8745 (p) REVERT: C 38 ASN cc_start: 0.9258 (t0) cc_final: 0.9012 (t0) REVERT: D 68 ASP cc_start: 0.9111 (t70) cc_final: 0.8573 (t0) REVERT: D 113 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8698 (mt-10) REVERT: E 56 LYS cc_start: 0.9245 (ttmm) cc_final: 0.9015 (ttpt) REVERT: F 25 ASN cc_start: 0.9131 (m-40) cc_final: 0.8736 (m110) REVERT: F 88 TYR cc_start: 0.9131 (m-80) cc_final: 0.8829 (m-80) REVERT: F 98 TYR cc_start: 0.9424 (m-10) cc_final: 0.9186 (m-10) REVERT: G 68 ASN cc_start: 0.8952 (m-40) cc_final: 0.8192 (m110) REVERT: G 71 ARG cc_start: 0.9117 (ttp80) cc_final: 0.8619 (ttp80) REVERT: G 72 ASP cc_start: 0.8893 (m-30) cc_final: 0.8452 (m-30) REVERT: G 91 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7768 (tm-30) REVERT: H 42 TYR cc_start: 0.8907 (t80) cc_final: 0.8581 (t80) REVERT: H 47 GLN cc_start: 0.9364 (tt0) cc_final: 0.9100 (tm-30) REVERT: H 88 THR cc_start: 0.9467 (m) cc_final: 0.9209 (p) REVERT: H 101 LEU cc_start: 0.9121 (mm) cc_final: 0.8837 (mm) REVERT: K 42 ARG cc_start: 0.7802 (mmm160) cc_final: 0.7419 (mmm160) REVERT: K 59 GLU cc_start: 0.8748 (pm20) cc_final: 0.8373 (pm20) REVERT: K 79 LYS cc_start: 0.8513 (tptt) cc_final: 0.8010 (tttp) REVERT: K 80 THR cc_start: 0.9279 (p) cc_final: 0.8966 (p) REVERT: K 81 ASP cc_start: 0.9134 (m-30) cc_final: 0.8797 (m-30) REVERT: L 43 VAL cc_start: 0.9310 (t) cc_final: 0.9050 (m) REVERT: M 927 MET cc_start: 0.9442 (ppp) cc_final: 0.9055 (pmm) REVERT: M 949 ARG cc_start: 0.9216 (mtp85) cc_final: 0.8899 (tpp80) REVERT: M 952 THR cc_start: 0.9318 (p) cc_final: 0.8655 (p) REVERT: M 953 ARG cc_start: 0.9299 (mtp85) cc_final: 0.9065 (mtp85) REVERT: M 954 GLN cc_start: 0.8732 (mp10) cc_final: 0.8262 (mp10) REVERT: R 11 ARG cc_start: 0.9137 (ptt-90) cc_final: 0.8639 (ptp-170) REVERT: R 76 MET cc_start: 0.4756 (pmm) cc_final: 0.4085 (tmm) outliers start: 17 outliers final: 16 residues processed: 348 average time/residue: 0.1271 time to fit residues: 62.0655 Evaluate side-chains 349 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 333 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 933 VAL Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 37 ASN Chi-restraints excluded: chain R residue 89 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 120 optimal weight: 40.0000 chunk 113 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 30.0000 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 20.0000 chunk 110 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 68 GLN E 125 GLN H 63 ASN K 68 GLN K 93 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 961 ASN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.133612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.076183 restraints weight = 30723.948| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.94 r_work: 0.2706 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15568 Z= 0.157 Angle : 0.632 14.496 22292 Z= 0.356 Chirality : 0.042 0.221 2533 Planarity : 0.005 0.050 1814 Dihedral : 29.501 172.439 4455 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.11 % Allowed : 20.36 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.55 (0.26), residues: 1081 helix: 2.21 (0.20), residues: 655 sheet: -0.32 (0.63), residues: 75 loop : -0.98 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 20 TYR 0.018 0.001 TYR H 83 PHE 0.021 0.001 PHE M 943 TRP 0.003 0.001 TRP R 96 HIS 0.002 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (15553) covalent geometry : angle 0.61308 / 0.36 (22281) hydrogen bonds : bond 0.04488 / 3.10 ( 884) hydrogen bonds : angle 3.27954 / 2.30 ( 2231) metal coordination : bond 0.00533 / 0.32 ( 14) metal coordination : angle 7.68913 / 4.71 ( 9) link_NAG-SER : bond 0.00274 / 0.14 ( 1) link_NAG-SER : angle 0.83658 / 0.45 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 336 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 LEU cc_start: 0.8921 (mt) cc_final: 0.8299 (tt) REVERT: A 965 HIS cc_start: 0.1991 (m-70) cc_final: 0.1522 (m-70) REVERT: A 985 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8570 (mmtm) REVERT: A 986 CYS cc_start: 0.8987 (t) cc_final: 0.8695 (p) REVERT: C 38 ASN cc_start: 0.9265 (t0) cc_final: 0.9020 (t0) REVERT: D 68 ASP cc_start: 0.9101 (t70) cc_final: 0.8543 (t0) REVERT: D 113 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8664 (mt-10) REVERT: E 56 LYS cc_start: 0.9262 (ttmm) cc_final: 0.9034 (ttpt) REVERT: F 25 ASN cc_start: 0.9160 (m-40) cc_final: 0.8773 (m110) REVERT: F 88 TYR cc_start: 0.9194 (m-80) cc_final: 0.8860 (m-80) REVERT: G 68 ASN cc_start: 0.8947 (m-40) cc_final: 0.8260 (m110) REVERT: G 71 ARG cc_start: 0.9119 (ttp80) cc_final: 0.8638 (ttp80) REVERT: G 72 ASP cc_start: 0.8904 (m-30) cc_final: 0.8480 (m-30) REVERT: G 91 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7805 (tm-30) REVERT: H 42 TYR cc_start: 0.8945 (t80) cc_final: 0.8605 (t80) REVERT: H 47 GLN cc_start: 0.9355 (tt0) cc_final: 0.9090 (tm-30) REVERT: H 88 THR cc_start: 0.9450 (m) cc_final: 0.9210 (p) REVERT: H 101 LEU cc_start: 0.9090 (mm) cc_final: 0.8807 (mm) REVERT: K 59 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8341 (pm20) REVERT: K 79 LYS cc_start: 0.8512 (tptt) cc_final: 0.8011 (tttp) REVERT: K 80 THR cc_start: 0.9245 (p) cc_final: 0.8872 (p) REVERT: K 81 ASP cc_start: 0.9139 (m-30) cc_final: 0.8803 (m-30) REVERT: L 43 VAL cc_start: 0.9338 (t) cc_final: 0.9083 (m) REVERT: M 949 ARG cc_start: 0.9199 (mtp85) cc_final: 0.8900 (tpp80) REVERT: M 952 THR cc_start: 0.9303 (p) cc_final: 0.8640 (p) REVERT: M 953 ARG cc_start: 0.9294 (mtp85) cc_final: 0.9057 (mtp85) REVERT: M 954 GLN cc_start: 0.8719 (mp10) cc_final: 0.8256 (mp10) REVERT: M 956 LYS cc_start: 0.9406 (mmmt) cc_final: 0.9090 (mmmt) REVERT: M 961 ASN cc_start: 0.8896 (t0) cc_final: 0.8638 (t0) REVERT: R 15 ARG cc_start: 0.9153 (tpp-160) cc_final: 0.8793 (tpp-160) outliers start: 19 outliers final: 15 residues processed: 340 average time/residue: 0.1201 time to fit residues: 57.1757 Evaluate side-chains 346 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 330 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 933 VAL Chi-restraints excluded: chain R residue 37 ASN Chi-restraints excluded: chain R residue 89 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 37 optimal weight: 0.5980 chunk 104 optimal weight: 0.0570 chunk 57 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 21 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 105 optimal weight: 0.7980 chunk 1 optimal weight: 40.0000 chunk 112 optimal weight: 0.0370 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 68 GLN E 93 GLN E 125 GLN H 63 ASN H 84 ASN K 68 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.135187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.078602 restraints weight = 31177.298| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.96 r_work: 0.2749 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15568 Z= 0.134 Angle : 0.638 16.449 22292 Z= 0.360 Chirality : 0.042 0.260 2533 Planarity : 0.005 0.116 1814 Dihedral : 29.442 172.083 4455 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.11 % Allowed : 21.25 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.62 (0.26), residues: 1081 helix: 2.25 (0.20), residues: 654 sheet: -0.37 (0.62), residues: 75 loop : -0.88 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 6 TYR 0.018 0.001 TYR H 83 PHE 0.029 0.001 PHE M 943 TRP 0.003 0.001 TRP R 36 HIS 0.002 0.000 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 (15553) covalent geometry : angle 0.62223 / 0.36 (22281) hydrogen bonds : bond 0.04286 / 2.97 ( 884) hydrogen bonds : angle 3.19221 / 2.24 ( 2231) metal coordination : bond 0.00449 / 0.27 ( 14) metal coordination : angle 7.10908 / 4.36 ( 9) link_NAG-SER : bond 0.00077 / 0.04 ( 1) link_NAG-SER : angle 0.36536 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 343 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 LEU cc_start: 0.8894 (mt) cc_final: 0.8277 (tt) REVERT: A 965 HIS cc_start: 0.1958 (m-70) cc_final: 0.1527 (m-70) REVERT: A 985 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8628 (mmtm) REVERT: A 986 CYS cc_start: 0.9046 (t) cc_final: 0.8758 (p) REVERT: C 38 ASN cc_start: 0.9227 (t0) cc_final: 0.8960 (t0) REVERT: D 68 ASP cc_start: 0.9086 (t70) cc_final: 0.8597 (t0) REVERT: D 113 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8624 (mt-10) REVERT: E 56 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8982 (ttpt) REVERT: F 25 ASN cc_start: 0.9139 (m-40) cc_final: 0.8740 (m110) REVERT: F 88 TYR cc_start: 0.9224 (m-80) cc_final: 0.8886 (m-80) REVERT: F 98 TYR cc_start: 0.9438 (m-10) cc_final: 0.9212 (m-10) REVERT: G 71 ARG cc_start: 0.9117 (ttp80) cc_final: 0.8645 (ttp80) REVERT: G 72 ASP cc_start: 0.8864 (m-30) cc_final: 0.8366 (m-30) REVERT: G 91 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7786 (tm-30) REVERT: H 42 TYR cc_start: 0.8917 (t80) cc_final: 0.8567 (t80) REVERT: H 47 GLN cc_start: 0.9351 (tt0) cc_final: 0.9090 (tm-30) REVERT: H 88 THR cc_start: 0.9447 (m) cc_final: 0.9242 (p) REVERT: H 101 LEU cc_start: 0.9082 (mm) cc_final: 0.8839 (mm) REVERT: K 59 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8226 (pm20) REVERT: K 79 LYS cc_start: 0.8436 (tptt) cc_final: 0.7948 (tttp) REVERT: K 80 THR cc_start: 0.9266 (p) cc_final: 0.8958 (p) REVERT: K 81 ASP cc_start: 0.9134 (m-30) cc_final: 0.8806 (m-30) REVERT: M 949 ARG cc_start: 0.9189 (mtp85) cc_final: 0.8916 (tpp80) REVERT: M 952 THR cc_start: 0.9297 (p) cc_final: 0.8668 (p) REVERT: M 953 ARG cc_start: 0.9298 (mtp85) cc_final: 0.9048 (mtp85) REVERT: M 954 GLN cc_start: 0.8724 (mp10) cc_final: 0.8255 (mp10) REVERT: M 956 LYS cc_start: 0.9347 (mmmt) cc_final: 0.9083 (mmmt) REVERT: M 959 LYS cc_start: 0.9239 (tptp) cc_final: 0.8812 (tppt) REVERT: R 76 MET cc_start: 0.4767 (pmm) cc_final: 0.4022 (tmm) outliers start: 19 outliers final: 9 residues processed: 349 average time/residue: 0.1261 time to fit residues: 61.3416 Evaluate side-chains 347 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 337 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 933 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 94 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN E 68 GLN E 113 HIS E 125 GLN G 73 ASN G 84 GLN H 63 ASN H 84 ASN K 68 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 961 ASN ** R 80 ASN ** 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 = 0.3988 r_free = 0.3988 target = 0.132716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.075049 restraints weight = 31030.309| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.98 r_work: 0.2689 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15568 Z= 0.212 Angle : 0.692 15.100 22292 Z= 0.382 Chirality : 0.043 0.257 2533 Planarity : 0.005 0.107 1814 Dihedral : 29.585 171.650 4455 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.89 % Allowed : 22.14 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.54 (0.26), residues: 1081 helix: 2.15 (0.20), residues: 654 sheet: -0.19 (0.68), residues: 63 loop : -0.88 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 11 TYR 0.021 0.002 TYR H 83 PHE 0.028 0.001 PHE M 943 TRP 0.006 0.001 TRP R 96 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (15553) covalent geometry : angle 0.67527 / 0.38 (22281) hydrogen bonds : bond 0.04775 / 3.31 ( 884) hydrogen bonds : angle 3.44162 / 2.41 ( 2231) metal coordination : bond 0.00896 / 0.58 ( 14) metal coordination : angle 7.56142 / 4.62 ( 9) link_NAG-SER : bond 0.00405 / 0.21 ( 1) link_NAG-SER : angle 1.15941 / 0.62 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 335 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 LEU cc_start: 0.8872 (mt) cc_final: 0.8276 (tt) REVERT: A 965 HIS cc_start: 0.2120 (m-70) cc_final: 0.1691 (m-70) REVERT: A 986 CYS cc_start: 0.9027 (t) cc_final: 0.8762 (p) REVERT: C 38 ASN cc_start: 0.9289 (t0) cc_final: 0.9059 (t0) REVERT: D 68 ASP cc_start: 0.9105 (t70) cc_final: 0.8554 (t0) REVERT: D 113 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8691 (mt-10) REVERT: E 56 LYS cc_start: 0.9287 (ttmm) cc_final: 0.9064 (ttpt) REVERT: F 25 ASN cc_start: 0.9169 (m-40) cc_final: 0.8783 (m110) REVERT: F 88 TYR cc_start: 0.9296 (m-80) cc_final: 0.8951 (m-80) REVERT: G 68 ASN cc_start: 0.8972 (m-40) cc_final: 0.8283 (m110) REVERT: G 71 ARG cc_start: 0.9131 (ttp80) cc_final: 0.8644 (ttp80) REVERT: G 72 ASP cc_start: 0.8887 (m-30) cc_final: 0.8380 (m-30) REVERT: G 91 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7856 (tm-30) REVERT: H 42 TYR cc_start: 0.8967 (t80) cc_final: 0.8598 (t80) REVERT: H 47 GLN cc_start: 0.9343 (tt0) cc_final: 0.9079 (tm-30) REVERT: H 101 LEU cc_start: 0.9126 (mm) cc_final: 0.8872 (mm) REVERT: K 59 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: K 79 LYS cc_start: 0.8529 (tptt) cc_final: 0.8032 (tttp) REVERT: K 80 THR cc_start: 0.9239 (p) cc_final: 0.8861 (p) REVERT: K 81 ASP cc_start: 0.9140 (m-30) cc_final: 0.8804 (m-30) REVERT: M 949 ARG cc_start: 0.9204 (mtp85) cc_final: 0.8929 (tpp80) REVERT: M 952 THR cc_start: 0.9298 (p) cc_final: 0.8621 (p) REVERT: M 953 ARG cc_start: 0.9330 (mtp85) cc_final: 0.9076 (mtp85) REVERT: M 954 GLN cc_start: 0.8729 (mp10) cc_final: 0.8289 (mp10) REVERT: R 11 ARG cc_start: 0.9040 (ptp-170) cc_final: 0.8365 (ptp-170) REVERT: R 76 MET cc_start: 0.4642 (pmm) cc_final: 0.3953 (tmm) outliers start: 17 outliers final: 14 residues processed: 342 average time/residue: 0.1217 time to fit residues: 58.6532 Evaluate side-chains 345 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 330 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 933 VAL Chi-restraints excluded: chain R residue 89 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 42 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN E 125 GLN G 73 ASN H 63 ASN H 95 GLN K 68 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** 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 = 0.3995 r_free = 0.3995 target = 0.133241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.075738 restraints weight = 30664.599| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.93 r_work: 0.2698 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 15568 Z= 0.203 Angle : 0.859 59.188 22292 Z= 0.495 Chirality : 0.043 0.332 2533 Planarity : 0.005 0.101 1814 Dihedral : 29.593 171.602 4455 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.56 % Allowed : 21.36 % Favored : 76.08 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.54 (0.26), residues: 1081 helix: 2.15 (0.20), residues: 654 sheet: -0.19 (0.68), residues: 63 loop : -0.88 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 11 TYR 0.019 0.002 TYR H 83 PHE 0.016 0.001 PHE M 943 TRP 0.006 0.001 TRP R 96 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (15553) covalent geometry : angle 0.84600 / 0.49 (22281) hydrogen bonds : bond 0.04740 / 3.29 ( 884) hydrogen bonds : angle 3.44672 / 2.41 ( 2231) metal coordination : bond 0.00889 / 0.55 ( 14) metal coordination : angle 7.53161 / 4.60 ( 9) link_NAG-SER : bond 0.00342 / 0.18 ( 1) link_NAG-SER : angle 1.20242 / 0.64 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3528.07 seconds wall clock time: 60 minutes 51.39 seconds (3651.39 seconds total)