Starting phenix.real_space_refine on Fri Sep 11 04:07:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vo0_32048/09_2026/7vo0_32048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vo0_32048/09_2026/7vo0_32048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vo0_32048/09_2026/7vo0_32048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vo0_32048/09_2026/7vo0_32048.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vo0_32048/09_2026/7vo0_32048.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vo0_32048/09_2026/7vo0_32048.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vo0_32048/09_2026/7vo0_32048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vo0_32048/09_2026/7vo0_32048.cif" } resolution = 3.4 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= 0.002 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 18 6.06 5 P 86 5.49 5 S 36 5.16 5 C 4435 2.51 5 N 1430 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7661 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 881 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "B" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 882 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "G" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2419 SG CYS G 90 17.020 35.919 74.138 1.00 14.11 S ATOM 2441 SG CYS G 93 14.658 38.603 75.561 1.00 14.02 S ATOM 2710 SG CYS G 130 14.131 34.547 74.640 1.00 13.95 S ATOM 2729 SG CYS G 133 14.223 38.200 72.447 1.00 12.72 S ATOM 2333 SG CYS G 79 22.903 29.119 87.999 1.00 8.52 S ATOM 3399 SG CYS H 90 47.171 17.297 77.955 1.00 15.08 S ATOM 3421 SG CYS H 93 50.676 16.458 76.618 1.00 15.80 S ATOM 3690 SG CYS H 130 48.162 13.693 76.952 1.00 14.71 S ATOM 3709 SG CYS H 133 49.706 15.440 80.059 1.00 13.87 S ATOM 3313 SG CYS H 79 39.498 21.082 63.805 1.00 12.35 S ATOM 4379 SG CYS K 90 67.435 35.188 121.307 1.00 14.64 S ATOM 4401 SG CYS K 93 69.485 38.036 119.820 1.00 11.63 S ATOM 4670 SG CYS K 130 71.181 34.650 120.418 1.00 14.11 S ATOM 4689 SG CYS K 133 70.136 36.993 123.291 1.00 13.78 S ATOM 4293 SG CYS K 79 62.768 28.600 107.613 1.00 10.21 S ATOM 5359 SG CYS L 90 36.790 17.905 117.231 1.00 14.03 S ATOM 5381 SG CYS L 93 33.278 16.685 118.266 1.00 15.09 S ATOM 5650 SG CYS L 130 36.117 14.200 117.874 1.00 15.43 S ATOM 5669 SG CYS L 133 34.660 16.009 114.807 1.00 12.84 S ATOM 5273 SG CYS L 79 44.495 20.993 131.110 1.00 15.73 S ATOM 6339 SG CYS M 90 25.503 75.233 95.065 1.00 11.24 S ATOM 6361 SG CYS M 93 22.323 74.046 93.241 1.00 11.91 S ATOM 6630 SG CYS M 130 23.831 77.865 94.260 1.00 13.46 S ATOM 6649 SG CYS M 133 21.716 74.801 96.257 1.00 15.34 S ATOM 6253 SG CYS M 79 36.178 76.922 83.660 1.00 9.11 S ATOM 7319 SG CYS N 90 60.394 75.070 99.755 1.00 10.61 S ATOM 7341 SG CYS N 93 63.487 73.535 101.597 1.00 10.62 S ATOM 7610 SG CYS N 130 63.136 77.242 101.261 1.00 13.41 S ATOM 7629 SG CYS N 133 63.978 75.057 98.267 1.00 15.58 S ATOM 7233 SG CYS N 79 50.376 76.774 111.528 1.00 7.87 S Time building chain proxies: 1.91, per 1000 atoms: 0.25 Number of scatterers: 7661 At special positions: 0 Unit cell: (85.8, 100.1, 159.5, 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 18 29.99 S 36 16.00 P 86 15.00 O 1656 8.00 N 1430 7.00 C 4435 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 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 399.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 93 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 133 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 130 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 87 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 85 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 79 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 86 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 122 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 84 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 93 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 133 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 130 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 79 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 87 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 86 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 84 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 122 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 93 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 133 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 90 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 130 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 79 " pdb="ZN ZN K 202 " - pdb=" NE2 HIS K 85 " pdb="ZN ZN K 202 " - pdb=" NE2 HIS K 87 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 122 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 84 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 86 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 133 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 90 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 93 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 130 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" NE2 HIS L 85 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 79 " pdb="ZN ZN L 202 " - pdb=" NE2 HIS L 87 " pdb=" ZN L 203 " pdb="ZN ZN L 203 " - pdb=" NE2 HIS L 86 " pdb="ZN ZN L 203 " - pdb=" NE2 HIS L 84 " pdb="ZN ZN L 203 " - pdb=" NE2 HIS L 122 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 133 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " Number of angles added : 36 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 48.7% alpha, 16.7% beta 22 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'G' and resid 13 through 26 Processing helix chain 'G' and resid 32 through 43 Processing helix chain 'G' and resid 47 through 62 removed outlier: 3.552A pdb=" N VAL G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.647A pdb=" N GLU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'H' and resid 13 through 26 Processing helix chain 'H' and resid 32 through 43 Processing helix chain 'H' and resid 47 through 61 Processing helix chain 'H' and resid 101 through 116 removed outlier: 3.946A pdb=" N GLU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 135 removed outlier: 4.230A pdb=" N ALA H 134 " --> pdb=" O CYS H 130 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY H 135 " --> pdb=" O ALA H 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 135' Processing helix chain 'K' and resid 13 through 26 Processing helix chain 'K' and resid 31 through 42 Processing helix chain 'K' and resid 47 through 62 Processing helix chain 'K' and resid 101 through 115 removed outlier: 3.770A pdb=" N GLU K 105 " --> pdb=" O GLY K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 135 removed outlier: 3.939A pdb=" N ALA K 134 " --> pdb=" O CYS K 130 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY K 135 " --> pdb=" O ALA K 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 130 through 135' Processing helix chain 'L' and resid 13 through 26 Processing helix chain 'L' and resid 32 through 43 Processing helix chain 'L' and resid 47 through 62 Processing helix chain 'L' and resid 101 through 115 removed outlier: 3.893A pdb=" N GLU L 105 " --> pdb=" O GLY L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 135 removed outlier: 4.323A pdb=" N ALA L 134 " --> pdb=" O CYS L 130 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 130 through 135' Processing helix chain 'M' and resid 13 through 26 removed outlier: 3.944A pdb=" N VAL M 19 " --> pdb=" O GLN M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 43 Processing helix chain 'M' and resid 47 through 62 Processing helix chain 'M' and resid 101 through 116 removed outlier: 3.938A pdb=" N GLU M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 135 Processing helix chain 'N' and resid 13 through 26 removed outlier: 3.529A pdb=" N VAL N 26 " --> pdb=" O ALA N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 43 Processing helix chain 'N' and resid 47 through 62 Processing helix chain 'N' and resid 101 through 116 removed outlier: 4.015A pdb=" N GLU N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 135 removed outlier: 4.197A pdb=" N ALA N 134 " --> pdb=" O CYS N 130 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY N 135 " --> pdb=" O ALA N 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 130 through 135' Processing sheet with id=AA1, first strand: chain 'G' and resid 30 through 31 removed outlier: 3.524A pdb=" N ARG G 77 " --> pdb=" O ASP G 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 96 through 99 removed outlier: 6.315A pdb=" N HIS G 87 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLY G 128 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL G 89 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU G 125 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N HIS H 87 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLY H 128 " --> pdb=" O HIS H 87 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL H 89 " --> pdb=" O GLY H 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 30 through 31 removed outlier: 3.824A pdb=" N ARG H 77 " --> pdb=" O ASP H 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 64 through 68 Processing sheet with id=AA5, first strand: chain 'K' and resid 96 through 99 removed outlier: 6.693A pdb=" N HIS K 87 " --> pdb=" O ILE K 126 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLY K 128 " --> pdb=" O HIS K 87 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL K 89 " --> pdb=" O GLY K 128 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N HIS L 87 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE L 126 " --> pdb=" O HIS L 87 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL L 89 " --> pdb=" O ILE L 126 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY L 128 " --> pdb=" O VAL L 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.802A pdb=" N ARG L 30 " --> pdb=" O TYR L 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 65 through 68 Processing sheet with id=AA8, first strand: chain 'M' and resid 96 through 99 removed outlier: 6.792A pdb=" N HIS M 87 " --> pdb=" O ILE M 126 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLY M 128 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL M 89 " --> pdb=" O GLY M 128 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU N 125 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS N 87 " --> pdb=" O ILE N 126 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLY N 128 " --> pdb=" O HIS N 87 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL N 89 " --> pdb=" O GLY N 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 65 through 68 removed outlier: 3.617A pdb=" N ARG N 77 " --> pdb=" O ASP N 65 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.90 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: 1896 1.33 - 1.45: 1974 1.45 - 1.57: 3876 1.57 - 1.70: 170 1.70 - 1.82: 42 Bond restraints: 7958 Sorted by residual: bond pdb=" C3' DG A 39 " pdb=" C2' DG A 39 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DT B 76 " pdb=" C2' DT B 76 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DC B 67 " pdb=" C2' DC B 67 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.17e+00 bond pdb=" C3' DA A 9 " pdb=" C2' DA A 9 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.08e+00 bond pdb=" N THR M 129 " pdb=" CA THR M 129 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.21e-02 6.83e+03 8.87e+00 ... (remaining 7953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 10731 1.65 - 3.29: 386 3.29 - 4.94: 27 4.94 - 6.59: 6 6.59 - 8.23: 1 Bond angle restraints: 11151 Sorted by residual: angle pdb=" N3 DT B 71 " pdb=" C4 DT B 71 " pdb=" O4 DT B 71 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT A 21 " pdb=" C4 DT A 21 " pdb=" O4 DT A 21 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT B 70 " pdb=" C4 DT B 70 " pdb=" O4 DT B 70 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT A 26 " pdb=" C4 DT A 26 " pdb=" O4 DT A 26 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT B 73 " pdb=" C4 DT B 73 " pdb=" O4 DT B 73 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 ... (remaining 11146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3607 17.84 - 35.68: 479 35.68 - 53.53: 319 53.53 - 71.37: 63 71.37 - 89.21: 10 Dihedral angle restraints: 4478 sinusoidal: 2240 harmonic: 2238 Sorted by residual: dihedral pdb=" CA TYR H 76 " pdb=" C TYR H 76 " pdb=" N ARG H 77 " pdb=" CA ARG H 77 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA HIS N 86 " pdb=" C HIS N 86 " pdb=" N HIS N 87 " pdb=" CA HIS N 87 " ideal model delta harmonic sigma weight residual -180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG M 16 " pdb=" CD ARG M 16 " pdb=" NE ARG M 16 " pdb=" CZ ARG M 16 " ideal model delta sinusoidal sigma weight residual -180.00 -137.99 -42.01 2 1.50e+01 4.44e-03 9.55e+00 ... (remaining 4475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 910 0.042 - 0.083: 240 0.083 - 0.125: 100 0.125 - 0.167: 9 0.167 - 0.208: 3 Chirality restraints: 1262 Sorted by residual: chirality pdb=" CB ILE G 126 " pdb=" CA ILE G 126 " pdb=" CG1 ILE G 126 " pdb=" CG2 ILE G 126 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA CYS G 130 " pdb=" N CYS G 130 " pdb=" C CYS G 130 " pdb=" CB CYS G 130 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA CYS M 130 " pdb=" N CYS M 130 " pdb=" C CYS M 130 " pdb=" CB CYS M 130 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 1259 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU L 105 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C GLU L 105 " 0.031 2.00e-02 2.50e+03 pdb=" O GLU L 105 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS L 106 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 52 " -0.020 2.00e-02 2.50e+03 1.12e-02 2.49e+00 pdb=" CG TYR G 52 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR G 52 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR G 52 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR G 52 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR G 52 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR G 52 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR G 52 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 85 " 0.012 2.00e-02 2.50e+03 1.25e-02 2.35e+00 pdb=" CG HIS H 85 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS H 85 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS H 85 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS H 85 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS H 85 " 0.020 2.00e-02 2.50e+03 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 51 2.53 - 3.12: 5479 3.12 - 3.72: 12059 3.72 - 4.31: 16033 4.31 - 4.90: 26103 Nonbonded interactions: 59725 Sorted by model distance: nonbonded pdb=" OD2 ASP L 65 " pdb="ZN ZN L 202 " model vdw 1.938 2.230 nonbonded pdb=" OE2 GLU N 105 " pdb="ZN ZN N 203 " model vdw 1.943 2.230 nonbonded pdb=" OE2 GLU G 105 " pdb="ZN ZN G 203 " model vdw 1.952 2.230 nonbonded pdb=" OD2 ASP N 65 " pdb="ZN ZN N 202 " model vdw 1.958 2.230 nonbonded pdb=" OE2 GLU M 105 " pdb="ZN ZN M 203 " model vdw 1.964 2.230 ... (remaining 59720 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 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.030 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 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 0.372 8018 Z= 0.429 Angle : 0.885 24.092 11187 Z= 0.523 Chirality : 0.045 0.208 1262 Planarity : 0.003 0.052 1160 Dihedral : 21.170 89.208 3038 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.17 % Allowed : 1.02 % Favored : 98.81 % 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: 0.39 (0.29), residues: 774 helix: 1.22 (0.27), residues: 384 sheet: -0.45 (0.37), residues: 156 loop : -0.69 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 14 TYR 0.022 0.002 TYR G 52 PHE 0.006 0.001 PHE L 127 TRP 0.024 0.003 TRP G 107 HIS 0.013 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.41 ( 7958) covalent geometry : angle 0.65556 / 0.51 (11151) hydrogen bonds : bond 0.19364 / 23.06 ( 368) hydrogen bonds : angle 7.48844 / 9.72 ( 1011) metal coordination : bond 0.04834 / 3.48 ( 60) metal coordination : angle 10.49795 / 16.31 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 28 GLU cc_start: 0.5842 (pt0) cc_final: 0.5344 (tt0) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1421 time to fit residues: 32.1747 Evaluate side-chains 122 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.0370 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.0870 chunk 74 optimal weight: 0.9990 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.191160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.160623 restraints weight = 12192.140| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.18 r_work: 0.3577 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 8018 Z= 0.160 Angle : 0.729 16.025 11187 Z= 0.367 Chirality : 0.044 0.192 1262 Planarity : 0.004 0.029 1160 Dihedral : 23.952 74.356 1778 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.38 % Allowed : 12.59 % Favored : 85.03 % 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: 0.45 (0.29), residues: 774 helix: 1.31 (0.26), residues: 384 sheet: -0.52 (0.38), residues: 156 loop : -0.67 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 30 TYR 0.020 0.002 TYR G 117 PHE 0.012 0.002 PHE G 29 TRP 0.015 0.002 TRP L 107 HIS 0.018 0.001 HIS N 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 ( 7958) covalent geometry : angle 0.63648 / 0.36 (11151) hydrogen bonds : bond 0.05703 / 6.08 ( 368) hydrogen bonds : angle 4.41272 / 5.76 ( 1011) metal coordination : bond 0.01621 / 1.43 ( 60) metal coordination : angle 6.30034 / 9.56 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 GLN cc_start: 0.8809 (tp40) cc_final: 0.8430 (mm-40) REVERT: H 38 MET cc_start: 0.8132 (mtt) cc_final: 0.7848 (mtm) REVERT: H 56 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6059 (mp10) REVERT: H 68 ARG cc_start: 0.8351 (mtp180) cc_final: 0.8091 (mtp180) REVERT: K 78 ARG cc_start: 0.8392 (tpt-90) cc_final: 0.8118 (ttt90) REVERT: N 115 HIS cc_start: 0.5685 (m90) cc_final: 0.5284 (m-70) outliers start: 14 outliers final: 7 residues processed: 156 average time/residue: 0.1249 time to fit residues: 24.5450 Evaluate side-chains 133 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain N residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN ** L 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.188673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.152466 restraints weight = 11908.574| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.26 r_work: 0.3508 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8018 Z= 0.196 Angle : 0.707 18.334 11187 Z= 0.360 Chirality : 0.044 0.153 1262 Planarity : 0.004 0.049 1160 Dihedral : 24.297 83.386 1778 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.55 % Allowed : 16.67 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.29), residues: 774 helix: 1.42 (0.26), residues: 384 sheet: -0.47 (0.41), residues: 132 loop : -0.35 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 30 TYR 0.018 0.002 TYR K 52 PHE 0.011 0.001 PHE G 29 TRP 0.010 0.002 TRP G 107 HIS 0.014 0.002 HIS G 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 ( 7958) covalent geometry : angle 0.61631 / 0.36 (11151) hydrogen bonds : bond 0.05432 / 5.95 ( 368) hydrogen bonds : angle 4.14049 / 5.45 ( 1011) metal coordination : bond 0.00755 / 0.80 ( 60) metal coordination : angle 6.12696 / 9.52 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.8035 (mmm-85) REVERT: H 56 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6100 (mp10) REVERT: K 78 ARG cc_start: 0.8498 (tpt-90) cc_final: 0.8237 (ttt90) outliers start: 15 outliers final: 11 residues processed: 137 average time/residue: 0.1209 time to fit residues: 20.8683 Evaluate side-chains 133 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 30.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN ** L 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.187348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.160639 restraints weight = 12154.410| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 1.64 r_work: 0.3555 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8018 Z= 0.176 Angle : 0.646 12.813 11187 Z= 0.336 Chirality : 0.042 0.151 1262 Planarity : 0.003 0.050 1160 Dihedral : 24.331 81.646 1778 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.57 % Allowed : 17.86 % Favored : 78.57 % 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: 0.71 (0.29), residues: 774 helix: 1.56 (0.26), residues: 384 sheet: -0.51 (0.41), residues: 132 loop : -0.53 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 14 TYR 0.014 0.002 TYR K 52 PHE 0.008 0.001 PHE N 29 TRP 0.007 0.001 TRP G 107 HIS 0.011 0.001 HIS G 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 ( 7958) covalent geometry : angle 0.57347 / 0.33 (11151) hydrogen bonds : bond 0.04830 / 5.15 ( 368) hydrogen bonds : angle 3.85303 / 5.07 ( 1011) metal coordination : bond 0.00463 / 0.52 ( 60) metal coordination : angle 5.26587 / 7.98 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.252 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: H 30 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.7955 (mmm-85) REVERT: H 56 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6144 (mp10) REVERT: K 78 ARG cc_start: 0.8425 (tpt-90) cc_final: 0.8196 (ttt90) REVERT: K 125 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7394 (mm-30) REVERT: L 91 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7920 (mtt-85) REVERT: N 56 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7927 (mp10) outliers start: 21 outliers final: 17 residues processed: 140 average time/residue: 0.1150 time to fit residues: 20.4379 Evaluate side-chains 137 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 91 ARG Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 33 GLN ** L 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.179278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.153893 restraints weight = 12214.220| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 1.63 r_work: 0.3376 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8018 Z= 0.233 Angle : 0.685 11.572 11187 Z= 0.360 Chirality : 0.045 0.155 1262 Planarity : 0.004 0.049 1160 Dihedral : 24.492 83.339 1778 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.25 % Allowed : 19.73 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.29), residues: 774 helix: 1.40 (0.25), residues: 384 sheet: -0.63 (0.42), residues: 132 loop : -0.66 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 16 TYR 0.018 0.002 TYR K 52 PHE 0.013 0.002 PHE N 29 TRP 0.012 0.002 TRP M 107 HIS 0.010 0.002 HIS L 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 ( 7958) covalent geometry : angle 0.62987 / 0.36 (11151) hydrogen bonds : bond 0.05368 / 5.94 ( 368) hydrogen bonds : angle 3.94185 / 5.24 ( 1011) metal coordination : bond 0.00682 / 0.70 ( 60) metal coordination : angle 4.80731 / 7.02 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ARG cc_start: 0.8319 (mmm-85) cc_final: 0.8029 (mmm-85) REVERT: H 56 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.6069 (mp10) REVERT: K 78 ARG cc_start: 0.8513 (tpt-90) cc_final: 0.8267 (ttt90) REVERT: L 26 VAL cc_start: 0.8655 (m) cc_final: 0.7974 (m) REVERT: L 91 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8047 (mtt-85) REVERT: M 33 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8434 (mt0) REVERT: N 115 HIS cc_start: 0.6790 (m-70) cc_final: 0.6174 (m-70) outliers start: 25 outliers final: 18 residues processed: 136 average time/residue: 0.1126 time to fit residues: 19.5168 Evaluate side-chains 139 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 91 ARG Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 4 optimal weight: 50.0000 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 84 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.181165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.143329 restraints weight = 12271.007| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.59 r_work: 0.3378 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.337 8018 Z= 0.201 Angle : 0.639 11.073 11187 Z= 0.336 Chirality : 0.042 0.151 1262 Planarity : 0.003 0.039 1160 Dihedral : 24.411 80.287 1778 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.25 % Allowed : 22.11 % Favored : 73.64 % 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: 0.63 (0.29), residues: 774 helix: 1.58 (0.26), residues: 384 sheet: -0.62 (0.42), residues: 132 loop : -0.69 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 14 TYR 0.013 0.002 TYR H 76 PHE 0.008 0.001 PHE G 29 TRP 0.022 0.001 TRP G 107 HIS 0.010 0.001 HIS G 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 7958) covalent geometry : angle 0.58088 / 0.33 (11151) hydrogen bonds : bond 0.04528 / 4.81 ( 368) hydrogen bonds : angle 3.71801 / 4.96 ( 1011) metal coordination : bond 0.04365 / 3.65 ( 60) metal coordination : angle 4.70883 / 6.62 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8243 (mm-40) REVERT: H 30 ARG cc_start: 0.8406 (mmm-85) cc_final: 0.8080 (mmm-85) REVERT: H 56 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6087 (mp10) REVERT: H 77 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6489 (ptm-80) REVERT: K 78 ARG cc_start: 0.8536 (tpt-90) cc_final: 0.8286 (ttt90) REVERT: L 91 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8295 (mtt-85) REVERT: L 129 THR cc_start: 0.7749 (p) cc_final: 0.7277 (p) REVERT: M 33 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8510 (mt0) REVERT: N 56 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7921 (mp10) outliers start: 25 outliers final: 19 residues processed: 140 average time/residue: 0.1241 time to fit residues: 21.8833 Evaluate side-chains 142 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 91 ARG Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 83 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 34 optimal weight: 0.0170 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.183478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.143087 restraints weight = 12127.534| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.59 r_work: 0.3374 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8018 Z= 0.150 Angle : 0.618 10.879 11187 Z= 0.325 Chirality : 0.041 0.162 1262 Planarity : 0.003 0.038 1160 Dihedral : 24.409 78.630 1778 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.91 % Allowed : 23.13 % Favored : 72.96 % 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: 0.79 (0.29), residues: 774 helix: 1.73 (0.26), residues: 384 sheet: -0.55 (0.43), residues: 132 loop : -0.66 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 30 TYR 0.012 0.001 TYR K 52 PHE 0.007 0.001 PHE H 29 TRP 0.023 0.001 TRP G 107 HIS 0.010 0.001 HIS G 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 ( 7958) covalent geometry : angle 0.56200 / 0.32 (11151) hydrogen bonds : bond 0.04349 / 4.57 ( 368) hydrogen bonds : angle 3.58620 / 4.76 ( 1011) metal coordination : bond 0.00565 / 0.57 ( 60) metal coordination : angle 4.55445 / 6.44 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8240 (mm-40) REVERT: H 30 ARG cc_start: 0.8371 (mmm-85) cc_final: 0.8048 (mmm-85) REVERT: H 56 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.6059 (mp10) REVERT: H 77 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6432 (ptm-80) REVERT: K 78 ARG cc_start: 0.8556 (tpt-90) cc_final: 0.8313 (ttt90) REVERT: M 95 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7694 (mmmt) REVERT: N 56 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7929 (mp10) outliers start: 23 outliers final: 19 residues processed: 136 average time/residue: 0.1294 time to fit residues: 21.8094 Evaluate side-chains 139 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 57 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.182088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.144689 restraints weight = 12291.746| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.65 r_work: 0.3398 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8018 Z= 0.141 Angle : 0.640 10.960 11187 Z= 0.329 Chirality : 0.041 0.166 1262 Planarity : 0.003 0.042 1160 Dihedral : 24.391 77.290 1778 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.08 % Allowed : 23.64 % Favored : 72.28 % 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: 0.86 (0.29), residues: 774 helix: 1.80 (0.26), residues: 384 sheet: -0.49 (0.43), residues: 132 loop : -0.64 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 14 TYR 0.011 0.001 TYR K 52 PHE 0.009 0.001 PHE H 29 TRP 0.026 0.002 TRP G 107 HIS 0.007 0.001 HIS G 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 7958) covalent geometry : angle 0.57076 / 0.33 (11151) hydrogen bonds : bond 0.04181 / 4.32 ( 368) hydrogen bonds : angle 3.50373 / 4.65 ( 1011) metal coordination : bond 0.00445 / 0.50 ( 60) metal coordination : angle 5.12375 / 7.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8287 (mm-40) REVERT: H 30 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.8053 (mmm-85) REVERT: H 56 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.5991 (mp10) REVERT: H 77 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6342 (ptm-80) REVERT: K 78 ARG cc_start: 0.8535 (tpt-90) cc_final: 0.8281 (ttt90) REVERT: M 33 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8506 (mt0) REVERT: N 56 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7898 (mp10) outliers start: 24 outliers final: 17 residues processed: 138 average time/residue: 0.1255 time to fit residues: 21.7362 Evaluate side-chains 140 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 57 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.182177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.142827 restraints weight = 12116.512| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.86 r_work: 0.3379 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8018 Z= 0.150 Angle : 0.661 13.160 11187 Z= 0.335 Chirality : 0.041 0.164 1262 Planarity : 0.003 0.049 1160 Dihedral : 24.407 76.552 1778 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.42 % Allowed : 22.62 % Favored : 72.96 % 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: 0.85 (0.29), residues: 774 helix: 1.82 (0.26), residues: 384 sheet: -0.50 (0.43), residues: 132 loop : -0.71 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 14 TYR 0.011 0.001 TYR K 52 PHE 0.009 0.001 PHE L 127 TRP 0.027 0.002 TRP G 107 HIS 0.008 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 7958) covalent geometry : angle 0.58232 / 0.33 (11151) hydrogen bonds : bond 0.04231 / 4.42 ( 368) hydrogen bonds : angle 3.49985 / 4.65 ( 1011) metal coordination : bond 0.00597 / 0.72 ( 60) metal coordination : angle 5.54377 / 7.57 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8297 (mm-40) REVERT: H 30 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.8071 (mmm-85) REVERT: H 56 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.5968 (mp10) REVERT: H 77 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6371 (ptm-80) REVERT: K 78 ARG cc_start: 0.8540 (tpt-90) cc_final: 0.8300 (ttt90) REVERT: M 33 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8526 (mt0) REVERT: N 56 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7906 (mp10) REVERT: N 115 HIS cc_start: 0.6865 (m-70) cc_final: 0.6283 (m-70) outliers start: 26 outliers final: 20 residues processed: 135 average time/residue: 0.1210 time to fit residues: 20.4738 Evaluate side-chains 142 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 95 LYS Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 22 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.182017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.147148 restraints weight = 11957.455| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.46 r_work: 0.3396 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8018 Z= 0.159 Angle : 0.660 10.863 11187 Z= 0.345 Chirality : 0.041 0.166 1262 Planarity : 0.003 0.039 1160 Dihedral : 24.437 76.374 1778 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.74 % Allowed : 22.96 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.29), residues: 774 helix: 1.75 (0.26), residues: 384 sheet: -0.52 (0.43), residues: 132 loop : -0.73 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 14 TYR 0.013 0.002 TYR K 52 PHE 0.009 0.001 PHE H 29 TRP 0.028 0.002 TRP G 107 HIS 0.005 0.001 HIS K 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 ( 7958) covalent geometry : angle 0.60378 / 0.34 (11151) hydrogen bonds : bond 0.04335 / 4.55 ( 368) hydrogen bonds : angle 3.54053 / 4.81 ( 1011) metal coordination : bond 0.00431 / 0.50 ( 60) metal coordination : angle 4.71639 / 6.78 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.8027 (mmm-85) REVERT: H 56 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6015 (mp10) REVERT: H 77 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6253 (ptm-80) REVERT: K 78 ARG cc_start: 0.8542 (tpt-90) cc_final: 0.8296 (ttt90) REVERT: M 33 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8516 (mt0) REVERT: N 56 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7900 (mp10) REVERT: N 115 HIS cc_start: 0.6922 (m-70) cc_final: 0.6297 (m-70) outliers start: 22 outliers final: 19 residues processed: 133 average time/residue: 0.1219 time to fit residues: 20.2435 Evaluate side-chains 139 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 95 LYS Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 78 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.183677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.145186 restraints weight = 12200.042| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.80 r_work: 0.3371 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8018 Z= 0.149 Angle : 0.637 10.780 11187 Z= 0.334 Chirality : 0.040 0.157 1262 Planarity : 0.003 0.035 1160 Dihedral : 24.445 75.666 1778 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.57 % Allowed : 22.96 % Favored : 73.47 % 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: 0.84 (0.29), residues: 774 helix: 1.80 (0.26), residues: 384 sheet: -0.54 (0.42), residues: 132 loop : -0.68 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 14 TYR 0.011 0.001 TYR K 52 PHE 0.010 0.001 PHE L 127 TRP 0.028 0.002 TRP G 107 HIS 0.005 0.001 HIS G 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 ( 7958) covalent geometry : angle 0.58331 / 0.33 (11151) hydrogen bonds : bond 0.04220 / 4.39 ( 368) hydrogen bonds : angle 3.50128 / 4.76 ( 1011) metal coordination : bond 0.00408 / 0.46 ( 60) metal coordination : angle 4.55531 / 6.72 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2075.86 seconds wall clock time: 36 minutes 9.46 seconds (2169.46 seconds total)