Starting phenix.real_space_refine on Fri Jul 25 11:11:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vo0_32048/07_2025/7vo0_32048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vo0_32048/07_2025/7vo0_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_32048/07_2025/7vo0_32048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vo0_32048/07_2025/7vo0_32048.map" model { file = "/net/cci-nas-00/data/ceres_data/7vo0_32048/07_2025/7vo0_32048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vo0_32048/07_2025/7vo0_32048.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.46, per 1000 atoms: 0.71 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: 1.93 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 2.80 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: 2.16 Time building geometry restraints manager: 2.19 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=" 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 bond pdb=" N CYS M 130 " pdb=" CA CYS M 130 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.27e-02 6.20e+03 8.67e+00 bond pdb=" N GLY G 128 " pdb=" CA GLY G 128 " ideal model delta sigma weight residual 1.448 1.477 -0.029 1.00e-02 1.00e+04 8.20e+00 bond pdb=" N CYS G 130 " pdb=" CA CYS G 130 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 7.95e+00 bond pdb=" N PHE M 127 " pdb=" CA PHE M 127 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.31e-02 5.83e+03 7.69e+00 ... (remaining 7953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 10872 1.65 - 3.29: 245 3.29 - 4.94: 27 4.94 - 6.59: 6 6.59 - 8.23: 1 Bond angle restraints: 11151 Sorted by residual: angle pdb=" N GLU K 109 " pdb=" CA GLU K 109 " pdb=" CB GLU K 109 " ideal model delta sigma weight residual 110.28 116.48 -6.20 1.55e+00 4.16e-01 1.60e+01 angle pdb=" CA GLY G 135 " pdb=" C GLY G 135 " pdb=" O GLY G 135 " ideal model delta sigma weight residual 121.41 118.26 3.15 8.80e-01 1.29e+00 1.28e+01 angle pdb=" CA GLY M 135 " pdb=" C GLY M 135 " pdb=" O GLY M 135 " ideal model delta sigma weight residual 121.41 118.28 3.13 8.80e-01 1.29e+00 1.27e+01 angle pdb=" C ALA K 108 " pdb=" N GLU K 109 " pdb=" CA GLU K 109 " ideal model delta sigma weight residual 120.31 114.92 5.39 1.52e+00 4.33e-01 1.26e+01 angle pdb=" CA PHE M 127 " pdb=" C PHE M 127 " pdb=" O PHE M 127 " ideal model delta sigma weight residual 121.47 117.76 3.71 1.15e+00 7.56e-01 1.04e+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: 992 0.042 - 0.083: 198 0.083 - 0.125: 65 0.125 - 0.167: 4 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: 3.760 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.700 Find NCS groups from input model: 0.270 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 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= 0.259 Angle : 0.823 24.092 11187 Z= 0.366 Chirality : 0.039 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.024 0.003 TRP G 107 HIS 0.013 0.001 HIS H 85 PHE 0.006 0.001 PHE L 127 TYR 0.022 0.002 TYR G 52 ARG 0.012 0.001 ARG L 14 Details of bonding type rmsd hydrogen bonds : bond 0.19364 ( 368) hydrogen bonds : angle 7.48844 ( 1011) metal coordination : bond 0.04834 ( 60) metal coordination : angle 10.49795 ( 36) covalent geometry : bond 0.00399 ( 7958) covalent geometry : angle 0.56967 (11151) *********************** 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 : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 117 TYR cc_start: 0.4659 (m-80) cc_final: 0.4413 (m-10) REVERT: M 28 GLU cc_start: 0.5841 (pt0) cc_final: 0.5518 (tt0) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.3051 time to fit residues: 67.9380 Evaluate side-chains 123 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.189039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.155054 restraints weight = 11847.574| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.28 r_work: 0.3537 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 8018 Z= 0.171 Angle : 0.626 13.949 11187 Z= 0.323 Chirality : 0.038 0.144 1262 Planarity : 0.003 0.029 1160 Dihedral : 24.075 83.914 1778 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.21 % Allowed : 14.12 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.29), residues: 774 helix: 1.60 (0.26), residues: 384 sheet: -0.49 (0.38), residues: 156 loop : -0.70 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 107 HIS 0.014 0.001 HIS G 115 PHE 0.006 0.001 PHE L 29 TYR 0.015 0.002 TYR K 52 ARG 0.011 0.001 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 368) hydrogen bonds : angle 3.98478 ( 1011) metal coordination : bond 0.01936 ( 60) metal coordination : angle 5.05717 ( 36) covalent geometry : bond 0.00361 ( 7958) covalent geometry : angle 0.55754 (11151) *********************** 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 168 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 GLN cc_start: 0.8798 (tp40) cc_final: 0.8224 (mm-40) REVERT: H 30 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7817 (mmm-85) REVERT: H 56 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.5966 (mp10) REVERT: H 78 ARG cc_start: 0.8198 (ptm160) cc_final: 0.7959 (ptm160) REVERT: K 78 ARG cc_start: 0.8468 (tpt-90) cc_final: 0.8203 (ttt90) REVERT: L 24 GLN cc_start: 0.8503 (mm110) cc_final: 0.8291 (mm110) REVERT: M 95 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7719 (mmmt) REVERT: N 56 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7945 (mp10) outliers start: 13 outliers final: 7 residues processed: 163 average time/residue: 0.2807 time to fit residues: 56.4786 Evaluate side-chains 134 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 8 optimal weight: 0.0050 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.182779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.156837 restraints weight = 12488.185| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 1.92 r_work: 0.3430 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8018 Z= 0.205 Angle : 0.624 13.201 11187 Z= 0.327 Chirality : 0.039 0.153 1262 Planarity : 0.003 0.025 1160 Dihedral : 24.220 78.844 1778 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.06 % Allowed : 15.82 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.29), residues: 774 helix: 1.54 (0.26), residues: 384 sheet: -0.29 (0.42), residues: 132 loop : -0.33 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 107 HIS 0.007 0.001 HIS K 41 PHE 0.010 0.002 PHE G 29 TYR 0.015 0.002 TYR K 52 ARG 0.006 0.001 ARG N 30 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 368) hydrogen bonds : angle 3.81094 ( 1011) metal coordination : bond 0.00471 ( 60) metal coordination : angle 4.79647 ( 36) covalent geometry : bond 0.00466 ( 7958) covalent geometry : angle 0.56295 (11151) *********************** 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 147 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 GLN cc_start: 0.8796 (tp40) cc_final: 0.8287 (mm-40) REVERT: H 30 ARG cc_start: 0.8351 (mmm-85) cc_final: 0.8149 (mmm-85) REVERT: H 56 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6141 (mp10) REVERT: K 78 ARG cc_start: 0.8488 (tpt-90) cc_final: 0.8227 (ttt90) REVERT: L 129 THR cc_start: 0.7655 (p) cc_final: 0.7276 (p) REVERT: M 95 LYS cc_start: 0.7843 (mmmt) cc_final: 0.7416 (mmmt) REVERT: N 56 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7892 (mp10) outliers start: 18 outliers final: 10 residues processed: 139 average time/residue: 0.2927 time to fit residues: 50.0288 Evaluate side-chains 128 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain M residue 26 VAL 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 66 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 HIS ** L 122 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 = 0.4365 r_free = 0.4365 target = 0.182046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.141662 restraints weight = 12100.975| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.79 r_work: 0.3371 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8018 Z= 0.171 Angle : 0.588 11.903 11187 Z= 0.307 Chirality : 0.037 0.143 1262 Planarity : 0.003 0.029 1160 Dihedral : 24.263 71.946 1778 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.06 % Allowed : 18.20 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.29), residues: 774 helix: 1.75 (0.26), residues: 384 sheet: -0.25 (0.43), residues: 132 loop : -0.42 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 107 HIS 0.009 0.001 HIS K 115 PHE 0.007 0.001 PHE N 29 TYR 0.013 0.002 TYR K 52 ARG 0.005 0.001 ARG L 14 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 368) hydrogen bonds : angle 3.51298 ( 1011) metal coordination : bond 0.00438 ( 60) metal coordination : angle 4.65604 ( 36) covalent geometry : bond 0.00385 ( 7958) covalent geometry : angle 0.52573 (11151) *********************** 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 148 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8596 (pttt) REVERT: H 24 GLN cc_start: 0.8968 (tp40) cc_final: 0.8747 (mm-40) REVERT: H 30 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.8011 (mmm-85) REVERT: H 56 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.5942 (mp10) REVERT: H 78 ARG cc_start: 0.8292 (ptm160) cc_final: 0.8054 (ptm160) REVERT: H 117 TYR cc_start: 0.7276 (m-10) cc_final: 0.6161 (m-10) REVERT: K 78 ARG cc_start: 0.8532 (tpt-90) cc_final: 0.8269 (ttt90) REVERT: L 24 GLN cc_start: 0.8530 (mm110) cc_final: 0.8314 (mm110) REVERT: L 129 THR cc_start: 0.8016 (p) cc_final: 0.7646 (p) REVERT: M 33 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8530 (mt0) REVERT: M 91 ARG cc_start: 0.6605 (ptt-90) cc_final: 0.6245 (mtm180) REVERT: M 95 LYS cc_start: 0.7791 (mmmt) cc_final: 0.7420 (mmmt) REVERT: N 56 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7919 (mp10) outliers start: 18 outliers final: 11 residues processed: 140 average time/residue: 0.2840 time to fit residues: 48.9412 Evaluate side-chains 136 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 L residue 38 MET Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain M residue 33 GLN 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 Chi-restraints excluded: chain N residue 81 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 0.0370 chunk 46 optimal weight: 1.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN L 56 GLN ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.181974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.147609 restraints weight = 12154.631| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.30 r_work: 0.3387 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8018 Z= 0.177 Angle : 0.581 9.746 11187 Z= 0.305 Chirality : 0.038 0.132 1262 Planarity : 0.003 0.022 1160 Dihedral : 24.474 73.786 1778 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.40 % Allowed : 19.39 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.29), residues: 774 helix: 1.82 (0.26), residues: 384 sheet: -0.29 (0.43), residues: 132 loop : -0.51 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 107 HIS 0.006 0.001 HIS K 41 PHE 0.009 0.001 PHE N 29 TYR 0.014 0.002 TYR K 52 ARG 0.006 0.001 ARG L 14 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 368) hydrogen bonds : angle 3.42770 ( 1011) metal coordination : bond 0.00435 ( 60) metal coordination : angle 4.17919 ( 36) covalent geometry : bond 0.00401 ( 7958) covalent geometry : angle 0.53118 (11151) *********************** 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 142 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8525 (pttt) REVERT: H 16 ARG cc_start: 0.8656 (ptp-110) cc_final: 0.7937 (mtt90) REVERT: H 24 GLN cc_start: 0.8945 (tp40) cc_final: 0.8554 (mm-40) REVERT: H 30 ARG cc_start: 0.8329 (mmm-85) cc_final: 0.8029 (mmm-85) REVERT: H 56 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6063 (mp10) REVERT: H 77 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.5895 (ptt-90) REVERT: H 117 TYR cc_start: 0.7250 (m-10) cc_final: 0.6111 (m-10) REVERT: K 78 ARG cc_start: 0.8549 (tpt-90) cc_final: 0.8278 (ttt90) REVERT: L 56 GLN cc_start: 0.8955 (tp-100) cc_final: 0.8650 (tp-100) REVERT: M 33 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8477 (mt0) REVERT: M 91 ARG cc_start: 0.6720 (ptt-90) cc_final: 0.6368 (mtm180) REVERT: M 95 LYS cc_start: 0.7722 (mmmt) cc_final: 0.7409 (mmmt) outliers start: 20 outliers final: 12 residues processed: 135 average time/residue: 0.3081 time to fit residues: 50.9830 Evaluate side-chains 127 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 H residue 77 ARG 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 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 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.183718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.146627 restraints weight = 12023.316| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.70 r_work: 0.3367 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8018 Z= 0.160 Angle : 0.576 10.309 11187 Z= 0.301 Chirality : 0.036 0.128 1262 Planarity : 0.003 0.029 1160 Dihedral : 24.419 73.079 1778 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.23 % Allowed : 20.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.29), residues: 774 helix: 1.90 (0.26), residues: 384 sheet: -0.26 (0.43), residues: 132 loop : -0.53 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 107 HIS 0.005 0.001 HIS K 41 PHE 0.011 0.001 PHE H 29 TYR 0.013 0.001 TYR H 76 ARG 0.006 0.001 ARG N 30 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 368) hydrogen bonds : angle 3.36860 ( 1011) metal coordination : bond 0.00396 ( 60) metal coordination : angle 4.37550 ( 36) covalent geometry : bond 0.00360 ( 7958) covalent geometry : angle 0.52013 (11151) *********************** 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 135 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.8901 (mtmm) cc_final: 0.8551 (pttt) REVERT: H 16 ARG cc_start: 0.8706 (ptp-110) cc_final: 0.7983 (mtt90) REVERT: H 24 GLN cc_start: 0.8969 (tp40) cc_final: 0.8553 (mm-40) REVERT: H 30 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7989 (mmm-85) REVERT: H 56 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.5922 (mp10) REVERT: H 117 TYR cc_start: 0.7047 (m-10) cc_final: 0.5945 (m-10) REVERT: K 78 ARG cc_start: 0.8558 (tpt-90) cc_final: 0.8288 (ttt90) REVERT: L 35 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8696 (tt) REVERT: L 56 GLN cc_start: 0.8975 (tp-100) cc_final: 0.8589 (tp-100) REVERT: M 91 ARG cc_start: 0.6764 (ptt-90) cc_final: 0.6421 (mtm180) REVERT: M 95 LYS cc_start: 0.7694 (mmmt) cc_final: 0.7379 (mmmt) outliers start: 19 outliers final: 13 residues processed: 128 average time/residue: 0.3031 time to fit residues: 47.1668 Evaluate side-chains 129 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 41 HIS 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 50 THR Chi-restraints excluded: chain N residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.183438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.154781 restraints weight = 11959.913| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.06 r_work: 0.3401 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8018 Z= 0.162 Angle : 0.566 9.529 11187 Z= 0.299 Chirality : 0.037 0.197 1262 Planarity : 0.003 0.026 1160 Dihedral : 24.411 73.922 1778 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.23 % Allowed : 21.26 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.29), residues: 774 helix: 1.90 (0.26), residues: 384 sheet: -0.25 (0.44), residues: 132 loop : -0.57 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 107 HIS 0.005 0.001 HIS K 41 PHE 0.009 0.001 PHE L 127 TYR 0.013 0.001 TYR K 52 ARG 0.006 0.001 ARG M 30 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 368) hydrogen bonds : angle 3.39180 ( 1011) metal coordination : bond 0.00393 ( 60) metal coordination : angle 4.05044 ( 36) covalent geometry : bond 0.00366 ( 7958) covalent geometry : angle 0.51789 (11151) *********************** 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 131 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 91 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.8166 (mtm-85) REVERT: G 95 LYS cc_start: 0.8887 (mtmm) cc_final: 0.8560 (pttt) REVERT: H 16 ARG cc_start: 0.8657 (ptp-110) cc_final: 0.8057 (mtt90) REVERT: H 24 GLN cc_start: 0.8968 (tp40) cc_final: 0.8711 (mm-40) REVERT: H 30 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.8036 (mmm-85) REVERT: H 56 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.5998 (mp10) REVERT: H 117 TYR cc_start: 0.6979 (m-10) cc_final: 0.5910 (m-10) REVERT: K 78 ARG cc_start: 0.8566 (tpt-90) cc_final: 0.8300 (ttt90) REVERT: L 35 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8677 (tt) REVERT: L 56 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8521 (tp-100) REVERT: M 33 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8495 (mt0) REVERT: M 91 ARG cc_start: 0.6748 (ptt-90) cc_final: 0.6379 (mtm180) REVERT: M 95 LYS cc_start: 0.7663 (mmmt) cc_final: 0.7369 (mmmt) outliers start: 19 outliers final: 14 residues processed: 123 average time/residue: 0.2884 time to fit residues: 43.5595 Evaluate side-chains 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 50 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 41 HIS 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 50 THR Chi-restraints excluded: chain N residue 81 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.0670 chunk 40 optimal weight: 0.0870 chunk 1 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 66 optimal weight: 0.0980 overall best weight: 0.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.186711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.159549 restraints weight = 12224.945| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 1.84 r_work: 0.3518 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8018 Z= 0.115 Angle : 0.548 9.714 11187 Z= 0.286 Chirality : 0.035 0.154 1262 Planarity : 0.002 0.023 1160 Dihedral : 24.101 74.272 1778 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.55 % Allowed : 21.94 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.29), residues: 774 helix: 2.11 (0.26), residues: 384 sheet: -0.22 (0.43), residues: 132 loop : -0.50 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 107 HIS 0.005 0.001 HIS G 115 PHE 0.008 0.001 PHE L 127 TYR 0.009 0.001 TYR H 76 ARG 0.005 0.000 ARG N 30 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 368) hydrogen bonds : angle 3.15396 ( 1011) metal coordination : bond 0.00355 ( 60) metal coordination : angle 4.03179 ( 36) covalent geometry : bond 0.00256 ( 7958) covalent geometry : angle 0.49830 (11151) *********************** 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 132 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 ASP cc_start: 0.7849 (t70) cc_final: 0.7374 (t0) REVERT: G 91 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.8108 (mtm-85) REVERT: G 95 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8445 (pttt) REVERT: H 8 VAL cc_start: -0.0897 (OUTLIER) cc_final: -0.1279 (t) REVERT: H 16 ARG cc_start: 0.8608 (ptp-110) cc_final: 0.8023 (mtt90) REVERT: H 30 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.7964 (mmm-85) REVERT: H 40 LYS cc_start: 0.9285 (ttpp) cc_final: 0.8999 (tppt) REVERT: H 117 TYR cc_start: 0.6618 (m-10) cc_final: 0.5486 (m-10) REVERT: K 78 ARG cc_start: 0.8493 (tpt-90) cc_final: 0.8251 (ttt90) REVERT: L 35 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8664 (tt) REVERT: L 56 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8493 (tp-100) REVERT: M 91 ARG cc_start: 0.6772 (ptt-90) cc_final: 0.6570 (mtm180) REVERT: M 95 LYS cc_start: 0.7547 (mmmt) cc_final: 0.7213 (mmmt) outliers start: 15 outliers final: 12 residues processed: 126 average time/residue: 0.2891 time to fit residues: 44.7238 Evaluate side-chains 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 41 HIS 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 50 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 0.0010 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.184083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.153062 restraints weight = 12365.437| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.33 r_work: 0.3384 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8018 Z= 0.164 Angle : 0.570 9.240 11187 Z= 0.299 Chirality : 0.036 0.144 1262 Planarity : 0.003 0.024 1160 Dihedral : 24.288 75.073 1778 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.72 % Allowed : 21.60 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.29), residues: 774 helix: 2.05 (0.26), residues: 384 sheet: -0.22 (0.44), residues: 132 loop : -0.51 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 107 HIS 0.005 0.001 HIS K 41 PHE 0.010 0.001 PHE L 127 TYR 0.012 0.001 TYR K 52 ARG 0.009 0.001 ARG M 30 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 368) hydrogen bonds : angle 3.30056 ( 1011) metal coordination : bond 0.00402 ( 60) metal coordination : angle 4.07446 ( 36) covalent geometry : bond 0.00373 ( 7958) covalent geometry : angle 0.52148 (11151) *********************** 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 126 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 91 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.8193 (mtm-85) REVERT: G 95 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8360 (pmtt) REVERT: H 8 VAL cc_start: -0.1282 (OUTLIER) cc_final: -0.1675 (t) REVERT: H 16 ARG cc_start: 0.8803 (ptp-110) cc_final: 0.8176 (mtt90) REVERT: H 30 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.8067 (mmm-85) REVERT: H 117 TYR cc_start: 0.6835 (m-10) cc_final: 0.5790 (m-10) REVERT: K 78 ARG cc_start: 0.8585 (tpt-90) cc_final: 0.8306 (ttt90) REVERT: L 35 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8681 (tt) REVERT: L 56 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8464 (tp-100) REVERT: M 91 ARG cc_start: 0.6820 (ptt-90) cc_final: 0.6595 (mtm180) outliers start: 16 outliers final: 13 residues processed: 120 average time/residue: 0.2885 time to fit residues: 42.5825 Evaluate side-chains 122 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 55 LEU 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 35 LEU Chi-restraints excluded: chain L residue 41 HIS 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 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 19 optimal weight: 0.0670 chunk 65 optimal weight: 0.4980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.185525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.162324 restraints weight = 12036.873| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 1.54 r_work: 0.3542 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8018 Z= 0.132 Angle : 0.544 9.012 11187 Z= 0.288 Chirality : 0.036 0.141 1262 Planarity : 0.002 0.020 1160 Dihedral : 24.143 75.619 1778 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.72 % Allowed : 21.43 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 774 helix: 2.08 (0.26), residues: 384 sheet: -0.23 (0.44), residues: 132 loop : -0.47 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 107 HIS 0.004 0.001 HIS G 115 PHE 0.009 0.001 PHE L 127 TYR 0.010 0.001 TYR K 52 ARG 0.008 0.000 ARG M 30 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 368) hydrogen bonds : angle 3.19170 ( 1011) metal coordination : bond 0.00356 ( 60) metal coordination : angle 3.77337 ( 36) covalent geometry : bond 0.00295 ( 7958) covalent geometry : angle 0.50063 (11151) ********************** 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 128 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8391 (pmtt) REVERT: G 107 TRP cc_start: 0.8271 (t60) cc_final: 0.7899 (t60) REVERT: H 8 VAL cc_start: -0.1226 (OUTLIER) cc_final: -0.1538 (t) REVERT: H 16 ARG cc_start: 0.8495 (ptp-110) cc_final: 0.7915 (mtt90) REVERT: H 117 TYR cc_start: 0.6512 (m-10) cc_final: 0.5430 (m-10) REVERT: K 78 ARG cc_start: 0.8486 (tpt-90) cc_final: 0.8228 (ttt90) REVERT: L 35 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8687 (tt) REVERT: L 56 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8369 (tp-100) outliers start: 16 outliers final: 13 residues processed: 121 average time/residue: 0.3038 time to fit residues: 44.7363 Evaluate side-chains 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 55 LEU 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 35 LEU Chi-restraints excluded: chain L residue 41 HIS 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 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 8 optimal weight: 0.0030 chunk 5 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.184017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.149746 restraints weight = 11945.302| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.27 r_work: 0.3405 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8018 Z= 0.166 Angle : 0.586 9.245 11187 Z= 0.305 Chirality : 0.036 0.140 1262 Planarity : 0.003 0.028 1160 Dihedral : 24.257 76.407 1778 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.55 % Allowed : 22.11 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.29), residues: 774 helix: 2.04 (0.26), residues: 384 sheet: -0.30 (0.44), residues: 132 loop : -0.52 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 107 HIS 0.005 0.001 HIS K 41 PHE 0.009 0.001 PHE L 127 TYR 0.013 0.001 TYR K 52 ARG 0.008 0.001 ARG M 30 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 368) hydrogen bonds : angle 3.28387 ( 1011) metal coordination : bond 0.00394 ( 60) metal coordination : angle 4.29497 ( 36) covalent geometry : bond 0.00377 ( 7958) covalent geometry : angle 0.53378 (11151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4308.32 seconds wall clock time: 74 minutes 31.76 seconds (4471.76 seconds total)