Starting phenix.real_space_refine on Wed Mar 12 07:25:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vo0_32048/03_2025/7vo0_32048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vo0_32048/03_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_32048/03_2025/7vo0_32048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vo0_32048/03_2025/7vo0_32048.map" model { file = "/net/cci-nas-00/data/ceres_data/7vo0_32048/03_2025/7vo0_32048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vo0_32048/03_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-5624/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: 5.38, per 1000 atoms: 0.70 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: 1.98 Conformation dependent library (CDL) restraints added in 903.8 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: 2.70 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: 2.17 Time building geometry restraints manager: 2.32 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: 1.160 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.350 Find NCS groups from input model: 0.250 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.970 ------------------------------------------------------------------------------- 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 : 0.004 0.037 7958 Z= 0.251 Angle : 0.570 8.235 11151 Z= 0.350 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 *********************** 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 : 0.660 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: 0.3124 time to fit residues: 69.8673 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 : 0.721 ------------------------------------------------------------------------------- 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 0.034 7958 Z= 0.216 Angle : 0.558 8.391 11151 Z= 0.319 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 *********************** 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 : 0.751 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: 0.2712 time to fit residues: 54.7957 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 : 0.667 ------------------------------------------------------------------------------- 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: 2.9990 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 7958 Z= 0.283 Angle : 0.563 7.076 11151 Z= 0.323 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 *********************** 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 : 0.696 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: 0.3051 time to fit residues: 52.4021 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 : 0.680 ------------------------------------------------------------------------------- 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 7958 Z= 0.234 Angle : 0.526 7.164 11151 Z= 0.303 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 *********************** 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 : 0.659 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: 0.2955 time to fit residues: 50.7155 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 : 0.722 ------------------------------------------------------------------------------- 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: 6.9990 chunk 35 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 0.0020 chunk 46 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.183275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.148808 restraints weight = 12222.181| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.42 r_work: 0.3383 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7958 Z= 0.201 Angle : 0.509 7.444 11151 Z= 0.291 Chirality : 0.036 0.131 1262 Planarity : 0.003 0.017 1160 Dihedral : 24.350 72.314 1778 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.23 % Allowed : 19.39 % Favored : 77.38 % 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: 1.12 (0.29), residues: 774 helix: 1.93 (0.26), residues: 384 sheet: -0.22 (0.43), residues: 132 loop : -0.48 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 107 HIS 0.005 0.001 HIS M 115 PHE 0.008 0.001 PHE H 29 TYR 0.011 0.001 TYR K 52 ARG 0.007 0.001 ARG L 14 *********************** 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 144 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8512 (pttt) REVERT: H 16 ARG cc_start: 0.8656 (ptp-110) cc_final: 0.7978 (mtt90) REVERT: H 24 GLN cc_start: 0.8967 (tp40) cc_final: 0.8531 (mm-40) REVERT: H 30 ARG cc_start: 0.8318 (mmm-85) cc_final: 0.8003 (mmm-85) REVERT: H 56 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.5944 (mp10) REVERT: H 77 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.5867 (ptt-90) REVERT: H 117 TYR cc_start: 0.7221 (m-10) cc_final: 0.6049 (m-10) REVERT: K 78 ARG cc_start: 0.8548 (tpt-90) cc_final: 0.8291 (ttt90) REVERT: L 56 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8670 (tp-100) REVERT: M 91 ARG cc_start: 0.6727 (ptt-90) cc_final: 0.6419 (mtm180) REVERT: M 95 LYS cc_start: 0.7737 (mmmt) cc_final: 0.7412 (mmmt) REVERT: N 56 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7945 (mp10) outliers start: 19 outliers final: 13 residues processed: 136 average time/residue: 0.3092 time to fit residues: 51.3624 Evaluate side-chains 131 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 23 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 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 0.0370 chunk 40 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.184134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.149077 restraints weight = 12053.920| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.63 r_work: 0.3381 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7958 Z= 0.216 Angle : 0.518 7.884 11151 Z= 0.297 Chirality : 0.036 0.128 1262 Planarity : 0.003 0.030 1160 Dihedral : 24.387 72.965 1778 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.72 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: 1.13 (0.29), residues: 774 helix: 1.95 (0.26), residues: 384 sheet: -0.20 (0.43), residues: 132 loop : -0.50 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 107 HIS 0.005 0.001 HIS K 41 PHE 0.011 0.001 PHE H 29 TYR 0.012 0.001 TYR H 76 ARG 0.007 0.001 ARG L 14 *********************** 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 137 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.696 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: 0.8521 (pttt) REVERT: H 16 ARG cc_start: 0.8695 (ptp-110) cc_final: 0.7980 (mtt90) REVERT: H 24 GLN cc_start: 0.8950 (tp40) cc_final: 0.8462 (mm-40) REVERT: H 30 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.7983 (mmm-85) REVERT: H 56 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.5936 (mp10) REVERT: H 78 ARG cc_start: 0.8263 (ptm160) cc_final: 0.8024 (ptm160) REVERT: H 117 TYR cc_start: 0.7014 (m-10) cc_final: 0.5917 (m-10) REVERT: K 78 ARG cc_start: 0.8550 (tpt-90) cc_final: 0.8284 (ttt90) REVERT: L 35 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8680 (tt) REVERT: L 56 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8586 (tp-100) REVERT: M 91 ARG cc_start: 0.6723 (ptt-90) cc_final: 0.6353 (mtm180) REVERT: M 95 LYS cc_start: 0.7675 (mmmt) cc_final: 0.7369 (mmmt) REVERT: N 56 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7932 (mp10) outliers start: 19 outliers final: 13 residues processed: 129 average time/residue: 0.2921 time to fit residues: 46.0359 Evaluate side-chains 131 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 41 HIS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 41 optimal weight: 0.0970 chunk 33 optimal weight: 4.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.183278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.146904 restraints weight = 12178.781| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.50 r_work: 0.3413 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7958 Z= 0.188 Angle : 0.500 7.702 11151 Z= 0.287 Chirality : 0.036 0.184 1262 Planarity : 0.003 0.025 1160 Dihedral : 24.294 73.599 1778 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.06 % Allowed : 21.26 % 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: 1.18 (0.29), residues: 774 helix: 2.02 (0.26), residues: 384 sheet: -0.15 (0.44), residues: 132 loop : -0.54 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 107 HIS 0.004 0.001 HIS M 115 PHE 0.009 0.001 PHE L 127 TYR 0.010 0.001 TYR K 52 ARG 0.006 0.001 ARG M 30 *********************** 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 135 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 91 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.8094 (mtm-85) REVERT: G 95 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8496 (pttt) REVERT: H 16 ARG cc_start: 0.8717 (ptp-110) cc_final: 0.8165 (mtt90) REVERT: H 24 GLN cc_start: 0.8943 (tp40) cc_final: 0.8410 (mm-40) REVERT: H 30 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7990 (mmm-85) REVERT: H 56 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.5914 (mp10) REVERT: H 78 ARG cc_start: 0.8203 (ptm160) cc_final: 0.7971 (ptm160) REVERT: H 117 TYR cc_start: 0.6831 (m-10) cc_final: 0.5723 (m-10) REVERT: K 78 ARG cc_start: 0.8549 (tpt-90) cc_final: 0.8293 (ttt90) REVERT: L 35 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8660 (tt) REVERT: L 56 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8529 (tp-100) REVERT: M 91 ARG cc_start: 0.6799 (ptt-90) cc_final: 0.6407 (mtm180) REVERT: M 95 LYS cc_start: 0.7615 (mmmt) cc_final: 0.7279 (mmmt) outliers start: 18 outliers final: 14 residues processed: 127 average time/residue: 0.2910 time to fit residues: 45.4251 Evaluate side-chains 127 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 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 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 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: 0.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 66 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.184870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.149510 restraints weight = 12167.160| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.30 r_work: 0.3459 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7958 Z= 0.194 Angle : 0.512 7.362 11151 Z= 0.290 Chirality : 0.036 0.156 1262 Planarity : 0.002 0.022 1160 Dihedral : 24.237 74.342 1778 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.40 % Allowed : 20.92 % 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: 2.04 (0.26), residues: 384 sheet: -0.18 (0.44), residues: 132 loop : -0.53 (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 0.009 0.001 PHE L 127 TYR 0.010 0.001 TYR K 52 ARG 0.005 0.000 ARG N 30 *********************** 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 136 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.763 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: 0.8324 (mtm-85) cc_final: 0.8105 (mtm-85) REVERT: G 95 LYS cc_start: 0.8725 (mtmm) cc_final: 0.8474 (pttt) REVERT: H 8 VAL cc_start: -0.0937 (OUTLIER) cc_final: -0.1357 (t) REVERT: H 16 ARG cc_start: 0.8786 (ptp-110) cc_final: 0.8153 (mtt90) REVERT: H 24 GLN cc_start: 0.8922 (tp40) cc_final: 0.8487 (mm-40) REVERT: H 30 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.8023 (mmm-85) REVERT: H 56 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.5919 (mp10) REVERT: H 117 TYR cc_start: 0.6786 (m-10) cc_final: 0.5694 (m-10) REVERT: K 78 ARG cc_start: 0.8536 (tpt-90) cc_final: 0.8277 (ttt90) REVERT: L 35 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8678 (tt) REVERT: L 56 GLN cc_start: 0.8951 (tp-100) cc_final: 0.8466 (tp-100) REVERT: M 91 ARG cc_start: 0.6766 (ptt-90) cc_final: 0.6549 (mtm180) REVERT: M 95 LYS cc_start: 0.7582 (mmmt) cc_final: 0.7266 (mmmt) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.2946 time to fit residues: 46.4266 Evaluate side-chains 131 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 8 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 41 HIS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 23 optimal weight: 0.0970 chunk 58 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4402 r_free = 0.4402 target = 0.184580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150406 restraints weight = 12186.398| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.38 r_work: 0.3405 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7958 Z= 0.205 Angle : 0.512 7.000 11151 Z= 0.292 Chirality : 0.036 0.145 1262 Planarity : 0.003 0.026 1160 Dihedral : 24.210 75.305 1778 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.23 % Allowed : 21.09 % 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: 2.01 (0.26), residues: 384 sheet: -0.15 (0.44), residues: 132 loop : -0.49 (0.35), 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 0.011 0.001 TYR K 52 ARG 0.005 0.000 ARG N 30 *********************** 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 132 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.678 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: 0.7833 (t70) cc_final: 0.7465 (t0) REVERT: G 91 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8181 (mtm-85) REVERT: G 95 LYS cc_start: 0.8768 (mtmm) cc_final: 0.8367 (pmtt) REVERT: H 8 VAL cc_start: -0.0826 (OUTLIER) cc_final: -0.1280 (t) REVERT: H 16 ARG cc_start: 0.8823 (ptp-110) cc_final: 0.8205 (mtt90) REVERT: H 30 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.8060 (mmm-85) REVERT: H 56 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.5957 (mp10) REVERT: H 117 TYR cc_start: 0.6787 (m-10) cc_final: 0.5756 (m-10) REVERT: K 78 ARG cc_start: 0.8560 (tpt-90) cc_final: 0.8290 (ttt90) REVERT: L 35 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8695 (tt) REVERT: L 56 GLN cc_start: 0.8943 (tp-100) cc_final: 0.8458 (tp-100) REVERT: M 91 ARG cc_start: 0.6840 (ptt-90) cc_final: 0.6603 (mtm180) REVERT: M 95 LYS cc_start: 0.7612 (mmmt) cc_final: 0.7294 (mmmt) outliers start: 19 outliers final: 15 residues processed: 125 average time/residue: 0.2938 time to fit residues: 45.1155 Evaluate side-chains 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 8 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 41 HIS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 83 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.185075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.150113 restraints weight = 12292.487| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.61 r_work: 0.3379 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7958 Z= 0.199 Angle : 0.512 7.111 11151 Z= 0.291 Chirality : 0.036 0.142 1262 Planarity : 0.003 0.021 1160 Dihedral : 24.194 75.936 1778 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.06 % Allowed : 21.26 % 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: 1.26 (0.29), residues: 774 helix: 2.09 (0.26), residues: 384 sheet: -0.20 (0.44), residues: 132 loop : -0.46 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 107 HIS 0.004 0.001 HIS G 84 PHE 0.010 0.001 PHE L 127 TYR 0.011 0.001 TYR K 52 ARG 0.005 0.000 ARG N 30 ********************** 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 129 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.743 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: 0.8462 (mtm-85) cc_final: 0.8236 (mtm-85) REVERT: G 95 LYS cc_start: 0.8769 (mtmm) cc_final: 0.8464 (pttt) REVERT: H 8 VAL cc_start: -0.1243 (OUTLIER) cc_final: -0.1665 (t) REVERT: H 16 ARG cc_start: 0.8831 (ptp-110) cc_final: 0.8229 (mtt90) REVERT: H 30 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.8057 (mmm-85) REVERT: H 56 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.5952 (mp10) REVERT: H 117 TYR cc_start: 0.6794 (m-10) cc_final: 0.5612 (m-10) REVERT: K 78 ARG cc_start: 0.8590 (tpt-90) cc_final: 0.8323 (ttt90) REVERT: L 35 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8669 (tt) REVERT: L 56 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8442 (tp-100) outliers start: 18 outliers final: 14 residues processed: 122 average time/residue: 0.3302 time to fit residues: 49.5407 Evaluate side-chains 126 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 8 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 41 HIS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 8 optimal weight: 0.0470 chunk 5 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 85 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4419 r_free = 0.4419 target = 0.186473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.148752 restraints weight = 12042.783| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.65 r_work: 0.3433 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7958 Z= 0.162 Angle : 0.491 7.102 11151 Z= 0.281 Chirality : 0.035 0.138 1262 Planarity : 0.002 0.028 1160 Dihedral : 23.984 76.761 1778 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.38 % Allowed : 21.94 % 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: 1.33 (0.29), residues: 774 helix: 2.11 (0.26), residues: 384 sheet: -0.18 (0.44), residues: 132 loop : -0.37 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 107 HIS 0.003 0.001 HIS G 115 PHE 0.009 0.001 PHE L 127 TYR 0.009 0.001 TYR K 52 ARG 0.007 0.000 ARG N 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4259.14 seconds wall clock time: 73 minutes 20.26 seconds (4400.26 seconds total)