Starting phenix.real_space_refine on Wed Feb 12 07:19:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vo0_32048/02_2025/7vo0_32048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vo0_32048/02_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_32048/02_2025/7vo0_32048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vo0_32048/02_2025/7vo0_32048.map" model { file = "/net/cci-nas-00/data/ceres_data/7vo0_32048/02_2025/7vo0_32048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vo0_32048/02_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-5592/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: 5.43, 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: 1.89 Conformation dependent library (CDL) restraints added in 899.8 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: 3.00 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: 2.25 Time building geometry restraints manager: 2.21 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.440 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.300 ------------------------------------------------------------------------------- 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 : 0.662 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: 0.3223 time to fit residues: 71.8956 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 : 0.710 ------------------------------------------------------------------------------- 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 = 0.4462 r_free = 0.4462 target = 0.189074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.155482 restraints weight = 11847.393| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.26 r_work: 0.3544 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 GLN cc_start: 0.8781 (tp40) cc_final: 0.8208 (mm-40) REVERT: H 30 ARG cc_start: 0.8091 (mmm-85) cc_final: 0.7810 (mmm-85) REVERT: H 56 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.5986 (mp10) REVERT: H 78 ARG cc_start: 0.8183 (ptm160) cc_final: 0.7944 (ptm160) REVERT: K 78 ARG cc_start: 0.8459 (tpt-90) cc_final: 0.8194 (ttt90) REVERT: L 24 GLN cc_start: 0.8484 (mm110) cc_final: 0.8270 (mm110) REVERT: M 95 LYS cc_start: 0.7913 (mmmt) cc_final: 0.7710 (mmmt) REVERT: N 56 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7940 (mp10) outliers start: 13 outliers final: 7 residues processed: 163 average time/residue: 0.2686 time to fit residues: 54.0348 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 : 0.738 ------------------------------------------------------------------------------- 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: 0.8980 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.182034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.149391 restraints weight = 12462.829| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.42 r_work: 0.3358 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7958 Z= 0.318 Angle : 0.580 7.190 11151 Z= 0.332 Chirality : 0.040 0.149 1262 Planarity : 0.003 0.028 1160 Dihedral : 24.256 80.421 1778 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.06 % Allowed : 16.33 % Favored : 80.61 % 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: 0.79 (0.29), residues: 774 helix: 1.48 (0.26), residues: 384 sheet: -0.33 (0.42), residues: 132 loop : -0.35 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 107 HIS 0.007 0.001 HIS K 41 PHE 0.010 0.002 PHE G 29 TYR 0.016 0.002 TYR K 52 ARG 0.005 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 145 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 GLN cc_start: 0.8851 (tp40) cc_final: 0.8385 (mm-40) REVERT: H 30 ARG cc_start: 0.8391 (mmm-85) cc_final: 0.8166 (mmm-85) REVERT: H 56 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6192 (mp10) REVERT: H 78 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8083 (ptm160) REVERT: K 78 ARG cc_start: 0.8534 (tpt-90) cc_final: 0.8266 (ttt90) REVERT: L 129 THR cc_start: 0.7895 (p) cc_final: 0.7478 (p) REVERT: M 95 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7486 (mmmt) outliers start: 18 outliers final: 10 residues processed: 137 average time/residue: 0.2989 time to fit residues: 50.3776 Evaluate side-chains 129 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 H residue 78 ARG 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: 0.9990 chunk 33 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 47 optimal weight: 0.0570 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 115 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 = 0.4399 r_free = 0.4399 target = 0.184448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.151929 restraints weight = 12329.920| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.29 r_work: 0.3412 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7958 Z= 0.213 Angle : 0.512 7.113 11151 Z= 0.296 Chirality : 0.037 0.141 1262 Planarity : 0.003 0.025 1160 Dihedral : 24.204 71.565 1778 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.06 % Allowed : 17.52 % Favored : 79.42 % 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: 0.98 (0.29), residues: 774 helix: 1.75 (0.26), residues: 384 sheet: -0.32 (0.42), residues: 132 loop : -0.40 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 107 HIS 0.008 0.001 HIS K 115 PHE 0.008 0.001 PHE G 29 TYR 0.012 0.001 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 : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 GLN cc_start: 0.8851 (tp40) cc_final: 0.8354 (mm-40) REVERT: H 30 ARG cc_start: 0.8319 (mmm-85) cc_final: 0.8062 (mmm-85) REVERT: H 56 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.5976 (mp10) REVERT: H 117 TYR cc_start: 0.7174 (m-10) cc_final: 0.6083 (m-10) REVERT: K 78 ARG cc_start: 0.8501 (tpt-90) cc_final: 0.8246 (ttt90) REVERT: K 95 LYS cc_start: 0.7707 (ptpp) cc_final: 0.7426 (ptpp) REVERT: M 33 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8525 (mt0) REVERT: M 95 LYS cc_start: 0.7789 (mmmt) cc_final: 0.7412 (mmmt) REVERT: N 56 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7912 (mp10) outliers start: 18 outliers final: 10 residues processed: 140 average time/residue: 0.3063 time to fit residues: 52.5001 Evaluate side-chains 133 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 0.0000 chunk 46 optimal weight: 3.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- 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 = 0.183338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.144658 restraints weight = 12201.194| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.94 r_work: 0.3387 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4018 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= 0.186 Angle : 0.511 7.475 11151 Z= 0.293 Chirality : 0.036 0.134 1262 Planarity : 0.003 0.031 1160 Dihedral : 24.254 71.127 1778 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.72 % Allowed : 19.22 % Favored : 78.06 % 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: 1.14 (0.29), residues: 774 helix: 1.94 (0.26), residues: 384 sheet: -0.23 (0.43), residues: 132 loop : -0.44 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 107 HIS 0.004 0.001 HIS G 115 PHE 0.008 0.001 PHE H 29 TYR 0.011 0.001 TYR K 52 ARG 0.006 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: 16 poor density : 128 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 16 ARG cc_start: 0.8676 (ptp-110) cc_final: 0.7951 (mtt90) REVERT: H 24 GLN cc_start: 0.8926 (tp40) cc_final: 0.8547 (mm-40) REVERT: H 30 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7995 (mmm-85) REVERT: H 56 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.5953 (mp10) REVERT: H 117 TYR cc_start: 0.7256 (m-10) cc_final: 0.6082 (m-10) REVERT: K 78 ARG cc_start: 0.8537 (tpt-90) cc_final: 0.8288 (ttt90) REVERT: K 95 LYS cc_start: 0.7790 (ptpp) cc_final: 0.7501 (ptpp) REVERT: L 24 GLN cc_start: 0.8552 (mm110) cc_final: 0.8344 (mm110) REVERT: L 56 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8662 (tp-100) REVERT: M 91 ARG cc_start: 0.6600 (ptt-90) cc_final: 0.6288 (mtm180) REVERT: M 95 LYS cc_start: 0.7745 (mmmt) cc_final: 0.7402 (mmmt) REVERT: N 56 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7910 (mp10) outliers start: 16 outliers final: 11 residues processed: 138 average time/residue: 0.3073 time to fit residues: 51.6710 Evaluate side-chains 130 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 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: 0.6980 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: 0.7980 chunk 77 optimal weight: 0.0060 chunk 40 optimal weight: 0.0670 chunk 82 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 overall best weight: 0.4534 ------------------------------------------------------------------------------- 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 = 0.4412 r_free = 0.4412 target = 0.185767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.153324 restraints weight = 12351.901| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.31 r_work: 0.3443 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4282 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= 0.178 Angle : 0.490 7.543 11151 Z= 0.282 Chirality : 0.036 0.135 1262 Planarity : 0.003 0.026 1160 Dihedral : 24.297 73.525 1778 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.06 % Allowed : 20.07 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.00 (0.26), residues: 384 sheet: -0.20 (0.43), residues: 132 loop : -0.45 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 107 HIS 0.004 0.001 HIS M 115 PHE 0.006 0.001 PHE H 29 TYR 0.010 0.001 TYR K 52 ARG 0.007 0.001 ARG N 30 *********************** 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: 18 poor density : 119 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 ASP cc_start: 0.7982 (t70) cc_final: 0.7771 (t0) REVERT: H 16 ARG cc_start: 0.8617 (ptp-110) cc_final: 0.7990 (mtt90) REVERT: H 24 GLN cc_start: 0.8938 (tp40) cc_final: 0.8550 (mm-40) REVERT: H 30 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.8019 (mmm-85) REVERT: H 56 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.5910 (mp10) REVERT: H 117 TYR cc_start: 0.6936 (m-10) cc_final: 0.5786 (m-10) REVERT: K 78 ARG cc_start: 0.8533 (tpt-90) cc_final: 0.8277 (ttt90) REVERT: K 95 LYS cc_start: 0.7971 (ptpp) cc_final: 0.7722 (ptpp) REVERT: K 125 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7375 (mm-30) REVERT: L 35 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8699 (tt) REVERT: L 56 GLN cc_start: 0.8974 (tp-100) cc_final: 0.8773 (tp40) REVERT: M 95 LYS cc_start: 0.7634 (mmmt) cc_final: 0.7317 (mmmt) REVERT: N 56 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7878 (mp10) outliers start: 18 outliers final: 12 residues processed: 131 average time/residue: 0.2926 time to fit residues: 46.9959 Evaluate side-chains 131 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 81 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: 1.9990 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 0.0070 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.184248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.149035 restraints weight = 12261.272| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.54 r_work: 0.3379 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7958 Z= 0.227 Angle : 0.518 6.571 11151 Z= 0.295 Chirality : 0.036 0.144 1262 Planarity : 0.003 0.031 1160 Dihedral : 24.350 73.473 1778 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.89 % Allowed : 20.92 % Favored : 76.19 % 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: 1.14 (0.29), residues: 774 helix: 1.96 (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 0.011 0.001 TRP G 107 HIS 0.005 0.001 HIS G 115 PHE 0.013 0.001 PHE H 29 TYR 0.014 0.001 TYR H 76 ARG 0.008 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: 17 poor density : 118 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 16 ARG cc_start: 0.8733 (ptp-110) cc_final: 0.8124 (mtt90) REVERT: H 24 GLN cc_start: 0.8969 (tp40) cc_final: 0.8759 (mm-40) REVERT: H 30 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.8039 (mmm-85) REVERT: H 56 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6005 (mp10) REVERT: H 117 TYR cc_start: 0.6963 (m-10) cc_final: 0.5872 (m-10) REVERT: K 78 ARG cc_start: 0.8552 (tpt-90) cc_final: 0.8283 (ttt90) REVERT: K 95 LYS cc_start: 0.8001 (ptpp) cc_final: 0.7716 (ptpp) REVERT: L 35 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8695 (tt) REVERT: L 56 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8514 (tp-100) REVERT: M 95 LYS cc_start: 0.7699 (mmmt) cc_final: 0.7378 (mmmt) outliers start: 17 outliers final: 13 residues processed: 127 average time/residue: 0.3029 time to fit residues: 47.0914 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 : 0.682 ------------------------------------------------------------------------------- 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 L residue 35 LEU Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 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: 0.5980 chunk 40 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.183158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.147962 restraints weight = 12345.377| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.49 r_work: 0.3398 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 7958 Z= 0.209 Angle : 0.501 6.441 11151 Z= 0.287 Chirality : 0.036 0.133 1262 Planarity : 0.003 0.025 1160 Dihedral : 24.255 74.234 1778 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: 1.15 (0.29), residues: 774 helix: 1.96 (0.26), residues: 384 sheet: -0.19 (0.44), residues: 132 loop : -0.48 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 107 HIS 0.004 0.001 HIS K 41 PHE 0.012 0.001 PHE H 29 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 135 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 VAL cc_start: -0.0978 (OUTLIER) cc_final: -0.1413 (t) REVERT: H 16 ARG cc_start: 0.8739 (ptp-110) cc_final: 0.8180 (mtt90) REVERT: H 24 GLN cc_start: 0.9004 (tp40) cc_final: 0.8760 (mm-40) REVERT: H 30 ARG cc_start: 0.8327 (mmm-85) cc_final: 0.8033 (mmm-85) REVERT: H 56 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.5939 (mp10) REVERT: H 117 TYR cc_start: 0.6793 (m-10) cc_final: 0.5627 (m-10) REVERT: K 78 ARG cc_start: 0.8573 (tpt-90) cc_final: 0.8306 (ttt90) REVERT: K 95 LYS cc_start: 0.7981 (ptpp) cc_final: 0.7727 (ptpp) REVERT: L 35 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8675 (tt) REVERT: L 56 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8469 (tp-100) REVERT: M 95 LYS cc_start: 0.7684 (mmmt) cc_final: 0.7362 (mmmt) outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 0.3045 time to fit residues: 46.9274 Evaluate side-chains 131 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 38 MET Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 23 optimal weight: 0.0010 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 15 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.184807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.151968 restraints weight = 12219.060| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.23 r_work: 0.3423 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7958 Z= 0.204 Angle : 0.518 7.972 11151 Z= 0.296 Chirality : 0.036 0.132 1262 Planarity : 0.003 0.021 1160 Dihedral : 24.209 75.089 1778 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.89 % Allowed : 21.60 % 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: 1.17 (0.29), residues: 774 helix: 1.98 (0.26), residues: 384 sheet: -0.19 (0.44), residues: 132 loop : -0.49 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 107 HIS 0.005 0.001 HIS K 41 PHE 0.012 0.001 PHE H 29 TYR 0.011 0.001 TYR K 52 ARG 0.009 0.000 ARG L 91 *********************** 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: 17 poor density : 115 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 VAL cc_start: -0.0860 (OUTLIER) cc_final: -0.1298 (t) REVERT: H 16 ARG cc_start: 0.8801 (ptp-110) cc_final: 0.8188 (mtt90) REVERT: H 24 GLN cc_start: 0.9005 (tp40) cc_final: 0.8797 (mm-40) REVERT: H 30 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.8038 (mmm-85) REVERT: H 56 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.5913 (mp10) REVERT: H 117 TYR cc_start: 0.6746 (m-10) cc_final: 0.5617 (m-10) REVERT: K 78 ARG cc_start: 0.8563 (tpt-90) cc_final: 0.8296 (ttt90) REVERT: K 95 LYS cc_start: 0.7988 (ptpp) cc_final: 0.7741 (ptpp) REVERT: L 35 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8655 (tt) REVERT: L 56 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8461 (tp-100) REVERT: M 95 LYS cc_start: 0.7649 (mmmt) cc_final: 0.7304 (mmmt) outliers start: 17 outliers final: 14 residues processed: 123 average time/residue: 0.3198 time to fit residues: 47.9724 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 : 1.059 ------------------------------------------------------------------------------- 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 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 38 MET Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 0.0170 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.4422 r_free = 0.4422 target = 0.186673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.156160 restraints weight = 12171.189| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.18 r_work: 0.3455 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7958 Z= 0.172 Angle : 0.500 7.217 11151 Z= 0.286 Chirality : 0.035 0.133 1262 Planarity : 0.002 0.027 1160 Dihedral : 24.026 75.820 1778 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.72 % Allowed : 21.26 % 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: 1.35 (0.29), residues: 774 helix: 2.13 (0.26), residues: 384 sheet: -0.12 (0.45), residues: 132 loop : -0.40 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 107 HIS 0.004 0.001 HIS G 115 PHE 0.012 0.001 PHE H 29 TYR 0.010 0.001 TYR K 52 ARG 0.007 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 136 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 VAL cc_start: -0.0894 (OUTLIER) cc_final: -0.1327 (t) REVERT: H 16 ARG cc_start: 0.8755 (ptp-110) cc_final: 0.8191 (mtt90) REVERT: H 30 ARG cc_start: 0.8298 (mmm-85) cc_final: 0.7980 (mmm-85) REVERT: H 40 LYS cc_start: 0.9333 (ttpp) cc_final: 0.9009 (tppt) REVERT: K 78 ARG cc_start: 0.8575 (tpt-90) cc_final: 0.8326 (ttt90) REVERT: K 95 LYS cc_start: 0.7933 (ptpp) cc_final: 0.7674 (ptpp) REVERT: L 56 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8465 (tp-100) REVERT: N 56 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7877 (mp10) outliers start: 16 outliers final: 11 residues processed: 128 average time/residue: 0.3168 time to fit residues: 49.1933 Evaluate side-chains 127 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 K residue 66 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 109 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 0.0370 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 28 optimal weight: 0.0770 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN ** 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 = 0.4407 r_free = 0.4407 target = 0.185197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.151753 restraints weight = 12011.625| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.48 r_work: 0.3400 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7958 Z= 0.192 Angle : 0.523 6.791 11151 Z= 0.296 Chirality : 0.036 0.132 1262 Planarity : 0.003 0.029 1160 Dihedral : 24.070 76.608 1778 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: 1.29 (0.29), residues: 774 helix: 2.07 (0.26), residues: 384 sheet: -0.16 (0.45), residues: 132 loop : -0.39 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 107 HIS 0.004 0.001 HIS K 41 PHE 0.011 0.001 PHE H 127 TYR 0.010 0.001 TYR K 52 ARG 0.007 0.001 ARG L 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4250.43 seconds wall clock time: 75 minutes 50.22 seconds (4550.22 seconds total)