Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 14:42:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo0_32048/04_2023/7vo0_32048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo0_32048/04_2023/7vo0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo0_32048/04_2023/7vo0_32048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo0_32048/04_2023/7vo0_32048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo0_32048/04_2023/7vo0_32048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo0_32048/04_2023/7vo0_32048.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 132": "OD1" <-> "OD2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "K GLU 125": "OE1" <-> "OE2" Residue "M GLU 25": "OE1" <-> "OE2" Residue "M GLU 28": "OE1" <-> "OE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "M GLU 125": "OE1" <-> "OE2" Residue "M ASP 132": "OD1" <-> "OD2" Residue "N GLU 27": "OE1" <-> "OE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 4.61, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 3.43 Conformation dependent library (CDL) restraints added in 912.3 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: 2.66 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: 2.05 Time building geometry restraints manager: 3.65 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: 99.77 - 106.63: 680 106.63 - 113.48: 4380 113.48 - 120.34: 2991 120.34 - 127.20: 2891 127.20 - 134.06: 209 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: 3579 17.84 - 35.68: 441 35.68 - 53.53: 313 53.53 - 71.37: 63 71.37 - 89.21: 10 Dihedral angle restraints: 4406 sinusoidal: 2168 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 4403 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 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: 1.390 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: 6.020 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 26.180 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- 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 : 21.096 89.208 2966 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 % 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.3149 time to fit residues: 69.8853 Evaluate side-chains 127 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9263 ------------------------------------------------------------------------------- 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: 0.9980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 0.0000 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 0.0980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 GLN L 84 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7958 Z= 0.188 Angle : 0.533 8.306 11151 Z= 0.305 Chirality : 0.037 0.145 1262 Planarity : 0.003 0.035 1160 Dihedral : 24.136 84.225 1706 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 2.55 % 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: 0.76 (0.30), residues: 774 helix: 1.70 (0.27), residues: 384 sheet: -0.51 (0.38), residues: 156 loop : -0.67 (0.37), residues: 234 *********************** 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 165 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 156 average time/residue: 0.2623 time to fit residues: 50.9012 Evaluate side-chains 127 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 0.677 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0747 time to fit residues: 1.7664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 0.0270 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 0.0010 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.8248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.3284 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= 0.248 Angle : 0.547 7.964 11151 Z= 0.313 Chirality : 0.038 0.176 1262 Planarity : 0.003 0.027 1160 Dihedral : 24.249 78.866 1706 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.70 % 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: 1.62 (0.26), residues: 384 sheet: -0.49 (0.38), residues: 156 loop : -0.76 (0.37), residues: 234 *********************** 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 139 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 134 average time/residue: 0.2857 time to fit residues: 47.2322 Evaluate side-chains 121 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0748 time to fit residues: 1.7033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.0670 chunk 58 optimal weight: 0.0030 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.3328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN K 56 GLN L 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 7958 Z= 0.158 Angle : 0.492 7.548 11151 Z= 0.282 Chirality : 0.036 0.148 1262 Planarity : 0.002 0.023 1160 Dihedral : 24.152 70.496 1706 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 1.19 % 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: 1.29 (0.30), residues: 774 helix: 1.96 (0.26), residues: 384 sheet: -0.08 (0.43), residues: 132 loop : -0.23 (0.37), residues: 258 *********************** 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 132 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 128 average time/residue: 0.2784 time to fit residues: 44.3349 Evaluate side-chains 120 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 0.688 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0768 time to fit residues: 1.4731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 GLN L 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7958 Z= 0.212 Angle : 0.511 9.156 11151 Z= 0.289 Chirality : 0.036 0.139 1262 Planarity : 0.003 0.029 1160 Dihedral : 24.420 72.977 1706 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.29), residues: 774 helix: 2.07 (0.26), residues: 384 sheet: -0.03 (0.44), residues: 132 loop : -0.25 (0.36), residues: 258 *********************** 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 122 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 120 average time/residue: 0.2924 time to fit residues: 43.1638 Evaluate side-chains 118 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.716 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0700 time to fit residues: 1.1208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 GLN ** L 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.4167 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= 0.246 Angle : 0.530 9.264 11151 Z= 0.297 Chirality : 0.037 0.169 1262 Planarity : 0.003 0.033 1160 Dihedral : 24.566 73.258 1706 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.87 % 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: 1.28 (0.29), residues: 774 helix: 1.97 (0.25), residues: 384 sheet: -0.05 (0.44), residues: 132 loop : -0.30 (0.36), residues: 258 *********************** 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 131 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 128 average time/residue: 0.2942 time to fit residues: 46.1364 Evaluate side-chains 115 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0692 time to fit residues: 1.5091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 GLN ** L 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7958 Z= 0.197 Angle : 0.521 9.838 11151 Z= 0.289 Chirality : 0.036 0.142 1262 Planarity : 0.003 0.038 1160 Dihedral : 24.442 73.768 1706 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.29), residues: 774 helix: 2.03 (0.26), residues: 384 sheet: -0.21 (0.43), residues: 132 loop : -0.29 (0.36), residues: 258 *********************** 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 120 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 117 average time/residue: 0.3130 time to fit residues: 45.4051 Evaluate side-chains 115 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0764 time to fit residues: 1.3786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 72 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 GLN ** L 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 7958 Z= 0.239 Angle : 0.541 9.377 11151 Z= 0.302 Chirality : 0.036 0.137 1262 Planarity : 0.003 0.031 1160 Dihedral : 24.475 74.665 1706 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.19 % 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: 1.18 (0.29), residues: 774 helix: 1.96 (0.25), residues: 384 sheet: -0.29 (0.43), residues: 132 loop : -0.33 (0.35), residues: 258 *********************** 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 118 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 113 average time/residue: 0.3068 time to fit residues: 42.3322 Evaluate side-chains 113 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.716 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0668 time to fit residues: 1.5362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 GLN ** L 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 7958 Z= 0.276 Angle : 0.567 9.428 11151 Z= 0.316 Chirality : 0.037 0.134 1262 Planarity : 0.003 0.032 1160 Dihedral : 24.504 75.786 1706 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 1.02 % 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: 1.00 (0.29), residues: 774 helix: 1.81 (0.25), residues: 384 sheet: -0.42 (0.42), residues: 132 loop : -0.40 (0.35), residues: 258 *********************** 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 115 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 113 average time/residue: 0.3024 time to fit residues: 41.9758 Evaluate side-chains 110 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 0.681 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0767 time to fit residues: 1.3214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 GLN ** L 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 7958 Z= 0.261 Angle : 0.574 9.513 11151 Z= 0.318 Chirality : 0.037 0.136 1262 Planarity : 0.003 0.038 1160 Dihedral : 24.487 76.467 1706 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.68 % 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: 1.00 (0.29), residues: 774 helix: 1.85 (0.25), residues: 384 sheet: -0.54 (0.42), residues: 132 loop : -0.41 (0.35), residues: 258 ********************** 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 115 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 113 average time/residue: 0.3071 time to fit residues: 42.6092 Evaluate side-chains 111 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 0.745 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0783 time to fit residues: 1.3609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 18 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 GLN ** L 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4398 r_free = 0.4398 target = 0.183892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.144135 restraints weight = 12130.472| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.60 r_work: 0.3384 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 7958 Z= 0.220 Angle : 0.547 9.400 11151 Z= 0.307 Chirality : 0.036 0.150 1262 Planarity : 0.003 0.035 1160 Dihedral : 24.408 77.021 1706 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.29), residues: 774 helix: 1.94 (0.26), residues: 384 sheet: -0.53 (0.42), residues: 132 loop : -0.45 (0.34), residues: 258 =============================================================================== Job complete usr+sys time: 1853.55 seconds wall clock time: 33 minutes 58.28 seconds (2038.28 seconds total)