Starting phenix.real_space_refine on Mon Mar 11 08:00:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo0_32048/03_2024/7vo0_32048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo0_32048/03_2024/7vo0_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_32048/03_2024/7vo0_32048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo0_32048/03_2024/7vo0_32048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo0_32048/03_2024/7vo0_32048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo0_32048/03_2024/7vo0_32048.pdb" } 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 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-dev-5265/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: 4.65, per 1000 atoms: 0.61 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: 3.59 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 93 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 133 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 130 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 87 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 85 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 79 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 86 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 122 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 84 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 93 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 133 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 130 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 79 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 87 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 86 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 84 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 122 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 93 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 133 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 90 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 130 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 79 " pdb="ZN ZN K 202 " - pdb=" NE2 HIS K 85 " pdb="ZN ZN K 202 " - pdb=" NE2 HIS K 87 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 122 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 84 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 86 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 133 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 90 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 93 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 130 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" NE2 HIS L 85 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 79 " pdb="ZN ZN L 202 " - pdb=" NE2 HIS L 87 " pdb=" ZN L 203 " pdb="ZN ZN L 203 " - pdb=" NE2 HIS L 86 " pdb="ZN ZN L 203 " - pdb=" NE2 HIS L 84 " pdb="ZN ZN L 203 " - pdb=" NE2 HIS L 122 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 133 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " Number of angles added : 36 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 48.7% alpha, 16.7% beta 22 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 2.87 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: 2.06 Time building geometry restraints manager: 3.66 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: 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 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: 1.260 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: 5.650 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 27.200 Find NCS groups from input model: 0.450 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.670 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 0.697 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: 0.3300 time to fit residues: 73.5548 Evaluate side-chains 123 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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: 0.6508 moved from start: 0.2637 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 8.195 11151 Z= 0.305 Chirality : 0.037 0.143 1262 Planarity : 0.003 0.033 1160 Dihedral : 23.996 83.542 1778 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.38 % Allowed : 13.95 % 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: 0.75 (0.30), residues: 774 helix: 1.69 (0.27), residues: 384 sheet: -0.52 (0.38), residues: 156 loop : -0.69 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 107 HIS 0.013 0.001 HIS G 115 PHE 0.006 0.001 PHE L 29 TYR 0.012 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 163 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 56 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6357 (mp10) REVERT: H 117 TYR cc_start: 0.4362 (m-80) cc_final: 0.4088 (m-10) REVERT: M 27 GLU cc_start: 0.5942 (pm20) cc_final: 0.5531 (pm20) outliers start: 14 outliers final: 6 residues processed: 155 average time/residue: 0.2707 time to fit residues: 52.2685 Evaluate side-chains 129 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 83 ASP 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: 0.6980 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 78 optimal weight: 0.0980 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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: 0.6542 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7958 Z= 0.187 Angle : 0.515 7.790 11151 Z= 0.296 Chirality : 0.037 0.177 1262 Planarity : 0.003 0.028 1160 Dihedral : 23.986 75.880 1778 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.72 % Allowed : 14.80 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.30), residues: 774 helix: 1.76 (0.26), residues: 384 sheet: -0.15 (0.42), residues: 132 loop : -0.18 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 107 HIS 0.008 0.001 HIS M 115 PHE 0.008 0.001 PHE L 29 TYR 0.012 0.001 TYR K 52 ARG 0.011 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 56 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6377 (mp10) REVERT: H 117 TYR cc_start: 0.4348 (m-80) cc_final: 0.4067 (m-10) REVERT: M 95 LYS cc_start: 0.6753 (mmmt) cc_final: 0.6521 (mmmt) outliers start: 16 outliers final: 11 residues processed: 139 average time/residue: 0.2516 time to fit residues: 44.0666 Evaluate side-chains 131 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain 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 Chi-restraints excluded: chain N residue 83 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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: 0.6564 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7958 Z= 0.192 Angle : 0.502 7.526 11151 Z= 0.288 Chirality : 0.037 0.146 1262 Planarity : 0.003 0.042 1160 Dihedral : 24.082 71.123 1778 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.72 % Allowed : 17.86 % 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: 1.23 (0.30), residues: 774 helix: 1.89 (0.26), residues: 384 sheet: -0.07 (0.43), residues: 132 loop : -0.24 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 107 HIS 0.005 0.001 HIS K 41 PHE 0.009 0.001 PHE H 29 TYR 0.012 0.001 TYR K 52 ARG 0.008 0.000 ARG H 30 *********************** 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 143 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 56 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6501 (mp10) REVERT: H 117 TYR cc_start: 0.4352 (m-80) cc_final: 0.4151 (m-10) outliers start: 16 outliers final: 9 residues processed: 135 average time/residue: 0.3002 time to fit residues: 50.1661 Evaluate side-chains 130 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 83 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7958 Z= 0.229 Angle : 0.524 9.038 11151 Z= 0.295 Chirality : 0.037 0.150 1262 Planarity : 0.003 0.034 1160 Dihedral : 24.286 71.931 1778 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.04 % Allowed : 19.90 % 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: 1.21 (0.29), residues: 774 helix: 1.89 (0.26), residues: 384 sheet: -0.10 (0.43), residues: 132 loop : -0.27 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 107 HIS 0.006 0.001 HIS K 41 PHE 0.007 0.001 PHE N 29 TYR 0.013 0.001 TYR K 52 ARG 0.011 0.001 ARG H 30 *********************** 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 134 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 56 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6469 (mp10) REVERT: H 117 TYR cc_start: 0.4591 (m-80) cc_final: 0.4364 (m-10) outliers start: 12 outliers final: 10 residues processed: 128 average time/residue: 0.2839 time to fit residues: 44.7706 Evaluate side-chains 129 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 41 HIS 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 83 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7958 Z= 0.246 Angle : 0.525 9.111 11151 Z= 0.295 Chirality : 0.037 0.163 1262 Planarity : 0.003 0.037 1160 Dihedral : 24.467 73.664 1778 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.40 % Allowed : 20.92 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.29), residues: 774 helix: 1.86 (0.25), residues: 384 sheet: -0.10 (0.43), residues: 132 loop : -0.29 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 107 HIS 0.006 0.001 HIS K 41 PHE 0.008 0.001 PHE N 29 TYR 0.014 0.002 TYR K 52 ARG 0.007 0.000 ARG H 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 141 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 56 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6487 (mp10) REVERT: M 33 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8391 (mt0) REVERT: N 56 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7302 (mp10) outliers start: 20 outliers final: 14 residues processed: 133 average time/residue: 0.3056 time to fit residues: 49.7376 Evaluate side-chains 133 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 41 HIS Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 56 GLN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 83 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.6617 moved from start: 0.4305 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= 0.220 Angle : 0.517 9.075 11151 Z= 0.290 Chirality : 0.036 0.136 1262 Planarity : 0.003 0.042 1160 Dihedral : 24.373 73.701 1778 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.23 % Allowed : 21.09 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.29), residues: 774 helix: 1.91 (0.26), residues: 384 sheet: -0.20 (0.43), residues: 132 loop : -0.30 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 107 HIS 0.006 0.001 HIS K 41 PHE 0.007 0.001 PHE N 29 TYR 0.012 0.001 TYR K 52 ARG 0.011 0.001 ARG H 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 fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ARG cc_start: 0.5849 (mmm-85) cc_final: 0.5377 (mmm-85) REVERT: H 56 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6440 (mp10) REVERT: M 33 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8357 (mt0) REVERT: N 56 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7314 (mp10) outliers start: 19 outliers final: 15 residues processed: 127 average time/residue: 0.3190 time to fit residues: 50.9290 Evaluate side-chains 131 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 41 HIS Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 20 SER 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 56 GLN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 83 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 GLN ** 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: 0.6678 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 7958 Z= 0.314 Angle : 0.568 9.209 11151 Z= 0.318 Chirality : 0.038 0.130 1262 Planarity : 0.003 0.036 1160 Dihedral : 24.568 76.208 1778 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.08 % Allowed : 21.09 % Favored : 74.83 % 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: 0.97 (0.29), residues: 774 helix: 1.78 (0.25), residues: 378 sheet: -0.33 (0.43), residues: 132 loop : -0.42 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 107 HIS 0.007 0.001 HIS K 41 PHE 0.011 0.002 PHE N 29 TYR 0.014 0.002 TYR K 52 ARG 0.011 0.001 ARG H 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 137 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 56 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6556 (mp10) REVERT: H 117 TYR cc_start: 0.4704 (m-10) cc_final: 0.4402 (m-10) REVERT: M 33 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8375 (mt0) REVERT: N 56 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7618 (mp10) outliers start: 24 outliers final: 16 residues processed: 126 average time/residue: 0.2903 time to fit residues: 45.0442 Evaluate side-chains 129 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 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 H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 56 GLN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 83 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 60 optimal weight: 0.0050 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 chunk 81 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 GLN ** 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: 0.6611 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7958 Z= 0.200 Angle : 0.523 9.067 11151 Z= 0.293 Chirality : 0.036 0.134 1262 Planarity : 0.003 0.029 1160 Dihedral : 24.258 75.416 1778 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.74 % Allowed : 21.60 % Favored : 74.66 % 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: 1.16 (0.29), residues: 774 helix: 1.93 (0.26), residues: 384 sheet: -0.35 (0.43), residues: 132 loop : -0.29 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 107 HIS 0.006 0.001 HIS M 85 PHE 0.006 0.001 PHE N 29 TYR 0.011 0.001 TYR K 52 ARG 0.005 0.000 ARG M 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ARG cc_start: 0.5603 (mmm-85) cc_final: 0.4905 (mmm-85) REVERT: H 56 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6374 (mp10) REVERT: H 117 TYR cc_start: 0.4689 (m-10) cc_final: 0.4355 (m-10) REVERT: M 33 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8381 (mt0) REVERT: N 56 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7328 (mp10) outliers start: 22 outliers final: 17 residues processed: 125 average time/residue: 0.2804 time to fit residues: 43.5321 Evaluate side-chains 129 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 41 HIS Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 56 GLN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 83 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 0.0870 chunk 85 optimal weight: 0.0030 chunk 78 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 GLN ** 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: 0.6593 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7958 Z= 0.188 Angle : 0.512 8.993 11151 Z= 0.290 Chirality : 0.035 0.133 1262 Planarity : 0.003 0.027 1160 Dihedral : 24.143 76.106 1778 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.89 % Allowed : 22.11 % Favored : 75.00 % 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: 1.24 (0.29), residues: 774 helix: 1.98 (0.26), residues: 384 sheet: -0.34 (0.43), residues: 132 loop : -0.23 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 107 HIS 0.005 0.001 HIS K 41 PHE 0.010 0.001 PHE H 29 TYR 0.010 0.001 TYR K 52 ARG 0.007 0.000 ARG M 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 133 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 56 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6319 (mp10) REVERT: H 91 ARG cc_start: 0.5390 (ptp90) cc_final: 0.5173 (ptt-90) REVERT: H 117 TYR cc_start: 0.4422 (m-10) cc_final: 0.4084 (m-10) REVERT: M 33 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8372 (mt0) REVERT: N 56 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7265 (mp10) outliers start: 17 outliers final: 13 residues processed: 124 average time/residue: 0.2810 time to fit residues: 43.1451 Evaluate side-chains 128 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 56 GLN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 83 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 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 = 0.4370 r_free = 0.4370 target = 0.181268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.146998 restraints weight = 12124.296| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.32 r_work: 0.3335 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7958 Z= 0.344 Angle : 0.608 9.174 11151 Z= 0.336 Chirality : 0.039 0.148 1262 Planarity : 0.003 0.037 1160 Dihedral : 24.464 77.105 1778 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.40 % Allowed : 22.11 % Favored : 74.49 % 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: 0.94 (0.29), residues: 774 helix: 1.81 (0.25), residues: 378 sheet: -0.56 (0.42), residues: 132 loop : -0.38 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 107 HIS 0.008 0.001 HIS K 41 PHE 0.013 0.002 PHE L 127 TYR 0.014 0.002 TYR K 52 ARG 0.009 0.001 ARG H 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1907.23 seconds wall clock time: 35 minutes 0.59 seconds (2100.59 seconds total)