Starting phenix.real_space_refine on Mon Dec 11 00:11:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/12_2023/7cr4_30447_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/12_2023/7cr4_30447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/12_2023/7cr4_30447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/12_2023/7cr4_30447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/12_2023/7cr4_30447_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr4_30447/12_2023/7cr4_30447_trim_updated.pdb" } resolution = 3.9 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= -0.000 sd= 0.002 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 S 88 5.16 5 Cl 4 4.86 5 C 10288 2.51 5 N 2724 2.21 5 O 2880 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D GLU 330": "OE1" <-> "OE2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 553": "NH1" <-> "NH2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F ARG 144": "NH1" <-> "NH2" Residue "F ARG 201": "NH1" <-> "NH2" Residue "F GLU 330": "OE1" <-> "OE2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ARG 553": "NH1" <-> "NH2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15988 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2855 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 6, 'TRANS': 342} Chain breaks: 2 Chain: "H" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1125 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2855 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 6, 'TRANS': 342} Chain breaks: 2 Chain: "C" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1125 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2855 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 6, 'TRANS': 342} Chain breaks: 2 Chain: "E" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1125 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2855 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 6, 'TRANS': 342} Chain breaks: 2 Chain: "G" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1125 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.53, per 1000 atoms: 0.53 Number of scatterers: 15988 At special positions: 0 Unit cell: (126.75, 126.75, 119.652, 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) Cl 4 17.00 S 88 16.00 F 4 9.00 O 2880 8.00 N 2724 7.00 C 10288 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.84 Conformation dependent library (CDL) restraints added in 2.6 seconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 4 sheets defined 74.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 91 through 114 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 123 through 148 Processing helix chain 'A' and resid 158 through 164 Processing helix chain 'A' and resid 167 through 183 removed outlier: 3.995A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.840A pdb=" N MET A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 254 removed outlier: 5.493A pdb=" N LYS A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 288 through 328 removed outlier: 3.892A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 333 through 349 Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 536 through 560 removed outlier: 4.220A pdb=" N ARG A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 593 Processing helix chain 'H' and resid 7 through 20 Processing helix chain 'H' and resid 30 through 40 Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 66 through 73 Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing helix chain 'H' and resid 83 through 92 Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 119 through 129 Processing helix chain 'H' and resid 139 through 147 Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 91 through 114 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 123 through 148 Processing helix chain 'B' and resid 158 through 164 Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.995A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.840A pdb=" N MET B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 254 removed outlier: 5.493A pdb=" N LYS B 230 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 288 through 328 removed outlier: 3.891A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 333 through 349 Processing helix chain 'B' and resid 358 through 365 Processing helix chain 'B' and resid 536 through 560 removed outlier: 4.219A pdb=" N ARG B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 593 Processing helix chain 'C' and resid 7 through 20 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 91 through 114 Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 123 through 148 Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 167 through 183 removed outlier: 3.995A pdb=" N LEU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 211 removed outlier: 3.839A pdb=" N MET D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 254 removed outlier: 5.492A pdb=" N LYS D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 288 through 328 removed outlier: 3.891A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 333 through 349 Processing helix chain 'D' and resid 358 through 365 Processing helix chain 'D' and resid 536 through 560 removed outlier: 4.220A pdb=" N ARG D 560 " --> pdb=" O LYS D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 593 Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 103 through 110 Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'F' and resid 71 through 85 Processing helix chain 'F' and resid 91 through 114 Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 123 through 148 Processing helix chain 'F' and resid 158 through 164 Processing helix chain 'F' and resid 167 through 183 removed outlier: 3.995A pdb=" N LEU F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 211 removed outlier: 3.840A pdb=" N MET F 211 " --> pdb=" O ARG F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 254 removed outlier: 5.493A pdb=" N LYS F 230 " --> pdb=" O TYR F 226 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU F 231 " --> pdb=" O ALA F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 275 Processing helix chain 'F' and resid 288 through 328 removed outlier: 3.891A pdb=" N THR F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER F 303 " --> pdb=" O LEU F 299 " (cutoff:3.500A) Proline residue: F 308 - end of helix Processing helix chain 'F' and resid 333 through 349 Processing helix chain 'F' and resid 358 through 365 Processing helix chain 'F' and resid 536 through 560 removed outlier: 4.219A pdb=" N ARG F 560 " --> pdb=" O LYS F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 593 Processing helix chain 'G' and resid 7 through 20 Processing helix chain 'G' and resid 30 through 40 Processing helix chain 'G' and resid 46 through 56 Processing helix chain 'G' and resid 66 through 73 Processing helix chain 'G' and resid 83 through 92 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 139 through 147 Processing sheet with id= A, first strand: chain 'H' and resid 100 through 102 removed outlier: 3.670A pdb=" N ILE H 101 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.670A pdb=" N ILE C 101 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.669A pdb=" N ILE E 101 " --> pdb=" O VAL E 137 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 100 through 102 removed outlier: 3.669A pdb=" N ILE G 101 " --> pdb=" O VAL G 137 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.63 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2592 1.30 - 1.43: 4474 1.43 - 1.56: 9106 1.56 - 1.68: 0 1.68 - 1.81: 152 Bond restraints: 16324 Sorted by residual: bond pdb=" C12 GB9 B1001 " pdb=" N2 GB9 B1001 " ideal model delta sigma weight residual 1.306 1.482 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" C12 GB9 F1001 " pdb=" N2 GB9 F1001 " ideal model delta sigma weight residual 1.306 1.482 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" C12 GB9 A1001 " pdb=" N2 GB9 A1001 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.70e+01 bond pdb=" C12 GB9 D1001 " pdb=" N2 GB9 D1001 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C5 GB9 A1001 " pdb=" C8 GB9 A1001 " ideal model delta sigma weight residual 1.386 1.529 -0.143 2.00e-02 2.50e+03 5.12e+01 ... (remaining 16319 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.82: 264 106.82 - 113.60: 9068 113.60 - 120.39: 6523 120.39 - 127.18: 6017 127.18 - 133.96: 140 Bond angle restraints: 22012 Sorted by residual: angle pdb=" CA LEU A 272 " pdb=" CB LEU A 272 " pdb=" CG LEU A 272 " ideal model delta sigma weight residual 116.30 106.80 9.50 3.50e+00 8.16e-02 7.37e+00 angle pdb=" CA LEU B 272 " pdb=" CB LEU B 272 " pdb=" CG LEU B 272 " ideal model delta sigma weight residual 116.30 106.83 9.47 3.50e+00 8.16e-02 7.32e+00 angle pdb=" CA LEU F 272 " pdb=" CB LEU F 272 " pdb=" CG LEU F 272 " ideal model delta sigma weight residual 116.30 106.83 9.47 3.50e+00 8.16e-02 7.32e+00 angle pdb=" CA LEU D 272 " pdb=" CB LEU D 272 " pdb=" CG LEU D 272 " ideal model delta sigma weight residual 116.30 106.89 9.41 3.50e+00 8.16e-02 7.23e+00 angle pdb=" C2 GB9 D1001 " pdb=" N1 GB9 D1001 " pdb=" C3 GB9 D1001 " ideal model delta sigma weight residual 128.33 120.50 7.83 3.00e+00 1.11e-01 6.81e+00 ... (remaining 22007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 8659 17.86 - 35.71: 849 35.71 - 53.57: 68 53.57 - 71.42: 12 71.42 - 89.28: 8 Dihedral angle restraints: 9596 sinusoidal: 3900 harmonic: 5696 Sorted by residual: dihedral pdb=" CA SER D 122 " pdb=" C SER D 122 " pdb=" N GLU D 123 " pdb=" CA GLU D 123 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER F 122 " pdb=" C SER F 122 " pdb=" N GLU F 123 " pdb=" CA GLU F 123 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER B 122 " pdb=" C SER B 122 " pdb=" N GLU B 123 " pdb=" CA GLU B 123 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 9593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1368 0.025 - 0.049: 621 0.049 - 0.074: 304 0.074 - 0.098: 83 0.098 - 0.123: 28 Chirality restraints: 2404 Sorted by residual: chirality pdb=" CA PRO F 308 " pdb=" N PRO F 308 " pdb=" C PRO F 308 " pdb=" CB PRO F 308 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA PRO B 308 " pdb=" N PRO B 308 " pdb=" C PRO B 308 " pdb=" CB PRO B 308 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA PRO A 308 " pdb=" N PRO A 308 " pdb=" C PRO A 308 " pdb=" CB PRO A 308 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 2401 not shown) Planarity restraints: 2780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 166 " 0.016 5.00e-02 4.00e+02 2.45e-02 9.64e-01 pdb=" N PRO F 167 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO F 167 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 167 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 166 " -0.016 5.00e-02 4.00e+02 2.45e-02 9.64e-01 pdb=" N PRO B 167 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 166 " 0.016 5.00e-02 4.00e+02 2.45e-02 9.62e-01 pdb=" N PRO D 167 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO D 167 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 167 " 0.014 5.00e-02 4.00e+02 ... (remaining 2777 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 222 2.45 - 3.06: 14863 3.06 - 3.67: 28560 3.67 - 4.29: 41763 4.29 - 4.90: 59929 Nonbonded interactions: 145337 Sorted by model distance: nonbonded pdb=" OH TYR B 571 " pdb=" O VAL F 567 " model vdw 1.833 2.440 nonbonded pdb=" NE2 GLN F 341 " pdb=" O MET G 110 " model vdw 1.905 2.520 nonbonded pdb=" OG SER A 179 " pdb=" F1 GB9 A1001 " model vdw 1.973 2.390 nonbonded pdb=" OG SER B 179 " pdb=" F1 GB9 B1001 " model vdw 1.973 2.390 nonbonded pdb=" OG SER F 179 " pdb=" F1 GB9 F1001 " model vdw 1.973 2.390 ... (remaining 145332 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 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 0.650 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: 0.020 Extract box with map and model: 3.880 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 44.370 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.008 0.176 16324 Z= 0.506 Angle : 0.650 9.501 22012 Z= 0.384 Chirality : 0.036 0.123 2404 Planarity : 0.003 0.025 2780 Dihedral : 13.143 89.277 5932 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 102.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.16), residues: 1936 helix: -1.78 (0.11), residues: 1484 sheet: None (None), residues: 0 loop : -1.63 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 146 HIS 0.007 0.002 HIS B 328 PHE 0.012 0.002 PHE A 261 TYR 0.013 0.002 TYR D 571 ARG 0.004 0.000 ARG D 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 1.968 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.2977 time to fit residues: 166.7265 Evaluate side-chains 281 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 174 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN H 42 GLN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN B 591 GLN C 42 GLN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS D 324 HIS D 328 HIS ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 HIS ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16324 Z= 0.334 Angle : 0.715 11.804 22012 Z= 0.383 Chirality : 0.042 0.191 2404 Planarity : 0.005 0.051 2780 Dihedral : 4.776 21.679 2180 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 33.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.52 % Allowed : 14.52 % Favored : 80.95 % 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: -1.08 (0.17), residues: 1936 helix: -0.36 (0.12), residues: 1524 sheet: None (None), residues: 0 loop : -1.56 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 344 HIS 0.007 0.001 HIS B 324 PHE 0.018 0.002 PHE B 297 TYR 0.024 0.002 TYR B 571 ARG 0.011 0.001 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 357 time to evaluate : 2.019 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 48 residues processed: 391 average time/residue: 0.2801 time to fit residues: 160.5918 Evaluate side-chains 347 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 299 time to evaluate : 1.738 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.1837 time to fit residues: 17.5165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 48 optimal weight: 30.0000 chunk 174 optimal weight: 6.9990 chunk 188 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 173 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 GLN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 GLN F 321 GLN F 324 HIS ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16324 Z= 0.322 Angle : 0.670 11.314 22012 Z= 0.365 Chirality : 0.040 0.198 2404 Planarity : 0.004 0.037 2780 Dihedral : 4.712 23.005 2180 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 31.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.81 % Allowed : 19.76 % Favored : 76.43 % 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: -0.48 (0.18), residues: 1936 helix: 0.08 (0.12), residues: 1520 sheet: None (None), residues: 0 loop : -1.39 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 288 HIS 0.004 0.001 HIS A 260 PHE 0.017 0.002 PHE B 297 TYR 0.022 0.002 TYR B 571 ARG 0.005 0.001 ARG F 581 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 333 time to evaluate : 2.344 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 35 residues processed: 379 average time/residue: 0.2841 time to fit residues: 158.8740 Evaluate side-chains 337 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 302 time to evaluate : 1.867 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1625 time to fit residues: 12.7231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 40.0000 chunk 131 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 19 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 185 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN H 144 GLN ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS C 61 ASN C 112 ASN C 144 GLN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 HIS E 61 ASN E 112 ASN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 144 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16324 Z= 0.240 Angle : 0.635 12.173 22012 Z= 0.337 Chirality : 0.039 0.221 2404 Planarity : 0.004 0.032 2780 Dihedral : 4.495 22.762 2180 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.63 % Allowed : 21.43 % Favored : 74.94 % 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: 0.16 (0.18), residues: 1936 helix: 0.53 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -1.18 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 344 HIS 0.017 0.001 HIS F 357 PHE 0.018 0.002 PHE D 240 TYR 0.022 0.002 TYR B 571 ARG 0.003 0.000 ARG F 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 349 time to evaluate : 1.963 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 28 residues processed: 386 average time/residue: 0.2789 time to fit residues: 159.9674 Evaluate side-chains 341 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 313 time to evaluate : 1.867 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1457 time to fit residues: 10.1744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 138 optimal weight: 30.0000 chunk 76 optimal weight: 40.0000 chunk 158 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 30.0000 chunk 166 optimal weight: 2.9990 chunk 46 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN H 61 ASN ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS D 341 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 GLN E 43 ASN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 HIS ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16324 Z= 0.292 Angle : 0.682 9.632 22012 Z= 0.364 Chirality : 0.041 0.211 2404 Planarity : 0.004 0.043 2780 Dihedral : 4.649 24.411 2180 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 29.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.39 % Allowed : 23.21 % Favored : 73.39 % 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: 0.15 (0.18), residues: 1936 helix: 0.51 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -1.09 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 288 HIS 0.003 0.001 HIS D 228 PHE 0.024 0.002 PHE B 240 TYR 0.019 0.002 TYR H 139 ARG 0.008 0.001 ARG B 581 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 329 time to evaluate : 1.865 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 25 residues processed: 371 average time/residue: 0.2681 time to fit residues: 148.9823 Evaluate side-chains 329 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 304 time to evaluate : 1.795 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1512 time to fit residues: 9.5953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS A 341 GLN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16324 Z= 0.202 Angle : 0.712 11.543 22012 Z= 0.364 Chirality : 0.041 0.195 2404 Planarity : 0.003 0.031 2780 Dihedral : 4.536 28.449 2180 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.38 % Allowed : 24.40 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1936 helix: 0.87 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.98 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 344 HIS 0.004 0.001 HIS F 575 PHE 0.032 0.002 PHE D 240 TYR 0.019 0.002 TYR B 347 ARG 0.005 0.000 ARG D 581 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 374 time to evaluate : 1.959 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 27 residues processed: 390 average time/residue: 0.2633 time to fit residues: 153.1690 Evaluate side-chains 336 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 309 time to evaluate : 1.762 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1441 time to fit residues: 9.5038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 30.0000 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 135 optimal weight: 0.0970 chunk 156 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 112 optimal weight: 0.1980 chunk 85 optimal weight: 0.0070 chunk 114 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 HIS ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16324 Z= 0.198 Angle : 0.753 13.736 22012 Z= 0.379 Chirality : 0.041 0.198 2404 Planarity : 0.003 0.035 2780 Dihedral : 4.527 31.567 2180 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.25 % Allowed : 26.96 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.70 (0.19), residues: 1936 helix: 0.88 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.84 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 344 HIS 0.002 0.000 HIS A 328 PHE 0.037 0.002 PHE E 90 TYR 0.021 0.001 TYR B 571 ARG 0.004 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 362 time to evaluate : 1.941 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 373 average time/residue: 0.2926 time to fit residues: 163.7060 Evaluate side-chains 321 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 307 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1617 time to fit residues: 6.4908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 20.0000 chunk 110 optimal weight: 0.1980 chunk 55 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 145 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 328 HIS ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16324 Z= 0.254 Angle : 0.769 12.977 22012 Z= 0.395 Chirality : 0.043 0.190 2404 Planarity : 0.004 0.031 2780 Dihedral : 4.618 32.903 2180 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 25.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.95 % Allowed : 29.29 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.60 (0.19), residues: 1936 helix: 0.79 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.80 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 344 HIS 0.006 0.001 HIS A 328 PHE 0.040 0.002 PHE D 555 TYR 0.026 0.002 TYR B 571 ARG 0.003 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 316 time to evaluate : 1.778 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 322 average time/residue: 0.2794 time to fit residues: 131.9541 Evaluate side-chains 302 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 289 time to evaluate : 1.813 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1501 time to fit residues: 5.9419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 172 optimal weight: 30.0000 chunk 103 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 135 optimal weight: 50.0000 chunk 52 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 HIS ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN C 54 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS F 328 HIS ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16324 Z= 0.292 Angle : 0.789 13.396 22012 Z= 0.410 Chirality : 0.043 0.203 2404 Planarity : 0.004 0.034 2780 Dihedral : 4.840 35.922 2180 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 28.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.01 % Allowed : 29.82 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.40 (0.19), residues: 1936 helix: 0.61 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.72 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 344 HIS 0.008 0.001 HIS A 328 PHE 0.034 0.002 PHE D 555 TYR 0.025 0.002 TYR B 141 ARG 0.005 0.000 ARG G 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 310 time to evaluate : 2.007 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 319 average time/residue: 0.2818 time to fit residues: 133.5773 Evaluate side-chains 315 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 302 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1510 time to fit residues: 6.1495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 30.0000 chunk 126 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 GLN G 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.6674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16324 Z= 0.241 Angle : 0.816 14.089 22012 Z= 0.416 Chirality : 0.044 0.308 2404 Planarity : 0.004 0.031 2780 Dihedral : 4.850 34.233 2180 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 26.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.36 % Allowed : 30.36 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.43 (0.19), residues: 1936 helix: 0.63 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -0.67 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 344 HIS 0.004 0.001 HIS A 328 PHE 0.034 0.002 PHE D 555 TYR 0.022 0.002 TYR F 562 ARG 0.005 0.000 ARG D 581 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 327 time to evaluate : 1.861 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 330 average time/residue: 0.2805 time to fit residues: 136.4293 Evaluate side-chains 303 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 301 time to evaluate : 1.674 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1865 time to fit residues: 3.1903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 HIS ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 HIS ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.126910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.088112 restraints weight = 65241.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.087416 restraints weight = 46347.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.088498 restraints weight = 25798.449| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.6862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16324 Z= 0.241 Angle : 0.824 15.944 22012 Z= 0.419 Chirality : 0.044 0.279 2404 Planarity : 0.004 0.072 2780 Dihedral : 4.841 32.963 2180 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 26.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.77 % Allowed : 30.60 % Favored : 68.63 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.40 (0.19), residues: 1936 helix: 0.60 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -0.60 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP F 344 HIS 0.006 0.001 HIS A 328 PHE 0.032 0.002 PHE D 555 TYR 0.023 0.002 TYR A 141 ARG 0.007 0.000 ARG G 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3395.85 seconds wall clock time: 62 minutes 52.35 seconds (3772.35 seconds total)