Starting phenix.real_space_refine (version: 1.21rc1) on Tue Aug 15 17:14:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/08_2023/7naf_24271_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/08_2023/7naf_24271.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/08_2023/7naf_24271_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/08_2023/7naf_24271_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/08_2023/7naf_24271_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/08_2023/7naf_24271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/08_2023/7naf_24271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/08_2023/7naf_24271_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/08_2023/7naf_24271_updated.pdb" } resolution = 3.13 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: 5 Type Number sf(0) Gaussians P 378 5.49 5 S 52 5.16 5 C 10433 2.51 5 N 3452 2.21 5 O 4553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 97": "OD1" <-> "OD2" Residue "u PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 98": "OE1" <-> "OE2" Residue "w TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "c TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 76": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 124": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 18868 Number of models: 1 Model: "" Number of chains: 17 Chain: "1" Number of atoms: 8046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 8046 Classifications: {'RNA': 378} Modifications used: {'rna2p': 1, 'rna2p_pur': 36, 'rna2p_pyr': 26, 'rna3p': 2, 'rna3p_pur': 154, 'rna3p_pyr': 158} Link IDs: {'rna2p': 63, 'rna3p': 314} Chain breaks: 23 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 1 Chain: "5" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 918 Classifications: {'peptide': 105} Link IDs: {'TRANS': 104} Chain breaks: 2 Chain: "8" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 332 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "V" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "u" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 543 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "w" Number of atoms: 2959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2959 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 346} Chain breaks: 1 Chain: "b" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 613 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain breaks: 2 Chain: "d" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 369 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain breaks: 1 Chain: "U" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 165 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "R" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 529 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain breaks: 2 Chain: "c" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 310 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 2 Chain: "B" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1493 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 6 Chain: "z" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "s" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 66 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "y" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1250 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 8 Chain: "q" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 3, 'TRANS': 24} Chain breaks: 1 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Classifications: {'peptide': 1, 'water': 2} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N SER w 29 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER w 29 " occ=0.50 residue: pdb=" N LEU w 138 " occ=0.50 ... (6 atoms not shown) pdb=" CD2 LEU w 138 " occ=0.50 Time building chain proxies: 9.41, per 1000 atoms: 0.50 Number of scatterers: 18868 At special positions: 0 Unit cell: (142.56, 153.36, 168.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 378 15.00 O 4553 8.00 N 3452 7.00 C 10433 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: 9.45 Conformation dependent library (CDL) restraints added in 1.6 seconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2500 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 14 sheets defined 33.5% alpha, 10.1% beta 80 base pairs and 163 stacking pairs defined. Time for finding SS restraints: 9.06 Creating SS restraints... Processing helix chain '5' and resid 33 through 41 Processing helix chain '5' and resid 45 through 93 removed outlier: 3.891A pdb=" N ASN 5 93 " --> pdb=" O LYS 5 89 " (cutoff:3.500A) Processing helix chain '5' and resid 218 through 230 Processing helix chain '8' and resid 6 through 14 removed outlier: 3.511A pdb=" N SER 8 13 " --> pdb=" O LYS 8 9 " (cutoff:3.500A) Processing helix chain '8' and resid 16 through 33 Processing helix chain 'V' and resid 122 through 125 No H-bonds generated for 'chain 'V' and resid 122 through 125' Processing helix chain 'V' and resid 127 through 132 Processing helix chain 'u' and resid 34 through 41 Processing helix chain 'u' and resid 53 through 57 Processing helix chain 'w' and resid 6 through 8 No H-bonds generated for 'chain 'w' and resid 6 through 8' Processing helix chain 'w' and resid 15 through 23 Processing helix chain 'w' and resid 28 through 39 removed outlier: 3.857A pdb=" N ILE w 33 " --> pdb=" O SER w 30 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE w 36 " --> pdb=" O ILE w 33 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN w 37 " --> pdb=" O ILE w 34 " (cutoff:3.500A) Processing helix chain 'w' and resid 59 through 67 Processing helix chain 'w' and resid 98 through 107 Processing helix chain 'w' and resid 129 through 147 removed outlier: 4.085A pdb=" N PHE w 133 " --> pdb=" O VAL w 129 " (cutoff:3.500A) Processing helix chain 'w' and resid 167 through 174 Processing helix chain 'w' and resid 210 through 213 Processing helix chain 'w' and resid 215 through 218 No H-bonds generated for 'chain 'w' and resid 215 through 218' Processing helix chain 'w' and resid 230 through 233 No H-bonds generated for 'chain 'w' and resid 230 through 233' Processing helix chain 'w' and resid 259 through 264 Processing helix chain 'w' and resid 268 through 272 Processing helix chain 'w' and resid 285 through 291 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 312 through 328 removed outlier: 3.689A pdb=" N MET w 317 " --> pdb=" O LYS w 313 " (cutoff:3.500A) Processing helix chain 'w' and resid 359 through 386 removed outlier: 3.663A pdb=" N GLN w 386 " --> pdb=" O LEU w 382 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 27 Processing helix chain 'b' and resid 39 through 55 Processing helix chain 'b' and resid 497 through 510 Processing helix chain 'd' and resid 16 through 19 No H-bonds generated for 'chain 'd' and resid 16 through 19' Processing helix chain 'd' and resid 25 through 35 removed outlier: 5.554A pdb=" N ALA d 29 " --> pdb=" O LYS d 26 " (cutoff:3.500A) Proline residue: d 30 - end of helix Processing helix chain 'd' and resid 55 through 60 Processing helix chain 'U' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 109 Processing helix chain 'R' and resid 117 through 128 removed outlier: 3.651A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 144 Processing helix chain 'c' and resid 50 through 53 No H-bonds generated for 'chain 'c' and resid 50 through 53' Processing helix chain 'c' and resid 74 through 81 Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 348 through 351 Processing helix chain 'B' and resid 373 through 380 Processing helix chain 'y' and resid 13 through 16 No H-bonds generated for 'chain 'y' and resid 13 through 16' Processing helix chain 'y' and resid 33 through 37 Processing helix chain 'y' and resid 78 through 83 Processing helix chain 'y' and resid 104 through 107 No H-bonds generated for 'chain 'y' and resid 104 through 107' Processing helix chain 'y' and resid 123 through 126 No H-bonds generated for 'chain 'y' and resid 123 through 126' Processing helix chain 'y' and resid 148 through 151 No H-bonds generated for 'chain 'y' and resid 148 through 151' Processing helix chain 'y' and resid 212 through 217 Processing helix chain 'q' and resid 286 through 292 Processing sheet with id= A, first strand: chain 'V' and resid 22 through 24 removed outlier: 6.644A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'V' and resid 85 through 87 Processing sheet with id= C, first strand: chain 'u' and resid 20 through 22 Processing sheet with id= D, first strand: chain 'w' and resid 89 through 92 removed outlier: 6.680A pdb=" N THR w 115 " --> pdb=" O ILE w 51 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU w 53 " --> pdb=" O THR w 115 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU w 117 " --> pdb=" O LEU w 53 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR w 155 " --> pdb=" O VAL w 116 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N HIS w 118 " --> pdb=" O THR w 155 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL w 157 " --> pdb=" O HIS w 118 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'w' and resid 256 through 258 removed outlier: 6.517A pdb=" N LYS w 277 " --> pdb=" O THR w 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 321 through 325 removed outlier: 5.403A pdb=" N ASP B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS B 50 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR B 55 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 213 through 215 removed outlier: 4.194A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 337 through 339 Processing sheet with id= I, first strand: chain 'B' and resid 225 through 227 removed outlier: 3.586A pdb=" N GLY B 225 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'y' and resid 2 through 4 removed outlier: 6.106A pdb=" N ALA y 204 " --> pdb=" O THR y 3 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'y' and resid 25 through 27 removed outlier: 5.569A pdb=" N VAL y 49 " --> pdb=" O VAL y 26 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'y' and resid 71 through 73 removed outlier: 5.877A pdb=" N GLN y 95 " --> pdb=" O VAL y 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'y' and resid 108 through 110 removed outlier: 6.304A pdb=" N GLU y 136 " --> pdb=" O ALA y 115 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL y 117 " --> pdb=" O GLU y 136 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE y 138 " --> pdb=" O VAL y 117 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'q' and resid 294 through 297 removed outlier: 3.591A pdb=" N ASP q 311 " --> pdb=" O ASN q 295 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLN q 297 " --> pdb=" O ILE q 309 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE q 309 " --> pdb=" O GLN q 297 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 200 hydrogen bonds 330 hydrogen bond angles 0 basepair planarities 80 basepair parallelities 163 stacking parallelities Total time for adding SS restraints: 8.36 Time building geometry restraints manager: 9.81 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: 3874 1.33 - 1.46: 6755 1.46 - 1.58: 8491 1.58 - 1.70: 731 1.70 - 1.83: 87 Bond restraints: 19938 Sorted by residual: bond pdb=" C2' A2M 12946 " pdb=" C1' A2M 12946 " ideal model delta sigma weight residual 1.305 1.555 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" O4' A2M 12946 " pdb=" C1' A2M 12946 " ideal model delta sigma weight residual 1.615 1.412 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" P A2M 12946 " pdb=" O5' A2M 12946 " ideal model delta sigma weight residual 1.647 1.828 -0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" C5 OMU 12921 " pdb=" C6 OMU 12921 " ideal model delta sigma weight residual 1.480 1.355 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C4' A2M 12946 " pdb=" O4' A2M 12946 " ideal model delta sigma weight residual 1.305 1.429 -0.124 2.00e-02 2.50e+03 3.85e+01 ... (remaining 19933 not shown) Histogram of bond angle deviations from ideal: 90.60 - 99.28: 3 99.28 - 107.96: 3406 107.96 - 116.64: 13024 116.64 - 125.32: 10660 125.32 - 134.00: 1462 Bond angle restraints: 28555 Sorted by residual: angle pdb=" C1' A2M 12946 " pdb=" N9 A2M 12946 " pdb=" C8 A2M 12946 " ideal model delta sigma weight residual 88.50 128.04 -39.54 3.00e+00 1.11e-01 1.74e+02 angle pdb=" N6 A2M 12946 " pdb=" C6 A2M 12946 " pdb=" N1 A2M 12946 " ideal model delta sigma weight residual 92.14 118.65 -26.51 3.00e+00 1.11e-01 7.81e+01 angle pdb=" C1' OMG 12922 " pdb=" N9 OMG 12922 " pdb=" C4 OMG 12922 " ideal model delta sigma weight residual 108.29 126.65 -18.36 3.00e+00 1.11e-01 3.75e+01 angle pdb=" C1' OMG 12922 " pdb=" N9 OMG 12922 " pdb=" C8 OMG 12922 " ideal model delta sigma weight residual 142.82 126.64 16.18 3.00e+00 1.11e-01 2.91e+01 angle pdb=" N1 A2M 12946 " pdb=" C2 A2M 12946 " pdb=" N3 A2M 12946 " ideal model delta sigma weight residual 120.08 131.42 -11.34 3.00e+00 1.11e-01 1.43e+01 ... (remaining 28550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 10875 35.25 - 70.50: 299 70.50 - 105.75: 42 105.75 - 141.00: 2 141.00 - 176.25: 7 Dihedral angle restraints: 11225 sinusoidal: 7388 harmonic: 3837 Sorted by residual: dihedral pdb=" O4' U 13019 " pdb=" C1' U 13019 " pdb=" N1 U 13019 " pdb=" C2 U 13019 " ideal model delta sinusoidal sigma weight residual 200.00 29.91 170.09 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U 12829 " pdb=" C1' U 12829 " pdb=" N1 U 12829 " pdb=" C2 U 12829 " ideal model delta sinusoidal sigma weight residual 200.00 53.89 146.11 1 1.50e+01 4.44e-03 7.81e+01 dihedral pdb=" O4' C 12825 " pdb=" C1' C 12825 " pdb=" N1 C 12825 " pdb=" C2 C 12825 " ideal model delta sinusoidal sigma weight residual 232.00 55.94 176.06 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 11222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3254 0.061 - 0.123: 224 0.123 - 0.184: 15 0.184 - 0.245: 5 0.245 - 0.307: 1 Chirality restraints: 3499 Sorted by residual: chirality pdb=" C2' A2M 12946 " pdb=" C3' A2M 12946 " pdb=" O2' A2M 12946 " pdb=" C1' A2M 12946 " both_signs ideal model delta sigma weight residual False -2.39 -2.70 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C1' A2M 12946 " pdb=" O4' A2M 12946 " pdb=" C2' A2M 12946 " pdb=" N9 A2M 12946 " both_signs ideal model delta sigma weight residual False 2.40 2.62 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C4' A2M 12946 " pdb=" C5' A2M 12946 " pdb=" O4' A2M 12946 " pdb=" C3' A2M 12946 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 3496 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12922 " -0.032 2.00e-02 2.50e+03 4.89e-01 5.37e+03 pdb=" C4' OMG 12922 " -0.401 2.00e-02 2.50e+03 pdb=" O4' OMG 12922 " -0.438 2.00e-02 2.50e+03 pdb=" C3' OMG 12922 " 0.577 2.00e-02 2.50e+03 pdb=" O3' OMG 12922 " 0.446 2.00e-02 2.50e+03 pdb=" C2' OMG 12922 " 0.248 2.00e-02 2.50e+03 pdb=" O2' OMG 12922 " -0.824 2.00e-02 2.50e+03 pdb=" C1' OMG 12922 " -0.252 2.00e-02 2.50e+03 pdb=" N9 OMG 12922 " 0.677 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 11857 " 0.024 2.00e-02 2.50e+03 1.32e-02 3.90e+00 pdb=" N1 C 11857 " -0.031 2.00e-02 2.50e+03 pdb=" C2 C 11857 " 0.000 2.00e-02 2.50e+03 pdb=" O2 C 11857 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C 11857 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C 11857 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C 11857 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C 11857 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C 11857 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11303 " -0.026 2.00e-02 2.50e+03 1.16e-02 3.70e+00 pdb=" N9 A 11303 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A 11303 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 11303 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 11303 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 11303 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A 11303 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A 11303 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A 11303 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 11303 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A 11303 " 0.003 2.00e-02 2.50e+03 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1290 2.72 - 3.26: 17270 3.26 - 3.81: 33304 3.81 - 4.35: 42130 4.35 - 4.90: 62399 Nonbonded interactions: 156393 Sorted by model distance: nonbonded pdb=" O2' G 11789 " pdb=" O5' G 11790 " model vdw 2.172 2.440 nonbonded pdb=" O2' C 12343 " pdb=" OP1 U 13056 " model vdw 2.192 2.440 nonbonded pdb=" O2' G 11899 " pdb=" O4 U 12334 " model vdw 2.215 2.440 nonbonded pdb=" O2 C 13060 " pdb=" O2' U 13332 " model vdw 2.221 2.440 nonbonded pdb=" OG1 THR B 54 " pdb=" O ASP B 360 " model vdw 2.226 2.440 ... (remaining 156388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 3.520 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: 18.160 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 58.540 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.005 0.250 19938 Z= 0.273 Angle : 0.622 39.539 28555 Z= 0.279 Chirality : 0.034 0.307 3499 Planarity : 0.011 0.489 2222 Dihedral : 15.397 176.246 8725 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.43 (0.24), residues: 1261 helix: 1.71 (0.24), residues: 479 sheet: -0.01 (0.45), residues: 146 loop : -0.76 (0.24), residues: 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.802 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3691 time to fit residues: 102.0966 Evaluate side-chains 149 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.804 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 224 ASN ** w 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** q 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 19938 Z= 0.212 Angle : 0.567 16.488 28555 Z= 0.293 Chirality : 0.035 0.219 3499 Planarity : 0.004 0.120 2222 Dihedral : 14.440 175.567 5906 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.33 (0.24), residues: 1261 helix: 1.60 (0.24), residues: 483 sheet: -0.18 (0.45), residues: 148 loop : -0.77 (0.24), residues: 630 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 1.645 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 159 average time/residue: 0.3440 time to fit residues: 81.3039 Evaluate side-chains 153 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 1.625 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1611 time to fit residues: 4.1733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** q 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 19938 Z= 0.318 Angle : 0.636 16.266 28555 Z= 0.327 Chirality : 0.039 0.238 3499 Planarity : 0.005 0.128 2222 Dihedral : 14.677 174.983 5906 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.04 (0.23), residues: 1261 helix: 1.26 (0.24), residues: 483 sheet: -0.21 (0.43), residues: 150 loop : -0.89 (0.24), residues: 628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.763 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 159 average time/residue: 0.3529 time to fit residues: 83.3926 Evaluate side-chains 143 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1767 time to fit residues: 3.5524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 16 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 100 optimal weight: 0.1980 chunk 149 optimal weight: 0.4980 chunk 158 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** w 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** q 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 19938 Z= 0.131 Angle : 0.536 16.104 28555 Z= 0.279 Chirality : 0.033 0.220 3499 Planarity : 0.004 0.121 2222 Dihedral : 14.435 176.897 5906 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.23 (0.24), residues: 1261 helix: 1.47 (0.24), residues: 482 sheet: 0.09 (0.45), residues: 137 loop : -0.86 (0.24), residues: 642 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 1.601 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 165 average time/residue: 0.3635 time to fit residues: 89.4917 Evaluate side-chains 149 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 1.757 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1784 time to fit residues: 3.4830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** w 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 19938 Z= 0.202 Angle : 0.565 15.931 28555 Z= 0.291 Chirality : 0.035 0.226 3499 Planarity : 0.004 0.122 2222 Dihedral : 14.464 175.725 5906 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.17 (0.24), residues: 1261 helix: 1.48 (0.24), residues: 481 sheet: -0.24 (0.44), residues: 150 loop : -0.87 (0.24), residues: 630 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 1.613 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 157 average time/residue: 0.3576 time to fit residues: 83.8016 Evaluate side-chains 150 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.649 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1728 time to fit residues: 3.9268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: w 235 ASN ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 19938 Z= 0.292 Angle : 0.621 15.889 28555 Z= 0.319 Chirality : 0.038 0.240 3499 Planarity : 0.005 0.125 2222 Dihedral : 14.655 175.317 5906 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.01 (0.24), residues: 1261 helix: 1.20 (0.24), residues: 485 sheet: -0.27 (0.44), residues: 147 loop : -0.89 (0.24), residues: 629 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.688 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 160 average time/residue: 0.3397 time to fit residues: 81.1435 Evaluate side-chains 149 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 1.718 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1717 time to fit residues: 4.5904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 19938 Z= 0.194 Angle : 0.570 16.022 28555 Z= 0.295 Chirality : 0.035 0.232 3499 Planarity : 0.004 0.122 2222 Dihedral : 14.537 176.379 5906 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.10 (0.24), residues: 1261 helix: 1.30 (0.24), residues: 482 sheet: 0.06 (0.44), residues: 143 loop : -0.90 (0.24), residues: 636 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 1.570 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 153 average time/residue: 0.3528 time to fit residues: 80.4348 Evaluate side-chains 146 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.645 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1802 time to fit residues: 3.3445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** q 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 19938 Z= 0.337 Angle : 0.656 15.880 28555 Z= 0.337 Chirality : 0.039 0.249 3499 Planarity : 0.005 0.126 2222 Dihedral : 14.768 174.917 5906 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.20 (0.23), residues: 1261 helix: 0.98 (0.24), residues: 483 sheet: -0.20 (0.43), residues: 146 loop : -0.98 (0.24), residues: 632 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 1.818 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 150 average time/residue: 0.3548 time to fit residues: 79.4164 Evaluate side-chains 143 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.654 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1840 time to fit residues: 3.0131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 139 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 84 GLN ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** q 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 19938 Z= 0.161 Angle : 0.561 16.068 28555 Z= 0.290 Chirality : 0.034 0.230 3499 Planarity : 0.004 0.121 2222 Dihedral : 14.499 176.944 5906 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.03 (0.24), residues: 1261 helix: 1.26 (0.24), residues: 481 sheet: -0.01 (0.45), residues: 137 loop : -0.93 (0.24), residues: 643 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.642 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 154 average time/residue: 0.3577 time to fit residues: 81.4658 Evaluate side-chains 149 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2604 time to fit residues: 3.6497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 163 optimal weight: 0.0770 chunk 150 optimal weight: 0.0000 chunk 130 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 overall best weight: 0.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 84 GLN ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN q 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 19938 Z= 0.127 Angle : 0.535 15.929 28555 Z= 0.277 Chirality : 0.033 0.213 3499 Planarity : 0.004 0.119 2222 Dihedral : 14.289 177.531 5906 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.26 (0.24), residues: 1261 helix: 1.42 (0.25), residues: 480 sheet: 0.37 (0.46), residues: 135 loop : -0.85 (0.24), residues: 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.720 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.3540 time to fit residues: 78.5143 Evaluate side-chains 138 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.726 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 0.0570 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.118950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097952 restraints weight = 34414.615| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.11 r_work: 0.3224 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 19938 Z= 0.326 Angle : 0.650 15.776 28555 Z= 0.332 Chirality : 0.038 0.245 3499 Planarity : 0.005 0.125 2222 Dihedral : 14.600 175.329 5906 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.06 (0.24), residues: 1261 helix: 1.11 (0.24), residues: 480 sheet: -0.04 (0.44), residues: 146 loop : -0.93 (0.24), residues: 635 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3296.03 seconds wall clock time: 61 minutes 35.19 seconds (3695.19 seconds total)