Starting phenix.real_space_refine on Sun Mar 17 20:15:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/03_2024/7naf_24271_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/03_2024/7naf_24271.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/03_2024/7naf_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_24271/03_2024/7naf_24271_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/03_2024/7naf_24271_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/03_2024/7naf_24271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/03_2024/7naf_24271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/03_2024/7naf_24271_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7naf_24271/03_2024/7naf_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-dev-5265/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: 9.72, per 1000 atoms: 0.52 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: 8.20 Conformation dependent library (CDL) restraints added in 1.7 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: 8.33 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: 7.90 Time building geometry restraints manager: 8.76 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: 11514 35.25 - 70.50: 920 70.50 - 105.75: 124 105.75 - 141.00: 2 141.00 - 176.25: 9 Dihedral angle restraints: 12569 sinusoidal: 8732 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 12566 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: 4.030 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: 18.250 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 54.260 Find NCS groups from input model: 0.440 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.720 ------------------------------------------------------------------------------- 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 : 21.366 176.246 10069 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 % Allowed : 0.00 % Favored : 100.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP u 51 HIS 0.004 0.001 HIS y 162 PHE 0.009 0.001 PHE b 45 TYR 0.013 0.001 TYR c 27 ARG 0.004 0.000 ARG B 58 *********************** 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 : 1.654 Fit side-chains REVERT: 5 7 ARG cc_start: 0.7051 (mmp-170) cc_final: 0.6603 (mmp80) REVERT: V 109 MET cc_start: 0.7730 (mpp) cc_final: 0.7349 (mpp) REVERT: w 18 TYR cc_start: 0.7822 (m-80) cc_final: 0.7448 (m-80) REVERT: b 38 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7527 (mtmm) REVERT: b 43 ARG cc_start: 0.8061 (mtm180) cc_final: 0.6332 (mtp180) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3619 time to fit residues: 99.8392 Evaluate side-chains 148 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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: 0.0708 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= 0.210 Angle : 0.566 18.250 28555 Z= 0.291 Chirality : 0.035 0.218 3499 Planarity : 0.004 0.128 2222 Dihedral : 22.385 175.868 7250 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.86 % Allowed : 7.20 % Favored : 91.94 % 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: 0.35 (0.24), residues: 1261 helix: 1.62 (0.24), residues: 483 sheet: -0.18 (0.45), residues: 148 loop : -0.77 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP u 51 HIS 0.004 0.001 HIS y 50 PHE 0.016 0.001 PHE 5 88 TYR 0.014 0.001 TYR R 124 ARG 0.005 0.000 ARG B 58 *********************** 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 161 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 1.518 Fit side-chains REVERT: 5 7 ARG cc_start: 0.7014 (mmp-170) cc_final: 0.6775 (mmp80) REVERT: 8 25 LYS cc_start: 0.5329 (ttpt) cc_final: 0.4923 (ttpp) REVERT: b 38 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7703 (mtpp) outliers start: 10 outliers final: 6 residues processed: 156 average time/residue: 0.3428 time to fit residues: 79.4165 Evaluate side-chains 149 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain q residue 288 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 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: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.7845 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 19938 Z= 0.345 Angle : 0.661 16.188 28555 Z= 0.339 Chirality : 0.039 0.245 3499 Planarity : 0.005 0.127 2222 Dihedral : 22.455 175.112 7250 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.72 % Allowed : 10.46 % Favored : 87.82 % 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: -0.05 (0.23), residues: 1261 helix: 1.17 (0.24), residues: 484 sheet: -0.43 (0.43), residues: 152 loop : -0.88 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP u 51 HIS 0.008 0.002 HIS y 50 PHE 0.035 0.002 PHE 5 88 TYR 0.016 0.002 TYR w 17 ARG 0.005 0.001 ARG w 189 *********************** 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 172 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 1.709 Fit side-chains REVERT: 5 7 ARG cc_start: 0.7086 (mmp-170) cc_final: 0.6805 (mmp80) REVERT: 8 25 LYS cc_start: 0.5490 (ttpt) cc_final: 0.5218 (ttpp) REVERT: b 38 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7691 (mtmm) REVERT: d 35 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7676 (mm-30) REVERT: y 197 MET cc_start: 0.8300 (ppp) cc_final: 0.7482 (ptt) outliers start: 20 outliers final: 14 residues processed: 165 average time/residue: 0.3328 time to fit residues: 82.4520 Evaluate side-chains 154 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain d residue 35 GLU Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain q residue 288 THR 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: 6.9990 chunk 16 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 ** 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: 0.7822 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19938 Z= 0.255 Angle : 0.600 16.053 28555 Z= 0.310 Chirality : 0.037 0.241 3499 Planarity : 0.005 0.124 2222 Dihedral : 22.420 176.139 7250 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.23 % Allowed : 12.44 % Favored : 85.33 % 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: 1.24 (0.24), residues: 477 sheet: -0.14 (0.43), residues: 146 loop : -0.98 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP w 287 HIS 0.006 0.001 HIS y 50 PHE 0.012 0.002 PHE V 11 TYR 0.014 0.001 TYR w 17 ARG 0.004 0.000 ARG w 101 *********************** 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 173 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.544 Fit side-chains REVERT: 5 7 ARG cc_start: 0.7064 (mmp-170) cc_final: 0.6857 (mmp80) REVERT: 8 25 LYS cc_start: 0.5434 (ttpt) cc_final: 0.5166 (ttpp) REVERT: V 77 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7714 (mt) REVERT: b 38 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7701 (mtmm) REVERT: B 227 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: y 197 MET cc_start: 0.8240 (ppp) cc_final: 0.7466 (ptt) outliers start: 26 outliers final: 15 residues processed: 167 average time/residue: 0.3299 time to fit residues: 83.2397 Evaluate side-chains 153 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain w residue 74 ILE Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 198 VAL Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain q residue 288 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 109 optimal weight: 0.0010 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 142 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0390 ------------------------------------------------------------------------------- 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: 0.7788 moved from start: 0.1321 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= 0.175 Angle : 0.556 16.036 28555 Z= 0.288 Chirality : 0.034 0.232 3499 Planarity : 0.004 0.122 2222 Dihedral : 22.337 176.652 7250 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.06 % Allowed : 14.07 % Favored : 83.88 % 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: 0.13 (0.24), residues: 1261 helix: 1.36 (0.24), residues: 482 sheet: 0.06 (0.44), residues: 143 loop : -0.91 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP w 287 HIS 0.004 0.001 HIS y 50 PHE 0.010 0.001 PHE w 133 TYR 0.013 0.001 TYR w 17 ARG 0.003 0.000 ARG w 101 *********************** 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 170 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 1.565 Fit side-chains REVERT: 5 7 ARG cc_start: 0.7066 (mmp-170) cc_final: 0.6803 (mmp80) REVERT: 8 25 LYS cc_start: 0.5382 (ttpt) cc_final: 0.5114 (ttpp) REVERT: V 77 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7698 (mt) REVERT: w 18 TYR cc_start: 0.7846 (m-80) cc_final: 0.7442 (m-80) REVERT: b 38 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7639 (mtmm) REVERT: B 227 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7210 (mt-10) REVERT: y 197 MET cc_start: 0.8201 (ppp) cc_final: 0.7621 (ptm) outliers start: 24 outliers final: 20 residues processed: 164 average time/residue: 0.3263 time to fit residues: 80.8510 Evaluate side-chains 162 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 41 THR Chi-restraints excluded: chain 5 residue 217 THR Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 52 THR Chi-restraints excluded: chain w residue 74 ILE Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 198 VAL Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain q residue 288 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 83 optimal weight: 0.0770 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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 ** 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: 0.7775 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19938 Z= 0.166 Angle : 0.547 15.979 28555 Z= 0.284 Chirality : 0.034 0.225 3499 Planarity : 0.004 0.121 2222 Dihedral : 22.279 176.776 7250 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.23 % Allowed : 14.58 % Favored : 83.19 % 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: 0.21 (0.24), residues: 1261 helix: 1.45 (0.24), residues: 481 sheet: 0.11 (0.45), residues: 137 loop : -0.87 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP w 287 HIS 0.004 0.001 HIS y 50 PHE 0.017 0.001 PHE 5 88 TYR 0.012 0.001 TYR w 17 ARG 0.003 0.000 ARG y 188 *********************** 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 174 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 1.410 Fit side-chains REVERT: 5 7 ARG cc_start: 0.7053 (mmp-170) cc_final: 0.6793 (mmp80) REVERT: 8 25 LYS cc_start: 0.5345 (ttpt) cc_final: 0.5081 (ttpp) REVERT: V 77 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7673 (mt) REVERT: b 38 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7655 (mtmm) REVERT: B 227 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7196 (mt-10) REVERT: y 197 MET cc_start: 0.8333 (ppp) cc_final: 0.7476 (ptt) outliers start: 26 outliers final: 24 residues processed: 167 average time/residue: 0.3304 time to fit residues: 82.5289 Evaluate side-chains 162 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 41 THR Chi-restraints excluded: chain 5 residue 217 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 52 THR Chi-restraints excluded: chain w residue 74 ILE Chi-restraints excluded: chain w residue 169 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 198 VAL Chi-restraints excluded: chain w residue 212 LEU Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain q residue 288 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 115 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ** 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: 0.7775 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19938 Z= 0.168 Angle : 0.545 15.973 28555 Z= 0.284 Chirality : 0.034 0.223 3499 Planarity : 0.004 0.121 2222 Dihedral : 22.239 176.694 7250 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.40 % Allowed : 15.27 % Favored : 82.33 % 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: 0.19 (0.24), residues: 1261 helix: 1.42 (0.24), residues: 481 sheet: 0.11 (0.45), residues: 137 loop : -0.87 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP w 287 HIS 0.004 0.001 HIS y 50 PHE 0.016 0.001 PHE 5 88 TYR 0.012 0.001 TYR w 17 ARG 0.002 0.000 ARG w 101 *********************** 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 173 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.662 Fit side-chains REVERT: 5 7 ARG cc_start: 0.7064 (mmp-170) cc_final: 0.6786 (mmp80) REVERT: 8 25 LYS cc_start: 0.5343 (ttpt) cc_final: 0.5084 (ttpp) REVERT: V 77 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7686 (mt) REVERT: b 38 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7649 (mtmm) REVERT: R 106 LEU cc_start: 0.8281 (mp) cc_final: 0.8032 (mp) REVERT: y 13 ILE cc_start: 0.8836 (mm) cc_final: 0.8617 (mm) REVERT: y 197 MET cc_start: 0.8326 (ppp) cc_final: 0.7449 (ptt) outliers start: 28 outliers final: 24 residues processed: 168 average time/residue: 0.3256 time to fit residues: 82.9306 Evaluate side-chains 163 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 41 THR Chi-restraints excluded: chain 5 residue 217 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 52 THR Chi-restraints excluded: chain w residue 74 ILE Chi-restraints excluded: chain w residue 169 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 198 VAL Chi-restraints excluded: chain w residue 199 CYS Chi-restraints excluded: chain w residue 212 LEU Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain y residue 141 THR Chi-restraints excluded: chain q residue 288 THR 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: 1.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 19938 Z= 0.425 Angle : 0.729 15.896 28555 Z= 0.371 Chirality : 0.042 0.262 3499 Planarity : 0.006 0.128 2222 Dihedral : 22.501 175.536 7250 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.83 % Allowed : 16.04 % Favored : 81.13 % 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: -0.37 (0.23), residues: 1261 helix: 0.83 (0.24), residues: 480 sheet: -0.38 (0.43), residues: 134 loop : -1.04 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP u 51 HIS 0.011 0.002 HIS y 50 PHE 0.019 0.002 PHE V 11 TYR 0.017 0.002 TYR b 46 ARG 0.005 0.001 ARG w 189 *********************** 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 180 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 1.388 Fit side-chains REVERT: 8 25 LYS cc_start: 0.5825 (ttpt) cc_final: 0.5578 (ttpp) REVERT: V 77 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7738 (mt) REVERT: w 18 TYR cc_start: 0.7902 (m-80) cc_final: 0.7455 (m-80) REVERT: w 216 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8037 (mtpp) REVERT: b 38 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7793 (mtmm) REVERT: R 106 LEU cc_start: 0.8384 (mp) cc_final: 0.8022 (mp) REVERT: y 197 MET cc_start: 0.8295 (ppp) cc_final: 0.7665 (ptt) outliers start: 33 outliers final: 27 residues processed: 175 average time/residue: 0.3238 time to fit residues: 85.2719 Evaluate side-chains 170 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 41 THR Chi-restraints excluded: chain 5 residue 217 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 52 THR Chi-restraints excluded: chain w residue 74 ILE Chi-restraints excluded: chain w residue 169 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 198 VAL Chi-restraints excluded: chain w residue 199 CYS Chi-restraints excluded: chain w residue 212 LEU Chi-restraints excluded: chain w residue 216 LYS Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain y residue 81 LEU Chi-restraints excluded: chain q residue 288 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 0.5980 chunk 151 optimal weight: 0.8980 chunk 138 optimal weight: 0.1980 chunk 147 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 84 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19938 Z= 0.139 Angle : 0.559 16.135 28555 Z= 0.290 Chirality : 0.034 0.229 3499 Planarity : 0.004 0.120 2222 Dihedral : 22.274 177.713 7250 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.89 % Allowed : 17.50 % Favored : 80.62 % 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: 0.05 (0.24), residues: 1261 helix: 1.28 (0.24), residues: 481 sheet: 0.08 (0.45), residues: 137 loop : -0.95 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 358 HIS 0.004 0.001 HIS y 50 PHE 0.016 0.001 PHE 5 88 TYR 0.012 0.001 TYR w 17 ARG 0.003 0.000 ARG y 188 *********************** 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 169 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.560 Fit side-chains revert: symmetry clash REVERT: 8 25 LYS cc_start: 0.5505 (ttpt) cc_final: 0.5213 (ttpp) REVERT: V 77 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7633 (mt) REVERT: u 1 MET cc_start: 0.8441 (tpt) cc_final: 0.7887 (tpt) REVERT: w 18 TYR cc_start: 0.7828 (m-80) cc_final: 0.7443 (m-80) REVERT: b 38 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7717 (mtmm) REVERT: U 86 LYS cc_start: 0.8440 (tptp) cc_final: 0.7901 (tppt) REVERT: R 106 LEU cc_start: 0.8262 (mp) cc_final: 0.8011 (mp) REVERT: B 227 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7160 (mt-10) REVERT: y 13 ILE cc_start: 0.8840 (mm) cc_final: 0.8608 (mm) REVERT: y 197 MET cc_start: 0.8221 (ppp) cc_final: 0.7350 (ptt) REVERT: q 314 VAL cc_start: 0.8137 (m) cc_final: 0.7930 (m) outliers start: 22 outliers final: 16 residues processed: 166 average time/residue: 0.3367 time to fit residues: 84.2722 Evaluate side-chains 159 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 41 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 52 THR Chi-restraints excluded: chain w residue 74 ILE Chi-restraints excluded: chain w residue 169 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 199 CYS Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 337 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.6980 chunk 155 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 84 GLN ** w 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19938 Z= 0.145 Angle : 0.546 15.936 28555 Z= 0.283 Chirality : 0.033 0.222 3499 Planarity : 0.004 0.120 2222 Dihedral : 22.203 176.774 7250 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.46 % Allowed : 17.92 % Favored : 80.62 % 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: 0.21 (0.24), residues: 1261 helix: 1.42 (0.25), residues: 480 sheet: 0.35 (0.45), residues: 133 loop : -0.91 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP w 287 HIS 0.004 0.001 HIS y 50 PHE 0.012 0.001 PHE 5 88 TYR 0.012 0.001 TYR w 17 ARG 0.002 0.000 ARG B 275 ********************** 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 157 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: 5 84 GLN cc_start: 0.7784 (pt0) cc_final: 0.7479 (pt0) REVERT: 8 25 LYS cc_start: 0.5550 (ttpt) cc_final: 0.5263 (ttpp) REVERT: V 77 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7672 (mt) REVERT: w 18 TYR cc_start: 0.7815 (m-80) cc_final: 0.7410 (m-80) REVERT: b 38 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7581 (mtmm) REVERT: R 106 LEU cc_start: 0.8218 (mp) cc_final: 0.7989 (mp) REVERT: B 227 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7189 (mt-10) REVERT: y 13 ILE cc_start: 0.8804 (mm) cc_final: 0.8581 (mm) REVERT: y 197 MET cc_start: 0.8273 (ppp) cc_final: 0.7437 (ptt) REVERT: q 314 VAL cc_start: 0.8165 (m) cc_final: 0.7955 (m) outliers start: 17 outliers final: 16 residues processed: 155 average time/residue: 0.3473 time to fit residues: 80.4949 Evaluate side-chains 154 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 41 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 52 THR Chi-restraints excluded: chain w residue 74 ILE Chi-restraints excluded: chain w residue 169 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 199 CYS Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 337 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 54 optimal weight: 0.0070 chunk 133 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.2802 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.120716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.099390 restraints weight = 34193.612| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.07 r_work: 0.3255 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19938 Z= 0.206 Angle : 0.571 15.942 28555 Z= 0.296 Chirality : 0.035 0.229 3499 Planarity : 0.004 0.122 2222 Dihedral : 22.218 176.213 7250 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.63 % Allowed : 17.75 % Favored : 80.62 % 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: 1.31 (0.25), residues: 481 sheet: 0.05 (0.45), residues: 137 loop : -0.89 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP u 51 HIS 0.006 0.001 HIS y 50 PHE 0.031 0.001 PHE 5 88 TYR 0.013 0.001 TYR w 17 ARG 0.003 0.000 ARG w 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3364.03 seconds wall clock time: 62 minutes 28.73 seconds (3748.73 seconds total)