Starting phenix.real_space_refine on Tue Mar 19 23:43:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvq_16268/03_2024/8bvq_16268_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvq_16268/03_2024/8bvq_16268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvq_16268/03_2024/8bvq_16268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvq_16268/03_2024/8bvq_16268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvq_16268/03_2024/8bvq_16268_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvq_16268/03_2024/8bvq_16268_trim_updated.pdb" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2650 atoms to isotropic. 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 S 32 5.16 5 C 7486 2.51 5 N 2029 2.21 5 O 2328 1.98 5 H 11250 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A PHE 738": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 219": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23125 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 12092 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 29, 'TRANS': 755} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 5337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 5337 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain: "C" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 793 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "D" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3478 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 12, 'TRANS': 206} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1294 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 131 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'NH2NOTPRO': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'UX8:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 10.17, per 1000 atoms: 0.44 Number of scatterers: 23125 At special positions: 0 Unit cell: (122.84, 106.24, 134.46, 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 32 16.00 O 2328 8.00 N 2029 7.00 C 7486 6.00 H 11250 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.58 Conformation dependent library (CDL) restraints added in 2.6 seconds 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2774 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 16 sheets defined 19.4% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.80 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 107 through 116 Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.828A pdb=" N ARG A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 379 through 392 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'C' and resid 34 through 37 Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 48 through 61 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 98 Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 138 through 153 Processing helix chain 'D' and resid 160 through 188 Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 210 through 224 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 229 through 240 Processing helix chain 'E' and resid 42 through 45 No H-bonds generated for 'chain 'E' and resid 42 through 45' Processing helix chain 'E' and resid 52 through 58 Processing sheet with id= A, first strand: chain 'A' and resid 150 through 158 removed outlier: 6.264A pdb=" N THR A 93 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU A 165 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ALA A 95 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 12.227A pdb=" N LEU A 167 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N ILE A 97 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 11.887A pdb=" N PHE A 169 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 180 through 183 removed outlier: 8.413A pdb=" N ASN A 181 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 256 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL A 183 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 258 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 321 through 329 removed outlier: 6.265A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.441A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.579A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 352 through 355 removed outlier: 8.467A pdb=" N ARG A 353 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 414 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLU A 355 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR A 416 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 425 through 433 removed outlier: 3.580A pdb=" N ILE A 519 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR A 617 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 618 through 620 Processing sheet with id= G, first strand: chain 'A' and resid 72 through 80 removed outlier: 6.663A pdb=" N LYS A 89 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL A 75 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLN A 87 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL A 77 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 85 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ARG A 79 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.026A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 122 through 124 Processing sheet with id= J, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.367A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 201 through 203 Processing sheet with id= L, first strand: chain 'B' and resid 252 through 254 Processing sheet with id= M, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.657A pdb=" N ALA B 307 " --> pdb=" O TRP B 317 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 331 through 333 removed outlier: 5.396A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 372 through 374 removed outlier: 4.108A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 72 through 74 removed outlier: 3.644A pdb=" N THR E 94 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.31 Time building geometry restraints manager: 19.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11250 1.02 - 1.22: 0 1.22 - 1.42: 5148 1.42 - 1.61: 6924 1.61 - 1.81: 64 Bond restraints: 23386 Sorted by residual: bond pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " ideal model delta sigma weight residual 1.525 1.334 0.191 2.10e-02 2.27e+03 8.24e+01 bond pdb=" CA UX8 G 3 " pdb=" CB UX8 G 3 " ideal model delta sigma weight residual 1.530 1.711 -0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" CB UX8 G 3 " pdb=" CG UX8 G 3 " ideal model delta sigma weight residual 1.493 1.648 -0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" CG UX8 G 3 " pdb=" CD2 UX8 G 3 " ideal model delta sigma weight residual 1.433 1.577 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" N UX8 G 3 " pdb=" CA UX8 G 3 " ideal model delta sigma weight residual 1.458 1.339 0.119 1.90e-02 2.77e+03 3.93e+01 ... (remaining 23381 not shown) Histogram of bond angle deviations from ideal: 69.26 - 84.09: 3 84.09 - 98.93: 0 98.93 - 113.76: 27420 113.76 - 128.60: 14476 128.60 - 143.43: 76 Bond angle restraints: 41975 Sorted by residual: angle pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " pdb=" O UX8 G 3 " ideal model delta sigma weight residual 120.80 143.43 -22.63 1.70e+00 3.46e-01 1.77e+02 angle pdb=" C PRO A 684 " pdb=" CA PRO A 684 " pdb=" HA PRO A 684 " ideal model delta sigma weight residual 109.00 69.26 39.74 3.00e+00 1.11e-01 1.75e+02 angle pdb=" N PRO A 684 " pdb=" CA PRO A 684 " pdb=" HA PRO A 684 " ideal model delta sigma weight residual 110.00 74.86 35.14 3.00e+00 1.11e-01 1.37e+02 angle pdb=" CB PRO A 684 " pdb=" CA PRO A 684 " pdb=" HA PRO A 684 " ideal model delta sigma weight residual 109.00 76.06 32.94 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " pdb=" N THR G 4 " ideal model delta sigma weight residual 116.20 103.08 13.12 2.00e+00 2.50e-01 4.30e+01 ... (remaining 41970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 9775 17.75 - 35.50: 964 35.50 - 53.25: 289 53.25 - 71.00: 78 71.00 - 88.74: 11 Dihedral angle restraints: 11117 sinusoidal: 5960 harmonic: 5157 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual 93.00 151.79 -58.79 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CA ASP A 614 " pdb=" CB ASP A 614 " pdb=" CG ASP A 614 " pdb=" OD1 ASP A 614 " ideal model delta sinusoidal sigma weight residual -30.00 -84.40 54.40 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CA ARG C 33 " pdb=" CB ARG C 33 " pdb=" CG ARG C 33 " pdb=" CD ARG C 33 " ideal model delta sinusoidal sigma weight residual 180.00 120.59 59.41 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 11114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1649 0.082 - 0.164: 145 0.164 - 0.246: 1 0.246 - 0.328: 0 0.328 - 0.409: 2 Chirality restraints: 1797 Sorted by residual: chirality pdb=" CB UX8 G 3 " pdb=" CA UX8 G 3 " pdb=" CG UX8 G 3 " pdb=" O9 UX8 G 3 " both_signs ideal model delta sigma weight residual False -2.38 -2.79 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA PRO A 684 " pdb=" N PRO A 684 " pdb=" C PRO A 684 " pdb=" CB PRO A 684 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA UX8 G 3 " pdb=" N UX8 G 3 " pdb=" C UX8 G 3 " pdb=" CB UX8 G 3 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 1794 not shown) Planarity restraints: 3598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 35 " -0.027 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO B 36 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 185 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C ASN A 185 " 0.026 2.00e-02 2.50e+03 pdb=" O ASN A 185 " -0.010 2.00e-02 2.50e+03 pdb=" N HIS A 186 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 31 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO D 32 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO D 32 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 32 " 0.018 5.00e-02 4.00e+02 ... (remaining 3595 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 531 2.12 - 2.74: 40751 2.74 - 3.36: 63840 3.36 - 3.98: 81787 3.98 - 4.60: 127409 Nonbonded interactions: 314318 Sorted by model distance: nonbonded pdb=" O HIS A 677 " pdb=" H THR A 692 " model vdw 1.503 1.850 nonbonded pdb=" OE1 GLU A 435 " pdb=" H GLU A 435 " model vdw 1.618 1.850 nonbonded pdb=" OG1 THR B 309 " pdb=" H VAL B 314 " model vdw 1.626 1.850 nonbonded pdb=" O LEU A 66 " pdb=" HG1 THR A 69 " model vdw 1.631 1.850 nonbonded pdb=" OD2 ASP A 362 " pdb="HH21 ARG A 366 " model vdw 1.635 1.850 ... (remaining 314313 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.350 Extract box with map and model: 6.750 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 74.770 Find NCS groups from input model: 0.450 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 12136 Z= 0.260 Angle : 0.551 22.631 16497 Z= 0.290 Chirality : 0.044 0.409 1797 Planarity : 0.003 0.040 2173 Dihedral : 16.055 88.745 4390 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.31 % Allowed : 23.46 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1503 helix: 2.48 (0.30), residues: 316 sheet: -0.90 (0.24), residues: 471 loop : -1.07 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 317 HIS 0.003 0.001 HIS A 677 PHE 0.015 0.001 PHE A 738 TYR 0.013 0.001 TYR D 184 ARG 0.005 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 1.750 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 183 GLU cc_start: 0.8235 (tp30) cc_final: 0.7579 (tt0) outliers start: 4 outliers final: 3 residues processed: 173 average time/residue: 0.4750 time to fit residues: 122.2483 Evaluate side-chains 165 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 808 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.0245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12136 Z= 0.161 Angle : 0.460 5.938 16497 Z= 0.241 Chirality : 0.042 0.366 1797 Planarity : 0.003 0.039 2173 Dihedral : 4.150 58.636 1673 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.57 % Allowed : 22.44 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.22), residues: 1503 helix: 2.51 (0.30), residues: 316 sheet: -0.75 (0.24), residues: 471 loop : -1.13 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 348 HIS 0.002 0.000 HIS A 677 PHE 0.007 0.001 PHE G 7 TYR 0.014 0.001 TYR D 184 ARG 0.004 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.784 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8510 (p) REVERT: A 501 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7236 (tt) REVERT: B 277 ILE cc_start: 0.5550 (pt) cc_final: 0.5350 (mt) REVERT: C 57 ILE cc_start: 0.8213 (pt) cc_final: 0.7966 (tp) REVERT: C 78 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7906 (mtpt) REVERT: D 183 GLU cc_start: 0.8208 (tp30) cc_final: 0.7538 (tt0) outliers start: 20 outliers final: 14 residues processed: 186 average time/residue: 0.4421 time to fit residues: 123.3370 Evaluate side-chains 182 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 0.0000 chunk 119 optimal weight: 0.0000 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 0.0370 chunk 108 optimal weight: 4.9990 overall best weight: 0.8070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.0335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12136 Z= 0.147 Angle : 0.453 6.201 16497 Z= 0.237 Chirality : 0.042 0.367 1797 Planarity : 0.003 0.039 2173 Dihedral : 4.110 58.609 1673 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.89 % Allowed : 22.60 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1503 helix: 2.58 (0.30), residues: 316 sheet: -0.75 (0.24), residues: 468 loop : -1.10 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 348 HIS 0.002 0.000 HIS A 677 PHE 0.007 0.001 PHE G 7 TYR 0.013 0.001 TYR D 184 ARG 0.001 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 1.935 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8510 (p) REVERT: A 501 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7231 (tt) REVERT: C 57 ILE cc_start: 0.8224 (pt) cc_final: 0.8002 (tp) REVERT: D 183 GLU cc_start: 0.8209 (tp30) cc_final: 0.7553 (tt0) outliers start: 24 outliers final: 18 residues processed: 189 average time/residue: 0.4445 time to fit residues: 127.6367 Evaluate side-chains 188 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.0526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12136 Z= 0.220 Angle : 0.474 6.446 16497 Z= 0.250 Chirality : 0.043 0.365 1797 Planarity : 0.003 0.044 2173 Dihedral : 4.211 58.262 1673 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.54 % Allowed : 20.94 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1503 helix: 2.41 (0.30), residues: 316 sheet: -0.81 (0.24), residues: 467 loop : -1.17 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 776 HIS 0.002 0.001 HIS A 533 PHE 0.009 0.001 PHE A 791 TYR 0.015 0.001 TYR D 184 ARG 0.002 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 1.737 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8515 (p) REVERT: A 501 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7332 (tt) REVERT: C 57 ILE cc_start: 0.8278 (pt) cc_final: 0.8068 (tp) REVERT: D 183 GLU cc_start: 0.8224 (tp30) cc_final: 0.7515 (tt0) outliers start: 45 outliers final: 34 residues processed: 205 average time/residue: 0.4221 time to fit residues: 130.7886 Evaluate side-chains 202 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12136 Z= 0.259 Angle : 0.491 5.861 16497 Z= 0.261 Chirality : 0.043 0.365 1797 Planarity : 0.003 0.046 2173 Dihedral : 4.338 57.793 1673 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.39 % Allowed : 21.81 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1503 helix: 2.21 (0.29), residues: 316 sheet: -0.86 (0.24), residues: 465 loop : -1.29 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 348 HIS 0.003 0.001 HIS A 533 PHE 0.011 0.001 PHE G 7 TYR 0.016 0.001 TYR D 80 ARG 0.002 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 1.924 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8518 (p) REVERT: A 501 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7395 (tt) REVERT: C 57 ILE cc_start: 0.8330 (pt) cc_final: 0.8125 (tp) outliers start: 43 outliers final: 33 residues processed: 201 average time/residue: 0.4232 time to fit residues: 129.8473 Evaluate side-chains 196 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 0.0980 chunk 66 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12136 Z= 0.198 Angle : 0.470 5.903 16497 Z= 0.249 Chirality : 0.042 0.366 1797 Planarity : 0.003 0.042 2173 Dihedral : 4.278 57.985 1673 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.76 % Allowed : 22.28 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.22), residues: 1503 helix: 2.34 (0.29), residues: 313 sheet: -0.83 (0.24), residues: 465 loop : -1.25 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 348 HIS 0.002 0.001 HIS A 677 PHE 0.009 0.001 PHE G 7 TYR 0.016 0.001 TYR D 80 ARG 0.003 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.684 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8517 (p) REVERT: A 501 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7389 (tt) REVERT: E 71 ASN cc_start: 0.7719 (m-40) cc_final: 0.7363 (t0) outliers start: 35 outliers final: 30 residues processed: 201 average time/residue: 0.4365 time to fit residues: 135.0675 Evaluate side-chains 197 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12136 Z= 0.291 Angle : 0.509 5.807 16497 Z= 0.271 Chirality : 0.043 0.365 1797 Planarity : 0.004 0.048 2173 Dihedral : 4.452 56.487 1673 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.62 % Allowed : 21.81 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.21), residues: 1503 helix: 2.03 (0.29), residues: 314 sheet: -0.97 (0.24), residues: 464 loop : -1.35 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 205 HIS 0.004 0.001 HIS A 533 PHE 0.014 0.001 PHE G 7 TYR 0.016 0.001 TYR D 184 ARG 0.003 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 165 time to evaluate : 1.730 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8512 (p) REVERT: A 501 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7571 (tt) outliers start: 46 outliers final: 39 residues processed: 201 average time/residue: 0.4023 time to fit residues: 125.0676 Evaluate side-chains 199 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12136 Z= 0.156 Angle : 0.467 5.936 16497 Z= 0.248 Chirality : 0.042 0.366 1797 Planarity : 0.003 0.043 2173 Dihedral : 4.290 57.534 1673 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.32 % Favored : 95.61 % Rotamer: Outliers : 2.76 % Allowed : 22.68 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1503 helix: 2.46 (0.30), residues: 306 sheet: -0.78 (0.24), residues: 448 loop : -1.17 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 376 HIS 0.002 0.001 HIS A 677 PHE 0.007 0.001 PHE A 785 TYR 0.014 0.001 TYR D 184 ARG 0.003 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 1.464 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8507 (p) REVERT: A 501 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7387 (tt) REVERT: D 121 ASP cc_start: 0.5678 (OUTLIER) cc_final: 0.5375 (t0) REVERT: D 183 GLU cc_start: 0.8245 (tp30) cc_final: 0.7568 (tt0) outliers start: 35 outliers final: 29 residues processed: 195 average time/residue: 0.4250 time to fit residues: 127.7021 Evaluate side-chains 191 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12136 Z= 0.227 Angle : 0.483 5.873 16497 Z= 0.256 Chirality : 0.043 0.365 1797 Planarity : 0.003 0.046 2173 Dihedral : 4.334 56.763 1673 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.83 % Allowed : 22.52 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1503 helix: 2.25 (0.29), residues: 313 sheet: -0.83 (0.24), residues: 449 loop : -1.27 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 776 HIS 0.002 0.001 HIS A 533 PHE 0.010 0.001 PHE A 791 TYR 0.015 0.001 TYR D 184 ARG 0.005 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 159 time to evaluate : 1.723 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 243 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8506 (p) REVERT: A 501 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7498 (tt) REVERT: D 121 ASP cc_start: 0.5967 (OUTLIER) cc_final: 0.5671 (t0) REVERT: D 183 GLU cc_start: 0.8252 (tp30) cc_final: 0.7608 (tt0) outliers start: 36 outliers final: 33 residues processed: 189 average time/residue: 0.4451 time to fit residues: 129.7570 Evaluate side-chains 192 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 0.0010 chunk 97 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 12136 Z= 0.135 Angle : 0.456 5.999 16497 Z= 0.240 Chirality : 0.042 0.367 1797 Planarity : 0.003 0.047 2173 Dihedral : 4.177 57.112 1673 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.13 % Favored : 95.81 % Rotamer: Outliers : 2.20 % Allowed : 23.07 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1503 helix: 2.57 (0.30), residues: 311 sheet: -0.67 (0.24), residues: 453 loop : -1.12 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 376 HIS 0.002 0.001 HIS A 677 PHE 0.006 0.001 PHE A 426 TYR 0.015 0.001 TYR D 80 ARG 0.005 0.000 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 1.862 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 243 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8506 (p) REVERT: A 501 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7330 (tt) REVERT: D 183 GLU cc_start: 0.8237 (tp30) cc_final: 0.7562 (tt0) outliers start: 28 outliers final: 24 residues processed: 188 average time/residue: 0.4395 time to fit residues: 126.6001 Evaluate side-chains 188 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.192675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137785 restraints weight = 44032.922| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.38 r_work: 0.3355 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12136 Z= 0.171 Angle : 0.460 5.947 16497 Z= 0.243 Chirality : 0.042 0.366 1797 Planarity : 0.003 0.048 2173 Dihedral : 4.165 56.643 1673 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 2.28 % Allowed : 23.31 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.22), residues: 1503 helix: 2.55 (0.30), residues: 311 sheet: -0.75 (0.24), residues: 466 loop : -1.13 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 376 HIS 0.002 0.001 HIS A 677 PHE 0.007 0.001 PHE A 426 TYR 0.014 0.001 TYR D 184 ARG 0.004 0.000 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5268.43 seconds wall clock time: 94 minutes 9.66 seconds (5649.66 seconds total)