Starting phenix.real_space_refine on Mon Mar 11 10:32:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/03_2024/6x0l_21978.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/03_2024/6x0l_21978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/03_2024/6x0l_21978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/03_2024/6x0l_21978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/03_2024/6x0l_21978.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/03_2024/6x0l_21978.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 40 5.49 5 S 45 5.16 5 C 4989 2.51 5 N 1379 2.21 5 O 1584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O ARG 38": "NH1" <-> "NH2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "O GLU 198": "OE1" <-> "OE2" Residue "O GLU 273": "OE1" <-> "OE2" Residue "O GLU 327": "OE1" <-> "OE2" Residue "O ARG 336": "NH1" <-> "NH2" Residue "P ARG 137": "NH1" <-> "NH2" Residue "P ARG 224": "NH1" <-> "NH2" Residue "P ARG 277": "NH1" <-> "NH2" Residue "P GLU 322": "OE1" <-> "OE2" Residue "P ARG 350": "NH1" <-> "NH2" Residue "P GLU 362": "OE1" <-> "OE2" Residue "R GLU 182": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8037 Number of models: 1 Model: "" Number of chains: 7 Chain: "O" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2488 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Chain: "P" Number of atoms: 3798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3798 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 452} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 929 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 9} Chain: "J" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 207 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "i" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 207 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "j" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 9} Time building chain proxies: 4.82, per 1000 atoms: 0.60 Number of scatterers: 8037 At special positions: 0 Unit cell: (115.54, 109.18, 91.16, 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 45 16.00 P 40 15.00 O 1584 8.00 N 1379 7.00 C 4989 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.3 seconds 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 40.4% alpha, 19.8% beta 20 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'O' and resid 37 through 46 removed outlier: 3.895A pdb=" N VAL O 41 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 64 removed outlier: 3.974A pdb=" N TYR O 54 " --> pdb=" O PRO O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 77 Processing helix chain 'O' and resid 82 through 88 removed outlier: 3.500A pdb=" N ILE O 86 " --> pdb=" O GLY O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 176 removed outlier: 3.785A pdb=" N LYS O 174 " --> pdb=" O THR O 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 200 Processing helix chain 'O' and resid 207 through 217 Processing helix chain 'O' and resid 244 through 257 Processing helix chain 'O' and resid 260 through 268 Processing helix chain 'O' and resid 268 through 284 Processing helix chain 'O' and resid 286 through 301 removed outlier: 4.404A pdb=" N GLY O 290 " --> pdb=" O ASP O 286 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY O 294 " --> pdb=" O GLY O 290 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 304 No H-bonds generated for 'chain 'O' and resid 302 through 304' Processing helix chain 'O' and resid 305 through 320 Proline residue: O 314 - end of helix Processing helix chain 'O' and resid 322 through 335 Processing helix chain 'P' and resid 155 through 172 Processing helix chain 'P' and resid 222 through 233 Processing helix chain 'P' and resid 234 through 248 removed outlier: 3.532A pdb=" N LYS P 246 " --> pdb=" O MET P 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 258 through 278 removed outlier: 3.868A pdb=" N ALA P 278 " --> pdb=" O ASP P 274 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 296 removed outlier: 3.559A pdb=" N MET P 286 " --> pdb=" O GLY P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 334 removed outlier: 3.583A pdb=" N LEU P 314 " --> pdb=" O THR P 310 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 353 removed outlier: 4.088A pdb=" N GLN P 347 " --> pdb=" O HIS P 343 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 376 Processing helix chain 'P' and resid 398 through 403 removed outlier: 3.764A pdb=" N ALA P 402 " --> pdb=" O GLY P 398 " (cutoff:3.500A) Processing helix chain 'P' and resid 421 through 429 removed outlier: 3.745A pdb=" N ILE P 425 " --> pdb=" O ASN P 421 " (cutoff:3.500A) Processing helix chain 'P' and resid 438 through 442 removed outlier: 3.575A pdb=" N GLY P 441 " --> pdb=" O PRO P 438 " (cutoff:3.500A) Processing helix chain 'P' and resid 453 through 459 removed outlier: 3.588A pdb=" N SER P 457 " --> pdb=" O MET P 453 " (cutoff:3.500A) Processing helix chain 'P' and resid 460 through 462 No H-bonds generated for 'chain 'P' and resid 460 through 462' Processing helix chain 'P' and resid 511 through 515 Processing helix chain 'P' and resid 550 through 552 No H-bonds generated for 'chain 'P' and resid 550 through 552' Processing helix chain 'R' and resid 155 through 172 Processing sheet with id=AA1, first strand: chain 'O' and resid 79 through 80 removed outlier: 6.690A pdb=" N MET O 129 " --> pdb=" O ILE O 118 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE O 120 " --> pdb=" O TYR O 127 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N TYR O 127 " --> pdb=" O ILE O 120 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR O 142 " --> pdb=" O PHE O 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 92 through 94 removed outlier: 3.711A pdb=" N GLY P 139 " --> pdb=" O TYR P 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 92 through 94 removed outlier: 4.695A pdb=" N MET P 105 " --> pdb=" O LEU P 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 96 through 97 Processing sheet with id=AA5, first strand: chain 'P' and resid 354 through 358 removed outlier: 5.159A pdb=" N MET P 386 " --> pdb=" O ASN P 565 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN P 565 " --> pdb=" O MET P 386 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU P 388 " --> pdb=" O GLN P 563 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN P 563 " --> pdb=" O LEU P 388 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG P 557 " --> pdb=" O VAL P 394 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS P 396 " --> pdb=" O ARG P 555 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ARG P 555 " --> pdb=" O LYS P 396 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU P 474 " --> pdb=" O ARG P 557 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU P 559 " --> pdb=" O LEU P 472 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU P 472 " --> pdb=" O LEU P 559 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS P 561 " --> pdb=" O GLY P 470 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLY P 470 " --> pdb=" O LYS P 561 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU P 471 " --> pdb=" O SER P 417 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER P 417 " --> pdb=" O LEU P 471 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 448 through 450 removed outlier: 5.852A pdb=" N ASN P 483 " --> pdb=" O LYS P 503 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 529 through 530 removed outlier: 6.758A pdb=" N TYR P 543 " --> pdb=" O LYS P 507 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ALA P 509 " --> pdb=" O TYR P 543 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 516 through 518 Processing sheet with id=AA9, first strand: chain 'R' and resid 93 through 94 removed outlier: 3.833A pdb=" N HIS R 93 " --> pdb=" O GLU R 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 132 " --> pdb=" O CYS R 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 93 through 94 removed outlier: 3.833A pdb=" N HIS R 93 " --> pdb=" O GLU R 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 96 through 97 332 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 3.47 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: 2121 1.33 - 1.45: 1667 1.45 - 1.57: 4354 1.57 - 1.69: 76 1.69 - 1.81: 73 Bond restraints: 8291 Sorted by residual: bond pdb=" CA PRO P 434 " pdb=" C PRO P 434 " ideal model delta sigma weight residual 1.514 1.536 -0.021 5.50e-03 3.31e+04 1.52e+01 bond pdb=" C1' DA i 82 " pdb=" N9 DA i 82 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C1' DA j -81 " pdb=" N9 DA j -81 " ideal model delta sigma weight residual 1.460 1.388 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C1' DA j -78 " pdb=" N9 DA j -78 " ideal model delta sigma weight residual 1.460 1.397 0.063 2.00e-02 2.50e+03 9.84e+00 bond pdb=" C PRO P 434 " pdb=" O PRO P 434 " ideal model delta sigma weight residual 1.246 1.219 0.026 8.50e-03 1.38e+04 9.71e+00 ... (remaining 8286 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.57: 339 105.57 - 112.67: 4250 112.67 - 119.78: 2872 119.78 - 126.89: 3698 126.89 - 134.00: 193 Bond angle restraints: 11352 Sorted by residual: angle pdb=" N THR O 93 " pdb=" CA THR O 93 " pdb=" C THR O 93 " ideal model delta sigma weight residual 113.18 108.03 5.15 1.33e+00 5.65e-01 1.50e+01 angle pdb=" N LYS O 174 " pdb=" CA LYS O 174 " pdb=" C LYS O 174 " ideal model delta sigma weight residual 112.90 108.19 4.71 1.31e+00 5.83e-01 1.29e+01 angle pdb=" CA LYS O 181 " pdb=" C LYS O 181 " pdb=" O LYS O 181 " ideal model delta sigma weight residual 122.63 118.17 4.46 1.29e+00 6.01e-01 1.19e+01 angle pdb=" C MET P 556 " pdb=" N ARG P 557 " pdb=" CA ARG P 557 " ideal model delta sigma weight residual 122.15 112.75 9.40 2.83e+00 1.25e-01 1.10e+01 angle pdb=" CA PRO P 434 " pdb=" C PRO P 434 " pdb=" O PRO P 434 " ideal model delta sigma weight residual 120.90 118.60 2.30 7.20e-01 1.93e+00 1.02e+01 ... (remaining 11347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 4630 34.73 - 69.46: 260 69.46 - 104.19: 10 104.19 - 138.92: 0 138.92 - 173.64: 1 Dihedral angle restraints: 4901 sinusoidal: 2294 harmonic: 2607 Sorted by residual: dihedral pdb=" CA GLY R 90 " pdb=" C GLY R 90 " pdb=" N LYS R 91 " pdb=" CA LYS R 91 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASN P 99 " pdb=" C ASN P 99 " pdb=" N ASP P 100 " pdb=" CA ASP P 100 " ideal model delta harmonic sigma weight residual -180.00 -159.89 -20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" C4' DA J 80 " pdb=" C3' DA J 80 " pdb=" O3' DA J 80 " pdb=" P DT J 81 " ideal model delta sinusoidal sigma weight residual 220.00 46.36 173.64 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 4898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 827 0.044 - 0.089: 280 0.089 - 0.133: 94 0.133 - 0.177: 15 0.177 - 0.222: 4 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CA ILE O 182 " pdb=" N ILE O 182 " pdb=" C ILE O 182 " pdb=" CB ILE O 182 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE O 176 " pdb=" N ILE O 176 " pdb=" C ILE O 176 " pdb=" CB ILE O 176 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" C1' DA i 82 " pdb=" O4' DA i 82 " pdb=" C2' DA i 82 " pdb=" N9 DA i 82 " both_signs ideal model delta sigma weight residual False 2.42 2.23 0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 1217 not shown) Planarity restraints: 1329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P 425 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C ILE P 425 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE P 425 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU P 426 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA i 80 " -0.032 2.00e-02 2.50e+03 1.39e-02 5.29e+00 pdb=" N9 DA i 80 " 0.006 2.00e-02 2.50e+03 pdb=" C8 DA i 80 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DA i 80 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DA i 80 " 0.009 2.00e-02 2.50e+03 pdb=" C6 DA i 80 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA i 80 " -0.024 2.00e-02 2.50e+03 pdb=" N1 DA i 80 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA i 80 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA i 80 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA i 80 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT j -82 " 0.024 2.00e-02 2.50e+03 1.22e-02 3.73e+00 pdb=" N1 DT j -82 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DT j -82 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT j -82 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DT j -82 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT j -82 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT j -82 " 0.019 2.00e-02 2.50e+03 pdb=" C5 DT j -82 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DT j -82 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT j -82 " -0.015 2.00e-02 2.50e+03 ... (remaining 1326 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 125 2.63 - 3.20: 7616 3.20 - 3.77: 13417 3.77 - 4.33: 17912 4.33 - 4.90: 27606 Nonbonded interactions: 66676 Sorted by model distance: nonbonded pdb=" C2' DA i 77 " pdb=" C7 DT i 78 " model vdw 2.067 3.860 nonbonded pdb=" OE2 GLU O 114 " pdb=" OH TYR O 317 " model vdw 2.101 2.440 nonbonded pdb=" OH TYR P 119 " pdb=" OP1 DT j -82 " model vdw 2.119 2.440 nonbonded pdb=" OH TYR O 109 " pdb=" O GLY O 301 " model vdw 2.161 2.440 nonbonded pdb=" N GLY P 506 " pdb=" OD1 ASN P 544 " model vdw 2.174 2.520 ... (remaining 66671 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 23.110 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 27.240 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 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 0.074 8291 Z= 0.303 Angle : 0.850 9.403 11352 Z= 0.487 Chirality : 0.050 0.222 1220 Planarity : 0.005 0.035 1329 Dihedral : 18.875 173.644 3223 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.13 % Allowed : 5.36 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.26), residues: 884 helix: -0.58 (0.26), residues: 317 sheet: -0.40 (0.40), residues: 157 loop : -1.62 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP P 135 HIS 0.009 0.002 HIS O 223 PHE 0.019 0.003 PHE P 113 TYR 0.023 0.002 TYR P 188 ARG 0.010 0.001 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: O 239 ARG cc_start: 0.7160 (ptp-170) cc_final: 0.6847 (ptp-110) REVERT: O 305 PHE cc_start: 0.6355 (m-10) cc_final: 0.6067 (m-10) REVERT: O 311 GLN cc_start: 0.7775 (mt0) cc_final: 0.7535 (mt0) REVERT: P 108 GLN cc_start: 0.7620 (tt0) cc_final: 0.7271 (tm-30) REVERT: P 241 MET cc_start: 0.7810 (tpt) cc_final: 0.7349 (tpt) REVERT: P 290 ASN cc_start: 0.7103 (m110) cc_final: 0.5827 (m110) REVERT: P 468 ASN cc_start: 0.6550 (p0) cc_final: 0.6346 (p0) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.2369 time to fit residues: 55.3369 Evaluate side-chains 111 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 303 HIS ** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 267 GLN ** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 519 ASN P 553 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8291 Z= 0.204 Angle : 0.684 8.528 11352 Z= 0.363 Chirality : 0.043 0.139 1220 Planarity : 0.004 0.030 1329 Dihedral : 19.835 162.661 1394 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.42 % Allowed : 12.63 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.29 (0.27), residues: 884 helix: 0.66 (0.28), residues: 321 sheet: -0.22 (0.38), residues: 161 loop : -0.80 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP P 414 HIS 0.003 0.001 HIS R 93 PHE 0.026 0.002 PHE R 132 TYR 0.019 0.002 TYR O 317 ARG 0.007 0.001 ARG O 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: O 222 PHE cc_start: 0.6118 (OUTLIER) cc_final: 0.5635 (m-10) REVERT: O 239 ARG cc_start: 0.7348 (ptp-170) cc_final: 0.6782 (ptp-110) REVERT: O 289 MET cc_start: 0.7018 (ttm) cc_final: 0.6788 (ttm) REVERT: O 296 ASP cc_start: 0.6206 (m-30) cc_final: 0.5998 (m-30) REVERT: O 327 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7207 (mm-30) REVERT: P 108 GLN cc_start: 0.7586 (tt0) cc_final: 0.7305 (tm-30) REVERT: P 144 MET cc_start: 0.7739 (tmm) cc_final: 0.6649 (tmm) REVERT: P 270 LYS cc_start: 0.7824 (tppt) cc_final: 0.7450 (tptt) REVERT: P 290 ASN cc_start: 0.6956 (m110) cc_final: 0.6592 (m110) REVERT: P 414 TRP cc_start: 0.6990 (m100) cc_final: 0.6783 (m100) REVERT: P 567 LEU cc_start: 0.4566 (OUTLIER) cc_final: 0.4316 (pp) outliers start: 19 outliers final: 10 residues processed: 138 average time/residue: 0.2168 time to fit residues: 40.7960 Evaluate side-chains 115 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 190 GLU Chi-restraints excluded: chain O residue 222 PHE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 541 LEU Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 56 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 123 ASN ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 HIS ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 261 GLN P 371 GLN ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 459 ASN ** R 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 8291 Z= 0.452 Angle : 0.837 8.327 11352 Z= 0.449 Chirality : 0.048 0.169 1220 Planarity : 0.005 0.057 1329 Dihedral : 19.901 158.362 1394 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 28.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.34 % Allowed : 15.94 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.64 (0.27), residues: 884 helix: 0.47 (0.27), residues: 319 sheet: -0.41 (0.39), residues: 166 loop : -1.11 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP R 135 HIS 0.008 0.002 HIS R 147 PHE 0.020 0.003 PHE R 163 TYR 0.025 0.003 TYR O 317 ARG 0.007 0.001 ARG O 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 100 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: O 141 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.7136 (t) REVERT: O 239 ARG cc_start: 0.7451 (ptp-170) cc_final: 0.6924 (ptp-110) REVERT: O 289 MET cc_start: 0.7336 (ttm) cc_final: 0.7135 (ttm) REVERT: P 193 MET cc_start: 0.8075 (mmm) cc_final: 0.7856 (mmt) REVERT: P 419 MET cc_start: 0.7580 (tpp) cc_final: 0.7250 (tpp) REVERT: R 135 TRP cc_start: 0.6944 (t-100) cc_final: 0.6721 (t-100) outliers start: 34 outliers final: 25 residues processed: 124 average time/residue: 0.1906 time to fit residues: 32.6185 Evaluate side-chains 117 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 174 LYS Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 190 GLU Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 299 CYS Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain O residue 323 ASN Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 195 TYR Chi-restraints excluded: chain P residue 225 VAL Chi-restraints excluded: chain P residue 273 GLU Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 386 MET Chi-restraints excluded: chain P residue 452 ASP Chi-restraints excluded: chain P residue 486 LEU Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 541 LEU Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 141 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8291 Z= 0.209 Angle : 0.671 11.915 11352 Z= 0.356 Chirality : 0.042 0.148 1220 Planarity : 0.003 0.030 1329 Dihedral : 19.697 157.360 1394 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.44 % Allowed : 17.47 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.28), residues: 884 helix: 0.82 (0.28), residues: 321 sheet: -0.13 (0.41), residues: 156 loop : -0.88 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 414 HIS 0.003 0.001 HIS P 343 PHE 0.022 0.002 PHE O 305 TYR 0.020 0.002 TYR P 543 ARG 0.003 0.000 ARG O 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 0.948 Fit side-chains REVERT: O 222 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.5489 (m-10) REVERT: O 239 ARG cc_start: 0.7268 (ptp-170) cc_final: 0.6777 (ptp-110) REVERT: O 268 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: O 296 ASP cc_start: 0.5807 (m-30) cc_final: 0.5599 (m-30) REVERT: P 105 MET cc_start: 0.8016 (tmm) cc_final: 0.7714 (tmm) REVERT: P 108 GLN cc_start: 0.7738 (tt0) cc_final: 0.7244 (tm-30) REVERT: P 270 LYS cc_start: 0.7750 (tppt) cc_final: 0.7370 (tptt) REVERT: P 419 MET cc_start: 0.7545 (tpp) cc_final: 0.7285 (tpp) REVERT: P 453 MET cc_start: 0.7700 (mmp) cc_final: 0.7011 (mtm) outliers start: 27 outliers final: 18 residues processed: 120 average time/residue: 0.2018 time to fit residues: 33.4510 Evaluate side-chains 111 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 190 GLU Chi-restraints excluded: chain O residue 211 LYS Chi-restraints excluded: chain O residue 222 PHE Chi-restraints excluded: chain O residue 268 PHE Chi-restraints excluded: chain O residue 299 CYS Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 195 TYR Chi-restraints excluded: chain P residue 273 GLU Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 452 ASP Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 541 LEU Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 22 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 415 HIS ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8291 Z= 0.177 Angle : 0.644 12.960 11352 Z= 0.340 Chirality : 0.041 0.171 1220 Planarity : 0.003 0.031 1329 Dihedral : 19.516 158.589 1394 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.32 % Allowed : 19.52 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.28), residues: 884 helix: 1.01 (0.29), residues: 321 sheet: -0.03 (0.42), residues: 156 loop : -0.77 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP P 414 HIS 0.003 0.001 HIS O 128 PHE 0.022 0.002 PHE O 305 TYR 0.015 0.002 TYR O 317 ARG 0.002 0.000 ARG O 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: O 222 PHE cc_start: 0.5903 (OUTLIER) cc_final: 0.5436 (m-10) REVERT: O 268 PHE cc_start: 0.7061 (OUTLIER) cc_final: 0.6740 (m-80) REVERT: O 296 ASP cc_start: 0.5923 (m-30) cc_final: 0.5410 (m-30) REVERT: P 144 MET cc_start: 0.8019 (tmm) cc_final: 0.7067 (tmm) REVERT: P 270 LYS cc_start: 0.7692 (tppt) cc_final: 0.7334 (tptt) REVERT: P 453 MET cc_start: 0.7628 (mmp) cc_final: 0.7054 (mtm) outliers start: 26 outliers final: 16 residues processed: 115 average time/residue: 0.2008 time to fit residues: 32.1703 Evaluate side-chains 115 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 190 GLU Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 222 PHE Chi-restraints excluded: chain O residue 268 PHE Chi-restraints excluded: chain O residue 299 CYS Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain O residue 323 ASN Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 452 ASP Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 377 HIS ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 459 ASN ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8291 Z= 0.179 Angle : 0.640 11.913 11352 Z= 0.334 Chirality : 0.041 0.181 1220 Planarity : 0.003 0.044 1329 Dihedral : 19.372 158.663 1394 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.32 % Allowed : 20.41 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.12 (0.29), residues: 884 helix: 1.11 (0.29), residues: 321 sheet: 0.05 (0.43), residues: 156 loop : -0.68 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP P 414 HIS 0.003 0.001 HIS P 377 PHE 0.022 0.002 PHE O 305 TYR 0.024 0.001 TYR O 317 ARG 0.003 0.000 ARG O 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 219 THR cc_start: 0.4131 (OUTLIER) cc_final: 0.3492 (m) REVERT: O 222 PHE cc_start: 0.5967 (OUTLIER) cc_final: 0.5508 (m-10) REVERT: O 268 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6635 (m-80) REVERT: O 296 ASP cc_start: 0.5979 (m-30) cc_final: 0.5508 (m-30) REVERT: O 317 TYR cc_start: 0.6967 (m-80) cc_final: 0.6546 (m-80) REVERT: P 144 MET cc_start: 0.7999 (tmm) cc_final: 0.7130 (tmm) REVERT: P 270 LYS cc_start: 0.7688 (tppt) cc_final: 0.7298 (tptt) REVERT: P 453 MET cc_start: 0.7748 (mmp) cc_final: 0.7017 (mtm) REVERT: R 135 TRP cc_start: 0.6493 (t-100) cc_final: 0.5948 (t-100) REVERT: R 136 MET cc_start: 0.7246 (mpp) cc_final: 0.5963 (mtt) REVERT: R 180 LYS cc_start: 0.7386 (pttp) cc_final: 0.6173 (pttt) outliers start: 26 outliers final: 19 residues processed: 117 average time/residue: 0.1951 time to fit residues: 31.6981 Evaluate side-chains 118 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 222 PHE Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 268 PHE Chi-restraints excluded: chain O residue 299 CYS Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain O residue 323 ASN Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain P residue 452 ASP Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 556 MET Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8291 Z= 0.223 Angle : 0.666 13.618 11352 Z= 0.346 Chirality : 0.042 0.198 1220 Planarity : 0.004 0.037 1329 Dihedral : 19.316 158.467 1394 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.46 % Allowed : 20.15 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.11 (0.29), residues: 884 helix: 1.14 (0.29), residues: 321 sheet: -0.17 (0.42), residues: 157 loop : -0.63 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP P 414 HIS 0.003 0.001 HIS R 147 PHE 0.020 0.002 PHE O 305 TYR 0.021 0.002 TYR O 317 ARG 0.004 0.000 ARG O 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 96 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: O 222 PHE cc_start: 0.6067 (OUTLIER) cc_final: 0.5599 (m-10) REVERT: O 268 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: O 296 ASP cc_start: 0.6104 (m-30) cc_final: 0.5487 (m-30) REVERT: P 144 MET cc_start: 0.8038 (tmm) cc_final: 0.7348 (tmm) REVERT: P 270 LYS cc_start: 0.7716 (tppt) cc_final: 0.7373 (tptt) REVERT: P 419 MET cc_start: 0.8044 (tpp) cc_final: 0.7595 (tpp) REVERT: P 453 MET cc_start: 0.7824 (mmp) cc_final: 0.7084 (mtm) outliers start: 35 outliers final: 25 residues processed: 122 average time/residue: 0.2018 time to fit residues: 33.9319 Evaluate side-chains 120 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 123 ASN Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 190 GLU Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 222 PHE Chi-restraints excluded: chain O residue 241 LEU Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 268 PHE Chi-restraints excluded: chain O residue 299 CYS Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain O residue 323 ASN Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 146 GLN Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 290 ASN Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 452 ASP Chi-restraints excluded: chain P residue 477 VAL Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain R residue 126 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 459 ASN ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8291 Z= 0.264 Angle : 0.693 12.396 11352 Z= 0.363 Chirality : 0.042 0.210 1220 Planarity : 0.004 0.036 1329 Dihedral : 19.378 158.276 1394 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.08 % Allowed : 21.05 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.09 (0.29), residues: 884 helix: 0.99 (0.29), residues: 321 sheet: -0.35 (0.43), residues: 157 loop : -0.72 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP P 414 HIS 0.004 0.001 HIS P 343 PHE 0.018 0.002 PHE O 305 TYR 0.022 0.002 TYR O 317 ARG 0.006 0.001 ARG O 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 93 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: O 222 PHE cc_start: 0.6356 (OUTLIER) cc_final: 0.5852 (m-10) REVERT: O 268 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6967 (m-80) REVERT: O 283 ASP cc_start: 0.7214 (m-30) cc_final: 0.6880 (p0) REVERT: O 296 ASP cc_start: 0.5981 (m-30) cc_final: 0.5383 (m-30) REVERT: P 270 LYS cc_start: 0.7729 (tppt) cc_final: 0.7415 (tptt) REVERT: P 453 MET cc_start: 0.7694 (mmp) cc_final: 0.7054 (mtm) REVERT: R 136 MET cc_start: 0.7491 (mpp) cc_final: 0.6098 (mtt) outliers start: 32 outliers final: 28 residues processed: 117 average time/residue: 0.2248 time to fit residues: 37.3002 Evaluate side-chains 121 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 123 ASN Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 190 GLU Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 222 PHE Chi-restraints excluded: chain O residue 241 LEU Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 268 PHE Chi-restraints excluded: chain O residue 299 CYS Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain O residue 323 ASN Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 146 GLN Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 290 ASN Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 452 ASP Chi-restraints excluded: chain P residue 477 VAL Chi-restraints excluded: chain P residue 519 ASN Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 556 MET Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain R residue 191 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 0.0270 chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 226 GLN P 428 HIS ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8291 Z= 0.168 Angle : 0.685 14.619 11352 Z= 0.349 Chirality : 0.041 0.215 1220 Planarity : 0.003 0.027 1329 Dihedral : 19.167 159.895 1394 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.19 % Allowed : 22.45 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.29), residues: 884 helix: 1.21 (0.29), residues: 320 sheet: -0.21 (0.43), residues: 157 loop : -0.58 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP P 414 HIS 0.002 0.001 HIS P 343 PHE 0.018 0.002 PHE R 132 TYR 0.031 0.001 TYR O 317 ARG 0.005 0.000 ARG O 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: O 219 THR cc_start: 0.4280 (OUTLIER) cc_final: 0.3816 (m) REVERT: O 222 PHE cc_start: 0.6063 (OUTLIER) cc_final: 0.5622 (m-10) REVERT: O 268 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: O 296 ASP cc_start: 0.5849 (m-30) cc_final: 0.5563 (m-30) REVERT: P 270 LYS cc_start: 0.7621 (tppt) cc_final: 0.7300 (tptt) REVERT: P 453 MET cc_start: 0.7730 (mmp) cc_final: 0.7152 (mtm) REVERT: R 105 MET cc_start: 0.8099 (tpp) cc_final: 0.7148 (tpt) REVERT: R 136 MET cc_start: 0.7248 (mpp) cc_final: 0.6032 (mtt) outliers start: 25 outliers final: 16 residues processed: 123 average time/residue: 0.1895 time to fit residues: 32.5488 Evaluate side-chains 111 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 222 PHE Chi-restraints excluded: chain O residue 256 VAL Chi-restraints excluded: chain O residue 268 PHE Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 273 GLU Chi-restraints excluded: chain P residue 452 ASP Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 556 MET Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain R residue 191 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 459 ASN ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8291 Z= 0.190 Angle : 0.698 13.311 11352 Z= 0.355 Chirality : 0.043 0.283 1220 Planarity : 0.003 0.032 1329 Dihedral : 19.098 160.854 1394 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.55 % Allowed : 22.70 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.29), residues: 884 helix: 1.06 (0.29), residues: 323 sheet: -0.23 (0.43), residues: 157 loop : -0.61 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP P 414 HIS 0.004 0.001 HIS O 223 PHE 0.017 0.002 PHE O 305 TYR 0.026 0.001 TYR O 317 ARG 0.006 0.000 ARG O 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: O 219 THR cc_start: 0.4324 (OUTLIER) cc_final: 0.3900 (m) REVERT: O 268 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: O 283 ASP cc_start: 0.6970 (p0) cc_final: 0.6396 (m-30) REVERT: O 296 ASP cc_start: 0.5959 (m-30) cc_final: 0.5358 (m-30) REVERT: P 270 LYS cc_start: 0.7722 (tppt) cc_final: 0.7317 (tptt) REVERT: P 453 MET cc_start: 0.7792 (mmp) cc_final: 0.7184 (mtm) REVERT: R 105 MET cc_start: 0.8117 (tpp) cc_final: 0.7226 (tpt) REVERT: R 136 MET cc_start: 0.7265 (mpp) cc_final: 0.6042 (mtt) outliers start: 20 outliers final: 14 residues processed: 114 average time/residue: 0.1888 time to fit residues: 30.5214 Evaluate side-chains 110 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 268 PHE Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain O residue 323 ASN Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 273 GLU Chi-restraints excluded: chain P residue 452 ASP Chi-restraints excluded: chain P residue 477 VAL Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 556 MET Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 30 optimal weight: 0.2980 chunk 75 optimal weight: 0.0370 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 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 = 0.3965 r_free = 0.3965 target = 0.106163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.097929 restraints weight = 32574.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.099436 restraints weight = 19483.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.100485 restraints weight = 12941.827| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8291 Z= 0.189 Angle : 0.693 13.632 11352 Z= 0.353 Chirality : 0.042 0.212 1220 Planarity : 0.003 0.030 1329 Dihedral : 19.053 162.281 1394 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.17 % Allowed : 23.72 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.29), residues: 884 helix: 1.04 (0.29), residues: 322 sheet: -0.24 (0.42), residues: 157 loop : -0.59 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP P 414 HIS 0.003 0.001 HIS O 223 PHE 0.017 0.002 PHE O 305 TYR 0.029 0.001 TYR O 317 ARG 0.007 0.000 ARG O 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1934.59 seconds wall clock time: 36 minutes 8.78 seconds (2168.78 seconds total)