Starting phenix.real_space_refine on Tue Feb 13 11:41:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/02_2024/8gnj_34166_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/02_2024/8gnj_34166.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/02_2024/8gnj_34166_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/02_2024/8gnj_34166_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/02_2024/8gnj_34166_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/02_2024/8gnj_34166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/02_2024/8gnj_34166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/02_2024/8gnj_34166_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/02_2024/8gnj_34166_updated.pdb" } resolution = 3.78 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= 0.015 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 1 5.49 5 S 28 5.16 5 C 3670 2.51 5 N 1042 2.21 5 O 1091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B GLU 604": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 689": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5832 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3821 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 16, 'TRANS': 475} Chain: "B" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1125 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "C" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.82, per 1000 atoms: 0.66 Number of scatterers: 5832 At special positions: 0 Unit cell: (92.536, 93.612, 117.284, 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 28 16.00 P 1 15.00 O 1091 8.00 N 1042 7.00 C 3670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 96 " distance=2.04 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: 2.37 Conformation dependent library (CDL) restraints added in 1.3 seconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 3 sheets defined 50.8% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 59 through 79 removed outlier: 3.514A pdb=" N LEU A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 3.917A pdb=" N GLN A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 104 removed outlier: 4.684A pdb=" N GLN A 97 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 101 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 102 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 122 removed outlier: 3.673A pdb=" N GLN A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A 121 " --> pdb=" O CYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 139 through 150 removed outlier: 4.029A pdb=" N ARG A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 4.115A pdb=" N ASP A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 removed outlier: 3.544A pdb=" N LEU A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.922A pdb=" N ARG A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 220 through 236 Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.942A pdb=" N VAL A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.578A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 No H-bonds generated for 'chain 'A' and resid 284 through 287' Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.508A pdb=" N GLU A 297 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 339 through 357 removed outlier: 3.606A pdb=" N ALA A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.662A pdb=" N SER A 366 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 378 Processing helix chain 'A' and resid 384 through 397 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 427 through 435 removed outlier: 3.803A pdb=" N CYS A 430 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU A 431 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 433 " --> pdb=" O CYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 460 through 476 removed outlier: 4.052A pdb=" N GLU A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 475 " --> pdb=" O THR A 471 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.747A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 508 removed outlier: 3.568A pdb=" N ARG A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR A 503 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A 507 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS A 508 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 532 through 543 Processing helix chain 'B' and resid 575 through 587 removed outlier: 3.852A pdb=" N HIS B 587 " --> pdb=" O HIS B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 613 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 673 through 677 removed outlier: 3.716A pdb=" N THR B 677 " --> pdb=" O ALA B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.653A pdb=" N ASN B 616 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N SER B 567 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 618 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 654 " --> pdb=" O LEU B 619 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.633A pdb=" N SER C 8 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 11 through 13 removed outlier: 3.783A pdb=" N ALA C 50 " --> pdb=" O TRP C 37 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ARG C 39 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL C 48 " --> pdb=" O ARG C 39 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 531 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: 1.62 Time building geometry restraints manager: 2.59 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: 1662 1.33 - 1.45: 1102 1.45 - 1.58: 3127 1.58 - 1.70: 1 1.70 - 1.82: 38 Bond restraints: 5930 Sorted by residual: bond pdb=" C3R NMN A1001 " pdb=" C4R NMN A1001 " ideal model delta sigma weight residual 1.304 1.532 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C4R NMN A1001 " pdb=" O4R NMN A1001 " ideal model delta sigma weight residual 1.615 1.442 0.173 2.00e-02 2.50e+03 7.50e+01 bond pdb=" C7 NMN A1001 " pdb=" N7 NMN A1001 " ideal model delta sigma weight residual 1.451 1.322 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" C1R NMN A1001 " pdb=" O4R NMN A1001 " ideal model delta sigma weight residual 1.305 1.409 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C SER A 319 " pdb=" O SER A 319 " ideal model delta sigma weight residual 1.236 1.284 -0.047 1.16e-02 7.43e+03 1.65e+01 ... (remaining 5925 not shown) Histogram of bond angle deviations from ideal: 97.10 - 104.49: 78 104.49 - 111.88: 2685 111.88 - 119.28: 2339 119.28 - 126.67: 2838 126.67 - 134.07: 86 Bond angle restraints: 8026 Sorted by residual: angle pdb=" N LYS A 80 " pdb=" CA LYS A 80 " pdb=" C LYS A 80 " ideal model delta sigma weight residual 113.20 105.31 7.89 1.21e+00 6.83e-01 4.25e+01 angle pdb=" N PRO A 549 " pdb=" CA PRO A 549 " pdb=" CB PRO A 549 " ideal model delta sigma weight residual 103.00 97.73 5.27 1.10e+00 8.26e-01 2.29e+01 angle pdb=" C GLU A 284 " pdb=" N ARG A 285 " pdb=" CA ARG A 285 " ideal model delta sigma weight residual 121.58 112.70 8.88 1.95e+00 2.63e-01 2.07e+01 angle pdb=" N LEU A 79 " pdb=" CA LEU A 79 " pdb=" C LEU A 79 " ideal model delta sigma weight residual 112.23 106.58 5.65 1.26e+00 6.30e-01 2.01e+01 angle pdb=" N HIS A 547 " pdb=" CA HIS A 547 " pdb=" C HIS A 547 " ideal model delta sigma weight residual 111.54 105.63 5.91 1.36e+00 5.41e-01 1.89e+01 ... (remaining 8021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 3225 17.51 - 35.02: 285 35.02 - 52.53: 57 52.53 - 70.04: 25 70.04 - 87.55: 9 Dihedral angle restraints: 3601 sinusoidal: 1458 harmonic: 2143 Sorted by residual: dihedral pdb=" CA VAL A 95 " pdb=" C VAL A 95 " pdb=" N PHE A 96 " pdb=" CA PHE A 96 " ideal model delta harmonic sigma weight residual 180.00 -153.87 -26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA GLY A 84 " pdb=" C GLY A 84 " pdb=" N ALA A 85 " pdb=" CA ALA A 85 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LYS C 76 " pdb=" C LYS C 76 " pdb=" N ASN C 77 " pdb=" CA ASN C 77 " ideal model delta harmonic sigma weight residual -180.00 -161.95 -18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 3598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 736 0.085 - 0.170: 152 0.170 - 0.256: 25 0.256 - 0.341: 2 0.341 - 0.426: 1 Chirality restraints: 916 Sorted by residual: chirality pdb=" CG LEU A 148 " pdb=" CB LEU A 148 " pdb=" CD1 LEU A 148 " pdb=" CD2 LEU A 148 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CA LYS A 80 " pdb=" N LYS A 80 " pdb=" C LYS A 80 " pdb=" CB LYS A 80 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA THR A 318 " pdb=" N THR A 318 " pdb=" C THR A 318 " pdb=" CB THR A 318 " both_signs ideal model delta sigma weight residual False 2.53 2.82 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 913 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 99 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C VAL A 99 " -0.073 2.00e-02 2.50e+03 pdb=" O VAL A 99 " 0.027 2.00e-02 2.50e+03 pdb=" N GLU A 100 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 545 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C MET A 545 " 0.069 2.00e-02 2.50e+03 pdb=" O MET A 545 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU A 546 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 63 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C ASP A 63 " 0.060 2.00e-02 2.50e+03 pdb=" O ASP A 63 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA A 64 " -0.020 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 34 2.43 - 3.05: 3610 3.05 - 3.66: 8998 3.66 - 4.28: 12663 4.28 - 4.90: 20637 Nonbonded interactions: 45942 Sorted by model distance: nonbonded pdb=" NH1 ARG A 216 " pdb=" NE2 GLN B 688 " model vdw 1.811 3.200 nonbonded pdb=" OE2 GLU A 400 " pdb=" O VAL A 401 " model vdw 2.030 3.040 nonbonded pdb=" CD1 LEU A 76 " pdb=" NZ LYS A 80 " model vdw 2.184 3.540 nonbonded pdb=" OG1 THR A 447 " pdb=" OE1 GLU A 450 " model vdw 2.200 2.440 nonbonded pdb=" OD1 ASP A 441 " pdb=" OH TYR A 503 " model vdw 2.258 2.440 ... (remaining 45937 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: 2.710 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: 6.600 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.460 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.012 0.228 5930 Z= 0.820 Angle : 1.338 14.332 8026 Z= 0.718 Chirality : 0.072 0.426 916 Planarity : 0.008 0.059 1040 Dihedral : 15.505 87.554 2214 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % 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: -3.73 (0.26), residues: 740 helix: -3.26 (0.18), residues: 384 sheet: -0.37 (0.71), residues: 56 loop : -1.50 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 638 HIS 0.019 0.003 HIS A 516 PHE 0.022 0.003 PHE A 96 TYR 0.011 0.003 TYR A 213 ARG 0.045 0.002 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.9160 (t80) cc_final: 0.8843 (t80) REVERT: A 284 GLU cc_start: 0.6353 (pt0) cc_final: 0.5927 (pt0) REVERT: A 312 LEU cc_start: 0.9201 (mt) cc_final: 0.8943 (mt) REVERT: A 326 ASP cc_start: 0.8951 (t0) cc_final: 0.8740 (t0) REVERT: A 335 ASP cc_start: 0.8176 (p0) cc_final: 0.7931 (p0) REVERT: A 391 LYS cc_start: 0.9065 (mttp) cc_final: 0.8590 (mttp) REVERT: B 581 LYS cc_start: 0.8836 (tptt) cc_final: 0.8428 (tptt) REVERT: B 606 LYS cc_start: 0.6862 (ttpt) cc_final: 0.6610 (ttpt) REVERT: B 617 PHE cc_start: 0.8252 (t80) cc_final: 0.7985 (t80) REVERT: C 14 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7692 (mm-40) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2604 time to fit residues: 73.7609 Evaluate side-chains 178 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5930 Z= 0.260 Angle : 0.718 9.397 8026 Z= 0.350 Chirality : 0.044 0.222 916 Planarity : 0.005 0.047 1040 Dihedral : 6.082 82.857 822 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.42 % Allowed : 15.94 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.29), residues: 740 helix: -1.91 (0.24), residues: 389 sheet: -0.43 (0.61), residues: 67 loop : -1.05 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 638 HIS 0.009 0.001 HIS A 516 PHE 0.024 0.003 PHE B 565 TYR 0.012 0.001 TYR A 348 ARG 0.008 0.001 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 TRP cc_start: 0.8145 (m-10) cc_final: 0.7932 (m-10) REVERT: A 249 ARG cc_start: 0.8520 (mmm160) cc_final: 0.8316 (mmm160) REVERT: A 310 ARG cc_start: 0.4106 (ttt180) cc_final: 0.3578 (ttm170) REVERT: A 335 ASP cc_start: 0.8272 (p0) cc_final: 0.8023 (p0) REVERT: A 497 ARG cc_start: 0.8394 (mtt180) cc_final: 0.8194 (mtp85) REVERT: B 581 LYS cc_start: 0.8811 (tptt) cc_final: 0.8468 (tptt) REVERT: B 589 PHE cc_start: 0.7963 (m-80) cc_final: 0.7662 (m-80) REVERT: B 617 PHE cc_start: 0.8306 (t80) cc_final: 0.7912 (t80) REVERT: C 14 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7570 (mm-40) outliers start: 15 outliers final: 10 residues processed: 190 average time/residue: 0.2282 time to fit residues: 53.1683 Evaluate side-chains 178 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 0.0570 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 269 HIS ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5930 Z= 0.229 Angle : 0.667 9.774 8026 Z= 0.321 Chirality : 0.043 0.195 916 Planarity : 0.004 0.041 1040 Dihedral : 6.088 88.365 822 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.19 % Allowed : 18.20 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.30), residues: 740 helix: -1.17 (0.26), residues: 376 sheet: 0.24 (0.69), residues: 57 loop : -0.67 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 638 HIS 0.006 0.001 HIS A 190 PHE 0.023 0.002 PHE A 192 TYR 0.011 0.001 TYR C 54 ARG 0.010 0.001 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 176 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8185 (pp20) REVERT: A 133 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7579 (mt) REVERT: A 149 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8651 (mm-30) REVERT: A 180 LEU cc_start: 0.9266 (tt) cc_final: 0.9037 (tp) REVERT: A 193 LYS cc_start: 0.8761 (ttmm) cc_final: 0.8503 (mtmm) REVERT: A 214 TRP cc_start: 0.8108 (m-10) cc_final: 0.7871 (m-10) REVERT: A 310 ARG cc_start: 0.3965 (ttt180) cc_final: 0.3348 (ttm170) REVERT: A 335 ASP cc_start: 0.8323 (p0) cc_final: 0.8054 (p0) REVERT: A 348 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7678 (t80) REVERT: B 581 LYS cc_start: 0.8806 (tptt) cc_final: 0.8510 (tptt) REVERT: B 606 LYS cc_start: 0.6538 (ttpt) cc_final: 0.6106 (ttpt) REVERT: B 612 MET cc_start: 0.8507 (mmp) cc_final: 0.7890 (mtm) REVERT: B 617 PHE cc_start: 0.8348 (t80) cc_final: 0.8001 (t80) REVERT: B 637 ASP cc_start: 0.6280 (p0) cc_final: 0.5615 (t0) REVERT: C 14 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7670 (mm-40) outliers start: 26 outliers final: 17 residues processed: 187 average time/residue: 0.2339 time to fit residues: 53.4917 Evaluate side-chains 182 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5930 Z= 0.281 Angle : 0.700 9.391 8026 Z= 0.335 Chirality : 0.044 0.216 916 Planarity : 0.004 0.040 1040 Dihedral : 6.192 88.429 822 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.83 % Allowed : 19.16 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.31), residues: 740 helix: -0.91 (0.27), residues: 370 sheet: 0.04 (0.61), residues: 67 loop : -0.58 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 638 HIS 0.008 0.001 HIS A 190 PHE 0.015 0.002 PHE A 308 TYR 0.013 0.001 TYR C 54 ARG 0.010 0.001 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8225 (pp20) REVERT: A 114 GLN cc_start: 0.8746 (pm20) cc_final: 0.8327 (pm20) REVERT: A 180 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9082 (tp) REVERT: A 214 TRP cc_start: 0.8071 (m-10) cc_final: 0.7804 (m-10) REVERT: A 255 PHE cc_start: 0.9038 (t80) cc_final: 0.8780 (t80) REVERT: A 310 ARG cc_start: 0.4303 (ttt180) cc_final: 0.3595 (ttm170) REVERT: A 473 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8435 (tp) REVERT: B 581 LYS cc_start: 0.8794 (tptt) cc_final: 0.8526 (tptt) REVERT: B 612 MET cc_start: 0.8424 (mmp) cc_final: 0.7922 (mtm) REVERT: B 617 PHE cc_start: 0.8315 (t80) cc_final: 0.7898 (t80) REVERT: B 637 ASP cc_start: 0.6322 (p0) cc_final: 0.5418 (t0) outliers start: 30 outliers final: 23 residues processed: 187 average time/residue: 0.2290 time to fit residues: 53.0011 Evaluate side-chains 185 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5930 Z= 0.230 Angle : 0.678 8.760 8026 Z= 0.323 Chirality : 0.043 0.221 916 Planarity : 0.004 0.041 1040 Dihedral : 6.130 88.643 822 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.19 % Allowed : 20.13 % Favored : 75.68 % 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: -0.92 (0.31), residues: 740 helix: -0.61 (0.28), residues: 364 sheet: 0.11 (0.61), residues: 67 loop : -0.56 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 103 HIS 0.005 0.001 HIS A 190 PHE 0.014 0.001 PHE A 308 TYR 0.010 0.001 TYR C 54 ARG 0.010 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8230 (pp20) REVERT: A 114 GLN cc_start: 0.8728 (pm20) cc_final: 0.8378 (pm20) REVERT: A 180 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9080 (tp) REVERT: A 214 TRP cc_start: 0.8021 (m-10) cc_final: 0.7753 (m-10) REVERT: A 310 ARG cc_start: 0.4263 (ttt180) cc_final: 0.3460 (ttm170) REVERT: A 329 ARG cc_start: 0.7667 (ttm-80) cc_final: 0.7452 (mtp-110) REVERT: A 391 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8709 (mtmm) REVERT: B 581 LYS cc_start: 0.8848 (tptt) cc_final: 0.8591 (tptt) REVERT: B 586 LEU cc_start: 0.8557 (mm) cc_final: 0.8348 (mm) REVERT: B 612 MET cc_start: 0.8448 (mmp) cc_final: 0.8118 (mtm) REVERT: B 617 PHE cc_start: 0.8325 (t80) cc_final: 0.7925 (t80) REVERT: B 637 ASP cc_start: 0.6204 (p0) cc_final: 0.5434 (t0) REVERT: B 693 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7759 (tm-30) outliers start: 26 outliers final: 22 residues processed: 183 average time/residue: 0.2229 time to fit residues: 50.3943 Evaluate side-chains 187 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.0570 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5930 Z= 0.180 Angle : 0.638 9.421 8026 Z= 0.301 Chirality : 0.041 0.157 916 Planarity : 0.004 0.046 1040 Dihedral : 5.842 86.423 822 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.31 % Allowed : 21.26 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.32), residues: 740 helix: -0.38 (0.28), residues: 369 sheet: 0.52 (0.70), residues: 57 loop : -0.46 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 103 HIS 0.006 0.001 HIS B 640 PHE 0.014 0.001 PHE A 308 TYR 0.009 0.001 TYR A 348 ARG 0.011 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8689 (pm20) cc_final: 0.8341 (pm20) REVERT: A 180 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9041 (tp) REVERT: A 214 TRP cc_start: 0.7976 (m-10) cc_final: 0.7732 (m-10) REVERT: A 473 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8318 (tp) REVERT: B 581 LYS cc_start: 0.8845 (tptt) cc_final: 0.8597 (tptt) REVERT: B 586 LEU cc_start: 0.8537 (mm) cc_final: 0.8291 (mm) REVERT: B 612 MET cc_start: 0.8380 (mmp) cc_final: 0.8152 (mtm) REVERT: B 617 PHE cc_start: 0.8350 (t80) cc_final: 0.7967 (t80) REVERT: B 637 ASP cc_start: 0.6155 (p0) cc_final: 0.5585 (t0) REVERT: C 95 TYR cc_start: 0.8930 (m-80) cc_final: 0.8687 (m-80) outliers start: 33 outliers final: 24 residues processed: 187 average time/residue: 0.2371 time to fit residues: 54.5216 Evaluate side-chains 190 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.0670 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 HIS ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5930 Z= 0.200 Angle : 0.651 9.344 8026 Z= 0.310 Chirality : 0.043 0.253 916 Planarity : 0.004 0.038 1040 Dihedral : 5.812 84.453 822 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.15 % Allowed : 23.35 % Favored : 71.50 % 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: -0.54 (0.32), residues: 740 helix: -0.29 (0.28), residues: 368 sheet: 0.62 (0.69), residues: 57 loop : -0.43 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 103 HIS 0.007 0.001 HIS A 190 PHE 0.014 0.001 PHE A 308 TYR 0.009 0.001 TYR A 348 ARG 0.009 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 170 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9097 (tp) REVERT: A 473 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8540 (tp) REVERT: B 581 LYS cc_start: 0.8835 (tptt) cc_final: 0.8604 (tptt) REVERT: B 586 LEU cc_start: 0.8524 (mm) cc_final: 0.8241 (mm) REVERT: B 617 PHE cc_start: 0.8353 (t80) cc_final: 0.7988 (t80) REVERT: B 638 TRP cc_start: 0.7033 (t-100) cc_final: 0.6811 (t-100) REVERT: C 95 TYR cc_start: 0.8923 (m-80) cc_final: 0.8684 (m-80) outliers start: 32 outliers final: 24 residues processed: 185 average time/residue: 0.2314 time to fit residues: 52.5698 Evaluate side-chains 189 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5930 Z= 0.221 Angle : 0.683 9.401 8026 Z= 0.327 Chirality : 0.043 0.238 916 Planarity : 0.004 0.038 1040 Dihedral : 5.889 88.027 822 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.48 % Allowed : 24.15 % Favored : 70.37 % 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: -0.51 (0.32), residues: 740 helix: -0.28 (0.28), residues: 363 sheet: 0.56 (0.69), residues: 57 loop : -0.39 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 103 HIS 0.007 0.001 HIS A 190 PHE 0.014 0.001 PHE A 308 TYR 0.010 0.001 TYR C 54 ARG 0.010 0.001 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8055 (t) cc_final: 0.7855 (t) REVERT: A 101 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7309 (tp30) REVERT: A 139 GLU cc_start: 0.6550 (pm20) cc_final: 0.6116 (pm20) REVERT: A 180 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9122 (tp) REVERT: A 329 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7718 (mtp-110) REVERT: A 450 GLU cc_start: 0.8012 (mp0) cc_final: 0.7570 (mp0) REVERT: A 473 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8589 (tp) REVERT: B 581 LYS cc_start: 0.8841 (tptt) cc_final: 0.8605 (tptt) REVERT: B 586 LEU cc_start: 0.8506 (mm) cc_final: 0.8206 (mm) REVERT: B 617 PHE cc_start: 0.8362 (t80) cc_final: 0.8025 (t80) REVERT: B 637 ASP cc_start: 0.5946 (p0) cc_final: 0.4953 (t0) REVERT: B 642 GLU cc_start: 0.7214 (mp0) cc_final: 0.6846 (mp0) REVERT: C 95 TYR cc_start: 0.8946 (m-80) cc_final: 0.8699 (m-80) outliers start: 34 outliers final: 25 residues processed: 180 average time/residue: 0.2250 time to fit residues: 50.5634 Evaluate side-chains 186 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5930 Z= 0.305 Angle : 0.727 10.523 8026 Z= 0.355 Chirality : 0.045 0.251 916 Planarity : 0.004 0.038 1040 Dihedral : 6.357 87.976 822 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.15 % Allowed : 24.32 % Favored : 70.53 % 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: -0.64 (0.32), residues: 740 helix: -0.37 (0.28), residues: 370 sheet: 0.20 (0.62), residues: 67 loop : -0.42 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 214 HIS 0.007 0.001 HIS A 190 PHE 0.017 0.002 PHE A 308 TYR 0.012 0.001 TYR C 54 ARG 0.009 0.001 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 180 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9152 (tp) REVERT: A 329 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7802 (mtp-110) REVERT: A 348 TYR cc_start: 0.7977 (t80) cc_final: 0.7730 (t80) REVERT: A 514 LEU cc_start: 0.8985 (tp) cc_final: 0.8614 (tt) REVERT: B 586 LEU cc_start: 0.8506 (mm) cc_final: 0.8189 (mm) REVERT: B 617 PHE cc_start: 0.8389 (t80) cc_final: 0.8147 (t80) REVERT: B 637 ASP cc_start: 0.6059 (p0) cc_final: 0.5105 (t0) REVERT: C 95 TYR cc_start: 0.8966 (m-80) cc_final: 0.8699 (m-80) outliers start: 32 outliers final: 26 residues processed: 178 average time/residue: 0.2225 time to fit residues: 49.2278 Evaluate side-chains 182 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 0.0670 chunk 67 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5930 Z= 0.195 Angle : 0.704 9.831 8026 Z= 0.339 Chirality : 0.043 0.211 916 Planarity : 0.003 0.037 1040 Dihedral : 6.185 89.740 822 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.38 % Allowed : 25.76 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.47 (0.32), residues: 740 helix: -0.22 (0.28), residues: 363 sheet: 0.57 (0.68), residues: 57 loop : -0.41 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 103 HIS 0.008 0.001 HIS A 190 PHE 0.017 0.002 PHE B 603 TYR 0.010 0.001 TYR C 54 ARG 0.009 0.001 ARG A 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9091 (tp) REVERT: A 245 MET cc_start: 0.8302 (mmt) cc_final: 0.8025 (mmt) REVERT: A 450 GLU cc_start: 0.8046 (mp0) cc_final: 0.7618 (mp0) REVERT: B 617 PHE cc_start: 0.8401 (t80) cc_final: 0.8197 (t80) REVERT: B 637 ASP cc_start: 0.5661 (p0) cc_final: 0.4871 (t0) REVERT: C 95 TYR cc_start: 0.8932 (m-80) cc_final: 0.8706 (m-80) outliers start: 21 outliers final: 18 residues processed: 179 average time/residue: 0.2070 time to fit residues: 46.6734 Evaluate side-chains 179 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 42 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.142418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114928 restraints weight = 11436.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112910 restraints weight = 10116.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113788 restraints weight = 10237.245| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5930 Z= 0.250 Angle : 0.752 11.825 8026 Z= 0.361 Chirality : 0.045 0.197 916 Planarity : 0.004 0.037 1040 Dihedral : 6.186 89.363 822 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.54 % Allowed : 26.09 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.32), residues: 740 helix: -0.13 (0.28), residues: 362 sheet: 0.53 (0.68), residues: 57 loop : -0.39 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP A 103 HIS 0.007 0.001 HIS B 640 PHE 0.016 0.002 PHE A 308 TYR 0.011 0.001 TYR C 54 ARG 0.011 0.001 ARG A 517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1895.55 seconds wall clock time: 34 minutes 38.69 seconds (2078.69 seconds total)