Starting phenix.real_space_refine on Thu Feb 15 09:35:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emv_28266/02_2024/8emv_28266.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emv_28266/02_2024/8emv_28266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emv_28266/02_2024/8emv_28266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emv_28266/02_2024/8emv_28266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emv_28266/02_2024/8emv_28266.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emv_28266/02_2024/8emv_28266.pdb" } resolution = 3.6 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 Anisotropic ADP refinement not supported. Converting 5939 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 31 5.16 5 C 3795 2.51 5 N 1013 2.21 5 O 1109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 391": "OD1" <-> "OD2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A ASP 435": "OD1" <-> "OD2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A ASP 576": "OD1" <-> "OD2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A PHE 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "A ARG 872": "NH1" <-> "NH2" 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: 5949 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5949 Unusual residues: {' CA': 1} Classifications: {'peptide': 747, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 47, 'TRANS': 699, None: 1} Not linked: pdbres="GLY A 881 " pdbres=" CA A1301 " Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 3.52, per 1000 atoms: 0.59 Number of scatterers: 5949 At special positions: 0 Unit cell: (62.64, 98.28, 103.68, 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) Ca 1 19.99 S 31 16.00 O 1109 8.00 N 1013 7.00 C 3795 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: 1.90 Conformation dependent library (CDL) restraints added in 1.2 seconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 6 sheets defined 33.3% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.743A pdb=" N ARG A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 148 through 163 removed outlier: 3.503A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 removed outlier: 4.287A pdb=" N ILE A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 3.641A pdb=" N GLU A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.662A pdb=" N ASP A 227 " --> pdb=" O ARG A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 268 through 280 removed outlier: 4.887A pdb=" N LEU A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 288 removed outlier: 3.736A pdb=" N GLU A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 300 removed outlier: 3.639A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.927A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 418 through 434 removed outlier: 3.672A pdb=" N PHE A 433 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 632 through 641 Processing helix chain 'A' and resid 661 through 666 Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.674A pdb=" N ARG A 706 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 816 No H-bonds generated for 'chain 'A' and resid 814 through 816' Processing helix chain 'A' and resid 868 through 881 removed outlier: 4.689A pdb=" N ALA A 878 " --> pdb=" O ARG A 874 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 65 removed outlier: 4.116A pdb=" N THR A 55 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR A 42 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 26 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.706A pdb=" N VAL A 361 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLU A 413 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 363 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 598 through 599 removed outlier: 5.978A pdb=" N GLU A 598 " --> pdb=" O MET A 617 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N SER A 619 " --> pdb=" O GLU A 598 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 644 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 618 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 671 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 781 through 786 removed outlier: 4.518A pdb=" N LYS A 785 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN A 726 " --> pdb=" O LYS A 785 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 839 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLY A 735 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA A 837 " --> pdb=" O GLY A 735 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 759 through 763 removed outlier: 5.058A pdb=" N LYS A 761 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 749 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ARG A 763 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 747 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLU A 800 " --> pdb=" O PHE A 805 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE A 805 " --> pdb=" O GLU A 800 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 570 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: 1.58 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1898 1.34 - 1.45: 878 1.45 - 1.57: 3246 1.57 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 6075 Sorted by residual: bond pdb=" C PRO A 370 " pdb=" N PRO A 371 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.20e-02 6.94e+03 2.04e+01 bond pdb=" C PRO A 454 " pdb=" N SER A 455 " ideal model delta sigma weight residual 1.329 1.233 0.095 3.03e-02 1.09e+03 9.92e+00 bond pdb=" C LEU A 835 " pdb=" N PRO A 836 " ideal model delta sigma weight residual 1.333 1.349 -0.016 1.17e-02 7.31e+03 1.99e+00 bond pdb=" CB CYS A 669 " pdb=" SG CYS A 669 " ideal model delta sigma weight residual 1.808 1.763 0.045 3.30e-02 9.18e+02 1.85e+00 bond pdb=" C LEU A 453 " pdb=" N PRO A 454 " ideal model delta sigma weight residual 1.330 1.346 -0.016 1.25e-02 6.40e+03 1.72e+00 ... (remaining 6070 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.39: 203 106.39 - 113.29: 3218 113.29 - 120.19: 2281 120.19 - 127.09: 2463 127.09 - 133.99: 62 Bond angle restraints: 8227 Sorted by residual: angle pdb=" C SER A 200 " pdb=" N GLU A 201 " pdb=" CA GLU A 201 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C GLY A 380 " pdb=" N PHE A 381 " pdb=" CA PHE A 381 " ideal model delta sigma weight residual 122.82 128.33 -5.51 1.42e+00 4.96e-01 1.50e+01 angle pdb=" N LEU A 835 " pdb=" CA LEU A 835 " pdb=" C LEU A 835 " ideal model delta sigma weight residual 109.81 117.69 -7.88 2.21e+00 2.05e-01 1.27e+01 angle pdb=" N PRO A 370 " pdb=" CA PRO A 370 " pdb=" C PRO A 370 " ideal model delta sigma weight residual 110.70 114.57 -3.87 1.22e+00 6.72e-01 1.00e+01 angle pdb=" CA PRO A 370 " pdb=" C PRO A 370 " pdb=" N PRO A 371 " ideal model delta sigma weight residual 117.93 121.50 -3.57 1.20e+00 6.94e-01 8.86e+00 ... (remaining 8222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 3225 16.47 - 32.94: 405 32.94 - 49.41: 65 49.41 - 65.88: 23 65.88 - 82.35: 7 Dihedral angle restraints: 3725 sinusoidal: 1539 harmonic: 2186 Sorted by residual: dihedral pdb=" CA LYS A 238 " pdb=" C LYS A 238 " pdb=" N PRO A 239 " pdb=" CA PRO A 239 " ideal model delta harmonic sigma weight residual 180.00 -150.53 -29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LYS A 236 " pdb=" C LYS A 236 " pdb=" N GLY A 237 " pdb=" CA GLY A 237 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PRO A 239 " pdb=" C PRO A 239 " pdb=" N TYR A 240 " pdb=" CA TYR A 240 " ideal model delta harmonic sigma weight residual 180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 3722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 548 0.039 - 0.078: 254 0.078 - 0.117: 77 0.117 - 0.156: 26 0.156 - 0.195: 10 Chirality restraints: 915 Sorted by residual: chirality pdb=" CB VAL A 116 " pdb=" CA VAL A 116 " pdb=" CG1 VAL A 116 " pdb=" CG2 VAL A 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CB VAL A 621 " pdb=" CA VAL A 621 " pdb=" CG1 VAL A 621 " pdb=" CG2 VAL A 621 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CA LEU A 835 " pdb=" N LEU A 835 " pdb=" C LEU A 835 " pdb=" CB LEU A 835 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 912 not shown) Planarity restraints: 1071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 369 " 0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO A 370 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 111 " -0.041 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO A 112 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 321 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO A 322 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.031 5.00e-02 4.00e+02 ... (remaining 1068 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2031 2.85 - 3.36: 5011 3.36 - 3.88: 9084 3.88 - 4.39: 10476 4.39 - 4.90: 18462 Nonbonded interactions: 45064 Sorted by model distance: nonbonded pdb=" N ASP A 225 " pdb=" OD1 ASP A 225 " model vdw 2.339 2.520 nonbonded pdb=" O SER A 591 " pdb=" OG SER A 591 " model vdw 2.340 2.440 nonbonded pdb=" OE1 GLU A 577 " pdb=" OG SER A 581 " model vdw 2.356 2.440 nonbonded pdb=" N ASP A 125 " pdb=" OD1 ASP A 125 " model vdw 2.377 2.520 nonbonded pdb=" O SER A 404 " pdb=" OG SER A 404 " model vdw 2.382 2.440 ... (remaining 45059 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 3.890 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 18.850 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 : 0.007 0.095 6075 Z= 0.453 Angle : 0.813 8.282 8227 Z= 0.461 Chirality : 0.052 0.195 915 Planarity : 0.007 0.070 1071 Dihedral : 15.162 82.355 2307 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % 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: -4.26 (0.24), residues: 739 helix: -3.01 (0.23), residues: 235 sheet: -2.29 (0.41), residues: 124 loop : -2.89 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 54 HIS 0.005 0.001 HIS A 808 PHE 0.018 0.002 PHE A 799 TYR 0.019 0.002 TYR A 648 ARG 0.012 0.001 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.772 Fit side-chains REVERT: A 228 LYS cc_start: 0.8684 (tttt) cc_final: 0.8369 (tptp) REVERT: A 291 MET cc_start: 0.8471 (ttm) cc_final: 0.8129 (ttm) REVERT: A 444 LYS cc_start: 0.8438 (tttm) cc_final: 0.8071 (tptm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2942 time to fit residues: 29.1159 Evaluate side-chains 56 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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: 1.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6075 Z= 0.166 Angle : 0.507 5.258 8227 Z= 0.266 Chirality : 0.042 0.152 915 Planarity : 0.005 0.044 1071 Dihedral : 4.616 25.571 816 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.07 % Allowed : 12.08 % Favored : 86.85 % 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: -2.71 (0.27), residues: 739 helix: -0.98 (0.31), residues: 237 sheet: -2.06 (0.41), residues: 121 loop : -2.25 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 131 HIS 0.002 0.001 HIS A 808 PHE 0.030 0.001 PHE A 197 TYR 0.012 0.001 TYR A 299 ARG 0.004 0.000 ARG A 695 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.768 Fit side-chains REVERT: A 291 MET cc_start: 0.8438 (ttm) cc_final: 0.8103 (ttm) REVERT: A 444 LYS cc_start: 0.8454 (tttm) cc_final: 0.7985 (tptm) REVERT: A 719 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8765 (mm) REVERT: A 772 PHE cc_start: 0.7914 (t80) cc_final: 0.7670 (t80) outliers start: 7 outliers final: 5 residues processed: 76 average time/residue: 0.2105 time to fit residues: 20.8358 Evaluate side-chains 70 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 719 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 0.0970 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6075 Z= 0.125 Angle : 0.481 6.437 8227 Z= 0.244 Chirality : 0.041 0.164 915 Planarity : 0.004 0.046 1071 Dihedral : 4.126 23.831 816 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.53 % Allowed : 13.91 % Favored : 84.56 % 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: -1.77 (0.29), residues: 739 helix: 0.10 (0.34), residues: 238 sheet: -1.38 (0.45), residues: 121 loop : -1.96 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 131 HIS 0.001 0.000 HIS A 808 PHE 0.028 0.001 PHE A 197 TYR 0.008 0.001 TYR A 746 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8416 (tttm) cc_final: 0.7979 (tptm) REVERT: A 772 PHE cc_start: 0.7835 (t80) cc_final: 0.7593 (t80) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 0.2067 time to fit residues: 19.3836 Evaluate side-chains 66 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 0.0060 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 0.0030 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6075 Z= 0.121 Angle : 0.469 6.087 8227 Z= 0.237 Chirality : 0.041 0.165 915 Planarity : 0.004 0.046 1071 Dihedral : 3.899 23.187 816 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.68 % Allowed : 14.68 % Favored : 83.64 % 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: -1.23 (0.30), residues: 739 helix: 0.66 (0.35), residues: 238 sheet: -1.02 (0.46), residues: 126 loop : -1.76 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 776 HIS 0.002 0.000 HIS A 808 PHE 0.028 0.001 PHE A 197 TYR 0.008 0.001 TYR A 746 ARG 0.002 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8410 (tttm) cc_final: 0.8012 (tptm) REVERT: A 772 PHE cc_start: 0.7768 (t80) cc_final: 0.7510 (t80) outliers start: 11 outliers final: 6 residues processed: 74 average time/residue: 0.1882 time to fit residues: 18.8369 Evaluate side-chains 67 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 451 VAL 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: 1.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.0040 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6075 Z= 0.206 Angle : 0.500 6.323 8227 Z= 0.254 Chirality : 0.042 0.166 915 Planarity : 0.004 0.050 1071 Dihedral : 4.045 23.835 816 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.45 % Allowed : 15.29 % Favored : 82.26 % 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: -1.10 (0.31), residues: 739 helix: 0.73 (0.35), residues: 245 sheet: -0.90 (0.45), residues: 126 loop : -1.71 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 776 HIS 0.003 0.001 HIS A 808 PHE 0.028 0.001 PHE A 197 TYR 0.012 0.001 TYR A 299 ARG 0.003 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.8510 (ttm) cc_final: 0.8007 (tpp) REVERT: A 444 LYS cc_start: 0.8414 (tttm) cc_final: 0.8013 (tptm) REVERT: A 740 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.7903 (p0) outliers start: 16 outliers final: 11 residues processed: 74 average time/residue: 0.1969 time to fit residues: 19.3587 Evaluate side-chains 70 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 740 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6075 Z= 0.312 Angle : 0.550 6.319 8227 Z= 0.281 Chirality : 0.044 0.155 915 Planarity : 0.004 0.052 1071 Dihedral : 4.379 24.313 816 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.21 % Allowed : 15.44 % Favored : 81.35 % 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: -1.06 (0.31), residues: 739 helix: 0.83 (0.35), residues: 238 sheet: -1.01 (0.43), residues: 123 loop : -1.63 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 54 HIS 0.004 0.001 HIS A 808 PHE 0.028 0.002 PHE A 197 TYR 0.014 0.001 TYR A 299 ARG 0.004 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 56 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8427 (tttm) cc_final: 0.7998 (tptm) REVERT: A 740 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.7969 (p0) outliers start: 21 outliers final: 15 residues processed: 73 average time/residue: 0.1745 time to fit residues: 17.2094 Evaluate side-chains 70 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 740 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 39 optimal weight: 0.0770 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6075 Z= 0.138 Angle : 0.489 7.210 8227 Z= 0.248 Chirality : 0.042 0.159 915 Planarity : 0.004 0.051 1071 Dihedral : 4.020 22.212 816 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.60 % Allowed : 16.51 % Favored : 80.89 % 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: -0.70 (0.31), residues: 739 helix: 1.19 (0.36), residues: 233 sheet: -0.87 (0.44), residues: 126 loop : -1.40 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 776 HIS 0.002 0.000 HIS A 808 PHE 0.010 0.001 PHE A 799 TYR 0.009 0.001 TYR A 746 ARG 0.002 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 291 MET cc_start: 0.8496 (ttm) cc_final: 0.8132 (tpp) REVERT: A 444 LYS cc_start: 0.8413 (tttm) cc_final: 0.8054 (tptm) REVERT: A 740 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7853 (p0) outliers start: 17 outliers final: 12 residues processed: 71 average time/residue: 0.2173 time to fit residues: 20.5703 Evaluate side-chains 69 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 790 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.0870 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6075 Z= 0.146 Angle : 0.478 7.475 8227 Z= 0.243 Chirality : 0.041 0.162 915 Planarity : 0.004 0.051 1071 Dihedral : 3.883 21.915 816 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.60 % Allowed : 16.67 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.31), residues: 739 helix: 1.29 (0.36), residues: 233 sheet: -0.89 (0.44), residues: 124 loop : -1.25 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 776 HIS 0.002 0.000 HIS A 808 PHE 0.010 0.001 PHE A 799 TYR 0.009 0.001 TYR A 299 ARG 0.004 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 291 MET cc_start: 0.8489 (ttm) cc_final: 0.8124 (tpp) REVERT: A 444 LYS cc_start: 0.8408 (tttm) cc_final: 0.8062 (tptm) REVERT: A 740 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7877 (p0) outliers start: 17 outliers final: 14 residues processed: 73 average time/residue: 0.2005 time to fit residues: 19.3819 Evaluate side-chains 71 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 790 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.0000 chunk 66 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6075 Z= 0.129 Angle : 0.481 7.721 8227 Z= 0.241 Chirality : 0.041 0.158 915 Planarity : 0.004 0.050 1071 Dihedral : 3.766 21.175 816 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.99 % Allowed : 17.28 % Favored : 80.73 % 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: -0.43 (0.31), residues: 739 helix: 1.39 (0.36), residues: 233 sheet: -0.81 (0.44), residues: 121 loop : -1.18 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 776 HIS 0.001 0.000 HIS A 808 PHE 0.027 0.001 PHE A 197 TYR 0.008 0.001 TYR A 746 ARG 0.003 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 291 MET cc_start: 0.8465 (ttm) cc_final: 0.8114 (tpp) REVERT: A 444 LYS cc_start: 0.8424 (tttm) cc_final: 0.8096 (tptm) REVERT: A 617 MET cc_start: 0.8245 (ptm) cc_final: 0.7936 (ttp) REVERT: A 740 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7865 (p0) outliers start: 13 outliers final: 12 residues processed: 70 average time/residue: 0.2132 time to fit residues: 19.4946 Evaluate side-chains 71 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 790 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 0.0770 chunk 46 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6075 Z= 0.162 Angle : 0.485 7.833 8227 Z= 0.246 Chirality : 0.041 0.154 915 Planarity : 0.004 0.050 1071 Dihedral : 3.827 21.424 816 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.14 % Allowed : 17.28 % Favored : 80.58 % 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: -0.41 (0.31), residues: 739 helix: 1.41 (0.36), residues: 233 sheet: -0.80 (0.44), residues: 121 loop : -1.17 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 776 HIS 0.002 0.001 HIS A 808 PHE 0.027 0.001 PHE A 197 TYR 0.009 0.001 TYR A 299 ARG 0.004 0.000 ARG A 470 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 291 MET cc_start: 0.8482 (ttm) cc_final: 0.8071 (tpp) REVERT: A 444 LYS cc_start: 0.8427 (tttm) cc_final: 0.8103 (tptm) REVERT: A 740 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7874 (p0) outliers start: 14 outliers final: 13 residues processed: 71 average time/residue: 0.2133 time to fit residues: 19.7976 Evaluate side-chains 72 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 790 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: 0.0570 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.087898 restraints weight = 8999.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.089953 restraints weight = 6267.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.091351 restraints weight = 4988.085| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.002 0.025 6075 Z= 0.134 Angle : 0.475 7.878 8227 Z= 0.239 Chirality : 0.041 0.147 915 Planarity : 0.004 0.049 1071 Dihedral : 3.719 20.577 816 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.29 % Allowed : 17.13 % Favored : 80.58 % 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: -0.29 (0.31), residues: 739 helix: 1.51 (0.35), residues: 233 sheet: -0.75 (0.44), residues: 121 loop : -1.08 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 776 HIS 0.001 0.000 HIS A 808 PHE 0.027 0.001 PHE A 197 TYR 0.009 0.001 TYR A 746 ARG 0.003 0.000 ARG A 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1486.65 seconds wall clock time: 27 minutes 41.90 seconds (1661.90 seconds total)