Starting phenix.real_space_refine on Mon Mar 11 08:04:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/03_2024/8et9_28589_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/03_2024/8et9_28589.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/03_2024/8et9_28589_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/03_2024/8et9_28589_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/03_2024/8et9_28589_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/03_2024/8et9_28589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/03_2024/8et9_28589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/03_2024/8et9_28589_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/03_2024/8et9_28589_trim_updated.pdb" } resolution = 3.61 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= 0.003 sd= 0.047 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 S 26 5.16 5 C 2570 2.51 5 N 638 2.21 5 O 655 1.98 5 H 3796 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7685 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 7685 Unusual residues: {'WRF': 1} Classifications: {'peptide': 517, 'undetermined': 1} Link IDs: {'PTRANS': 27, 'TRANS': 489, None: 1} Not linked: pdbres="ARG A 534 " pdbres="WRF A 601 " Chain breaks: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 Time building chain proxies: 3.90, per 1000 atoms: 0.51 Number of scatterers: 7685 At special positions: 0 Unit cell: (118.8, 58.32, 68.04, 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 26 16.00 O 655 8.00 N 638 7.00 C 2570 6.00 H 3796 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 143 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.86 Conformation dependent library (CDL) restraints added in 771.4 milliseconds 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 950 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 1 sheets defined 71.0% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 17 through 43 removed outlier: 4.094A pdb=" N LEU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 31 " --> pdb=" O CYS A 27 " (cutoff:3.500A) Proline residue: A 35 - end of helix removed outlier: 3.879A pdb=" N VAL A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL A 41 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 62 removed outlier: 3.544A pdb=" N GLU A 58 " --> pdb=" O PRO A 54 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 73 removed outlier: 4.058A pdb=" N ASN A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.541A pdb=" N CYS A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 89' Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 146 through 174 removed outlier: 3.802A pdb=" N ASP A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR A 169 " --> pdb=" O MET A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 196 removed outlier: 3.962A pdb=" N ALA A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 228 removed outlier: 3.704A pdb=" N VAL A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLY A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 234 through 258 removed outlier: 3.936A pdb=" N GLN A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.507A pdb=" N LEU A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TRP A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N CYS A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.636A pdb=" N LYS A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 342 through 368 removed outlier: 3.936A pdb=" N LEU A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 401 removed outlier: 3.878A pdb=" N PHE A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Proline residue: A 389 - end of helix removed outlier: 4.912A pdb=" N ASP A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 422 Processing helix chain 'A' and resid 430 through 457 removed outlier: 3.965A pdb=" N THR A 434 " --> pdb=" O TRP A 430 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 455 " --> pdb=" O CYS A 451 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 491 removed outlier: 6.005A pdb=" N ASN A 464 " --> pdb=" O PHE A 461 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 467 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 468 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL A 469 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 473 " --> pdb=" O CYS A 470 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 481 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Proline residue: A 482 - end of helix removed outlier: 4.623A pdb=" N VAL A 485 " --> pdb=" O PRO A 482 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 490 " --> pdb=" O ARG A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 removed outlier: 3.707A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 530 Processing sheet with id= A, first strand: chain 'A' and resid 49 through 51 218 hydrogen bonds defined for protein. 594 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: 2.36 Time building geometry restraints manager: 6.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 3788 1.02 - 1.22: 23 1.22 - 1.41: 1637 1.41 - 1.61: 2304 1.61 - 1.81: 38 Bond restraints: 7790 Sorted by residual: bond pdb=" CA THR A 444 " pdb=" C THR A 444 " ideal model delta sigma weight residual 1.524 1.445 0.079 1.32e-02 5.74e+03 3.56e+01 bond pdb=" NE ARG A 440 " pdb=" HE ARG A 440 " ideal model delta sigma weight residual 0.860 0.969 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C TYR A 362 " pdb=" O TYR A 362 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.15e-02 7.56e+03 2.72e+01 bond pdb=" CA GLN A 242 " pdb=" C GLN A 242 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" C GLN A 242 " pdb=" O GLN A 242 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.17e-02 7.31e+03 1.11e+01 ... (remaining 7785 not shown) Histogram of bond angle deviations from ideal: 100.63 - 107.30: 285 107.30 - 113.97: 8988 113.97 - 120.64: 2859 120.64 - 127.31: 1887 127.31 - 133.98: 59 Bond angle restraints: 14078 Sorted by residual: angle pdb=" N THR A 444 " pdb=" CA THR A 444 " pdb=" C THR A 444 " ideal model delta sigma weight residual 111.69 104.82 6.87 1.23e+00 6.61e-01 3.12e+01 angle pdb=" C MET A 441 " pdb=" N GLY A 442 " pdb=" CA GLY A 442 " ideal model delta sigma weight residual 120.03 126.10 -6.07 1.12e+00 7.97e-01 2.94e+01 angle pdb=" O ILE A 443 " pdb=" C ILE A 443 " pdb=" N THR A 444 " ideal model delta sigma weight residual 121.87 116.41 5.46 1.01e+00 9.80e-01 2.92e+01 angle pdb=" O GLY A 439 " pdb=" C GLY A 439 " pdb=" N ARG A 440 " ideal model delta sigma weight residual 122.19 126.68 -4.49 9.60e-01 1.09e+00 2.19e+01 angle pdb=" CA GLY A 439 " pdb=" C GLY A 439 " pdb=" N ARG A 440 " ideal model delta sigma weight residual 117.04 112.46 4.58 9.90e-01 1.02e+00 2.14e+01 ... (remaining 14073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 3405 16.75 - 33.49: 188 33.49 - 50.24: 66 50.24 - 66.99: 44 66.99 - 83.74: 2 Dihedral angle restraints: 3705 sinusoidal: 1905 harmonic: 1800 Sorted by residual: dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS A 122 " pdb=" CB CYS A 122 " ideal model delta sinusoidal sigma weight residual -86.00 -125.26 39.26 1 1.00e+01 1.00e-02 2.17e+01 dihedral pdb=" CB CYS A 89 " pdb=" SG CYS A 89 " pdb=" SG CYS A 143 " pdb=" CB CYS A 143 " ideal model delta sinusoidal sigma weight residual 93.00 60.10 32.90 1 1.00e+01 1.00e-02 1.54e+01 dihedral pdb=" CA LYS A 518 " pdb=" CB LYS A 518 " pdb=" CG LYS A 518 " pdb=" CD LYS A 518 " ideal model delta sinusoidal sigma weight residual -180.00 -126.26 -53.74 3 1.50e+01 4.44e-03 9.23e+00 ... (remaining 3702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 541 0.055 - 0.110: 85 0.110 - 0.165: 6 0.165 - 0.220: 1 0.220 - 0.275: 1 Chirality restraints: 634 Sorted by residual: chirality pdb=" CA PHE A 388 " pdb=" N PHE A 388 " pdb=" C PHE A 388 " pdb=" CB PHE A 388 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA TYR A 362 " pdb=" N TYR A 362 " pdb=" C TYR A 362 " pdb=" CB TYR A 362 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA LEU A 385 " pdb=" N LEU A 385 " pdb=" C LEU A 385 " pdb=" CB LEU A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 631 not shown) Planarity restraints: 1165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 388 " 0.065 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO A 389 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 443 " -0.020 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ILE A 443 " 0.066 2.00e-02 2.50e+03 pdb=" O ILE A 443 " -0.024 2.00e-02 2.50e+03 pdb=" N THR A 444 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 443 " 0.017 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" N THR A 444 " -0.056 2.00e-02 2.50e+03 pdb=" CA THR A 444 " 0.014 2.00e-02 2.50e+03 pdb=" H THR A 444 " 0.025 2.00e-02 2.50e+03 ... (remaining 1162 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 266 2.17 - 2.78: 14697 2.78 - 3.38: 21397 3.38 - 3.99: 25397 3.99 - 4.60: 40885 Nonbonded interactions: 102642 Sorted by model distance: nonbonded pdb="HD11 ILE A 398 " pdb=" HE2 PHE A 452 " model vdw 1.560 2.270 nonbonded pdb=" O LEU A 43 " pdb=" HG SER A 134 " model vdw 1.592 1.850 nonbonded pdb=" O ILE A 462 " pdb=" H GLY A 466 " model vdw 1.617 1.850 nonbonded pdb=" O ILE A 350 " pdb="HD22 ASN A 354 " model vdw 1.637 1.850 nonbonded pdb=" O VAL A 485 " pdb=" H ALA A 489 " model vdw 1.640 1.850 ... (remaining 102637 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 2.050 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 28.170 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 3994 Z= 0.313 Angle : 0.613 6.868 5456 Z= 0.400 Chirality : 0.039 0.275 634 Planarity : 0.006 0.099 678 Dihedral : 10.837 83.735 1346 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.52 % Allowed : 4.97 % Favored : 94.50 % 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: 1.38 (0.36), residues: 511 helix: 1.78 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.01 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 355 HIS 0.001 0.000 HIS A 49 PHE 0.015 0.001 PHE A 388 TYR 0.010 0.001 TYR A 73 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.9083 (mp) cc_final: 0.8832 (mt) REVERT: A 173 ARG cc_start: 0.7502 (ttt180) cc_final: 0.7000 (ttt-90) REVERT: A 203 MET cc_start: 0.7721 (tmm) cc_final: 0.7465 (tmm) REVERT: A 264 TRP cc_start: 0.7457 (m-90) cc_final: 0.7152 (m-10) REVERT: A 276 PHE cc_start: 0.7787 (m-10) cc_final: 0.7268 (m-80) REVERT: A 301 LYS cc_start: 0.8411 (ttpt) cc_final: 0.7965 (tptp) REVERT: A 367 MET cc_start: 0.5771 (mmt) cc_final: 0.4503 (mmt) REVERT: A 389 PRO cc_start: 0.8302 (Cg_exo) cc_final: 0.8050 (Cg_endo) outliers start: 2 outliers final: 2 residues processed: 131 average time/residue: 0.3287 time to fit residues: 53.3813 Evaluate side-chains 93 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 246 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 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 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3994 Z= 0.194 Angle : 0.516 4.233 5456 Z= 0.272 Chirality : 0.035 0.126 634 Planarity : 0.004 0.059 678 Dihedral : 4.439 44.508 553 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.88 % Allowed : 12.30 % Favored : 84.82 % 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: 1.58 (0.37), residues: 511 helix: 1.94 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -0.92 (0.44), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 355 HIS 0.007 0.001 HIS A 368 PHE 0.009 0.001 PHE A 447 TYR 0.009 0.001 TYR A 73 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7619 (ttm) cc_final: 0.7370 (ttp) REVERT: A 173 ARG cc_start: 0.7558 (ttt180) cc_final: 0.7205 (ttt-90) REVERT: A 203 MET cc_start: 0.7763 (tmm) cc_final: 0.7459 (tmm) REVERT: A 264 TRP cc_start: 0.7504 (m-90) cc_final: 0.7076 (m-10) REVERT: A 313 LYS cc_start: 0.7674 (tmmt) cc_final: 0.7260 (tmtt) REVERT: A 353 TYR cc_start: 0.8357 (t80) cc_final: 0.8104 (t80) REVERT: A 367 MET cc_start: 0.5717 (mmt) cc_final: 0.4558 (mmt) REVERT: A 445 MET cc_start: 0.7653 (mtp) cc_final: 0.7417 (mtm) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.2857 time to fit residues: 38.7205 Evaluate side-chains 101 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 0.3980 chunk 46 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3994 Z= 0.164 Angle : 0.491 5.082 5456 Z= 0.254 Chirality : 0.034 0.131 634 Planarity : 0.004 0.045 678 Dihedral : 4.257 46.394 552 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.66 % Allowed : 13.35 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.37), residues: 511 helix: 1.94 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -0.97 (0.44), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 355 HIS 0.006 0.001 HIS A 368 PHE 0.014 0.001 PHE A 174 TYR 0.008 0.001 TYR A 73 ARG 0.003 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7643 (ttm) cc_final: 0.7383 (ttp) REVERT: A 173 ARG cc_start: 0.7510 (ttt180) cc_final: 0.7123 (ttt-90) REVERT: A 203 MET cc_start: 0.7767 (tmm) cc_final: 0.7488 (tmm) REVERT: A 264 TRP cc_start: 0.7499 (m-90) cc_final: 0.7118 (m-10) REVERT: A 276 PHE cc_start: 0.7653 (m-80) cc_final: 0.7365 (m-80) REVERT: A 353 TYR cc_start: 0.8308 (t80) cc_final: 0.8080 (t80) REVERT: A 367 MET cc_start: 0.5475 (mmt) cc_final: 0.4467 (mmt) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 0.2611 time to fit residues: 35.7957 Evaluate side-chains 101 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3994 Z= 0.266 Angle : 0.543 4.638 5456 Z= 0.291 Chirality : 0.036 0.128 634 Planarity : 0.004 0.040 678 Dihedral : 4.473 45.588 552 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.14 % Allowed : 16.23 % Favored : 80.63 % 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: 0.91 (0.36), residues: 511 helix: 1.53 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -1.35 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 355 HIS 0.007 0.002 HIS A 368 PHE 0.013 0.001 PHE A 23 TYR 0.009 0.001 TYR A 128 ARG 0.003 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7775 (ttm) cc_final: 0.7531 (ttm) REVERT: A 173 ARG cc_start: 0.7584 (ttt180) cc_final: 0.7192 (ttt-90) REVERT: A 203 MET cc_start: 0.7872 (tmm) cc_final: 0.7596 (tmm) REVERT: A 264 TRP cc_start: 0.7636 (m-90) cc_final: 0.7340 (m-10) REVERT: A 367 MET cc_start: 0.5679 (mmt) cc_final: 0.4551 (mmt) outliers start: 12 outliers final: 10 residues processed: 101 average time/residue: 0.2682 time to fit residues: 35.0991 Evaluate side-chains 102 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 50.0000 chunk 28 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3994 Z= 0.281 Angle : 0.546 4.763 5456 Z= 0.297 Chirality : 0.036 0.129 634 Planarity : 0.004 0.038 678 Dihedral : 4.583 45.749 552 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.93 % Allowed : 17.28 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.37), residues: 511 helix: 1.40 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -1.25 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 355 HIS 0.007 0.002 HIS A 368 PHE 0.023 0.002 PHE A 276 TYR 0.009 0.001 TYR A 128 ARG 0.003 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7586 (ttt180) cc_final: 0.7199 (ttt-90) REVERT: A 194 MET cc_start: 0.8823 (ttt) cc_final: 0.8526 (ttt) REVERT: A 203 MET cc_start: 0.7925 (tmm) cc_final: 0.7580 (tmm) REVERT: A 264 TRP cc_start: 0.7639 (m-90) cc_final: 0.7235 (m-10) REVERT: A 367 MET cc_start: 0.5692 (mmt) cc_final: 0.4550 (mmt) outliers start: 15 outliers final: 9 residues processed: 104 average time/residue: 0.2605 time to fit residues: 35.6992 Evaluate side-chains 101 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3994 Z= 0.168 Angle : 0.499 4.390 5456 Z= 0.258 Chirality : 0.034 0.132 634 Planarity : 0.004 0.040 678 Dihedral : 4.414 46.759 552 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.14 % Allowed : 17.28 % Favored : 79.58 % 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: 0.95 (0.36), residues: 511 helix: 1.54 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -1.28 (0.43), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 HIS 0.007 0.001 HIS A 368 PHE 0.019 0.001 PHE A 276 TYR 0.009 0.001 TYR A 200 ARG 0.001 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7539 (ttt180) cc_final: 0.7145 (ttt-90) REVERT: A 194 MET cc_start: 0.8801 (ttt) cc_final: 0.8479 (ttt) REVERT: A 203 MET cc_start: 0.7836 (tmm) cc_final: 0.7518 (tmm) REVERT: A 264 TRP cc_start: 0.7641 (m-90) cc_final: 0.7345 (m-10) REVERT: A 367 MET cc_start: 0.5430 (mmt) cc_final: 0.4481 (mmt) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.2726 time to fit residues: 35.9454 Evaluate side-chains 99 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 40.0000 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3994 Z= 0.258 Angle : 0.541 4.703 5456 Z= 0.290 Chirality : 0.035 0.131 634 Planarity : 0.004 0.037 678 Dihedral : 4.563 47.084 552 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.66 % Allowed : 18.06 % Favored : 78.27 % 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: 0.72 (0.36), residues: 511 helix: 1.36 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -1.27 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 355 HIS 0.006 0.001 HIS A 368 PHE 0.013 0.001 PHE A 276 TYR 0.008 0.001 TYR A 128 ARG 0.003 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7571 (ttt180) cc_final: 0.7178 (ttt-90) REVERT: A 194 MET cc_start: 0.8855 (ttt) cc_final: 0.8547 (ttt) REVERT: A 203 MET cc_start: 0.7910 (tmm) cc_final: 0.7578 (tmm) REVERT: A 264 TRP cc_start: 0.7721 (m-90) cc_final: 0.7249 (m-10) REVERT: A 289 TRP cc_start: 0.8119 (t-100) cc_final: 0.7842 (t-100) REVERT: A 367 MET cc_start: 0.5597 (mmt) cc_final: 0.4613 (mmt) outliers start: 14 outliers final: 12 residues processed: 102 average time/residue: 0.2671 time to fit residues: 35.8233 Evaluate side-chains 102 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3994 Z= 0.251 Angle : 0.542 4.725 5456 Z= 0.290 Chirality : 0.035 0.128 634 Planarity : 0.004 0.035 678 Dihedral : 4.582 47.317 552 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.40 % Allowed : 18.85 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.36), residues: 511 helix: 1.30 (0.28), residues: 335 sheet: None (None), residues: 0 loop : -1.36 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 HIS 0.008 0.002 HIS A 368 PHE 0.013 0.001 PHE A 23 TYR 0.008 0.001 TYR A 257 ARG 0.004 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7551 (ttt180) cc_final: 0.7167 (ttt-90) REVERT: A 194 MET cc_start: 0.8851 (ttt) cc_final: 0.8560 (ttt) REVERT: A 203 MET cc_start: 0.7934 (tmm) cc_final: 0.7607 (tmm) REVERT: A 264 TRP cc_start: 0.7689 (m-90) cc_final: 0.7211 (m-10) REVERT: A 289 TRP cc_start: 0.8112 (t-100) cc_final: 0.7788 (t-100) REVERT: A 353 TYR cc_start: 0.8433 (t80) cc_final: 0.8001 (t80) REVERT: A 367 MET cc_start: 0.5632 (mmt) cc_final: 0.4639 (mmt) outliers start: 13 outliers final: 12 residues processed: 101 average time/residue: 0.2601 time to fit residues: 34.2438 Evaluate side-chains 102 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 0.0060 chunk 46 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3994 Z= 0.161 Angle : 0.500 4.396 5456 Z= 0.257 Chirality : 0.034 0.132 634 Planarity : 0.004 0.038 678 Dihedral : 4.415 48.440 552 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.09 % Allowed : 20.94 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.37), residues: 511 helix: 1.50 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.43 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 355 HIS 0.008 0.001 HIS A 368 PHE 0.010 0.001 PHE A 276 TYR 0.008 0.001 TYR A 200 ARG 0.001 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7676 (ttm) cc_final: 0.7420 (ttm) REVERT: A 173 ARG cc_start: 0.7509 (ttt180) cc_final: 0.7140 (ttt-90) REVERT: A 194 MET cc_start: 0.8808 (ttt) cc_final: 0.8518 (ttt) REVERT: A 203 MET cc_start: 0.7853 (tmm) cc_final: 0.7524 (tmm) REVERT: A 264 TRP cc_start: 0.7649 (m-90) cc_final: 0.7304 (m-10) REVERT: A 353 TYR cc_start: 0.8368 (t80) cc_final: 0.7943 (t80) REVERT: A 367 MET cc_start: 0.5401 (mmt) cc_final: 0.4551 (mmt) outliers start: 8 outliers final: 7 residues processed: 93 average time/residue: 0.2747 time to fit residues: 33.3806 Evaluate side-chains 91 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3994 Z= 0.164 Angle : 0.510 5.880 5456 Z= 0.263 Chirality : 0.034 0.133 634 Planarity : 0.004 0.039 678 Dihedral : 4.356 47.750 552 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.83 % Allowed : 21.20 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.37), residues: 511 helix: 1.61 (0.29), residues: 341 sheet: None (None), residues: 0 loop : -1.34 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 355 HIS 0.007 0.001 HIS A 368 PHE 0.021 0.001 PHE A 139 TYR 0.007 0.001 TYR A 257 ARG 0.002 0.000 ARG A 463 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7715 (ttm) cc_final: 0.7484 (ttm) REVERT: A 173 ARG cc_start: 0.7511 (ttt180) cc_final: 0.7152 (ttt-90) REVERT: A 194 MET cc_start: 0.8818 (ttt) cc_final: 0.8515 (ttt) REVERT: A 203 MET cc_start: 0.7838 (tmm) cc_final: 0.7524 (tmm) REVERT: A 264 TRP cc_start: 0.7666 (m-90) cc_final: 0.7318 (m-10) REVERT: A 367 MET cc_start: 0.5342 (mmt) cc_final: 0.4565 (mmt) outliers start: 7 outliers final: 7 residues processed: 88 average time/residue: 0.2899 time to fit residues: 33.0650 Evaluate side-chains 91 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 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 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.174501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139907 restraints weight = 15154.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.146027 restraints weight = 6198.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.149997 restraints weight = 3552.234| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3994 Z= 0.189 Angle : 0.512 5.244 5456 Z= 0.268 Chirality : 0.034 0.130 634 Planarity : 0.004 0.037 678 Dihedral : 4.382 47.607 552 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.36 % Allowed : 20.68 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.37), residues: 511 helix: 1.61 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.25 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 355 HIS 0.008 0.001 HIS A 368 PHE 0.017 0.001 PHE A 139 TYR 0.007 0.001 TYR A 200 ARG 0.002 0.000 ARG A 463 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2449.28 seconds wall clock time: 43 minutes 57.82 seconds (2637.82 seconds total)