Starting phenix.real_space_refine on Fri Dec 8 07:32:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/12_2023/8et9_28589_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/12_2023/8et9_28589.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/12_2023/8et9_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_28589/12_2023/8et9_28589_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/12_2023/8et9_28589_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/12_2023/8et9_28589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/12_2023/8et9_28589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/12_2023/8et9_28589_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/12_2023/8et9_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-1.21rc1-5172/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: 3.87, per 1000 atoms: 0.50 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: 6.05 Conformation dependent library (CDL) restraints added in 875.3 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: 1.54 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: 2.62 Time building geometry restraints manager: 6.30 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: 3370 16.75 - 33.49: 177 33.49 - 50.24: 45 50.24 - 66.99: 6 66.99 - 83.74: 2 Dihedral angle restraints: 3600 sinusoidal: 1800 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 3597 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: 0.370 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: 0.120 Extract box with map and model: 2.010 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 28.840 Find NCS groups from input model: 0.140 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- 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 : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 131 average time/residue: 0.3391 time to fit residues: 54.5688 Evaluate side-chains 91 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.610 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0960 time to fit residues: 1.1443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.6746 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3994 Z= 0.203 Angle : 0.527 4.541 5456 Z= 0.277 Chirality : 0.035 0.127 634 Planarity : 0.004 0.032 678 Dihedral : 3.887 15.843 550 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.62 % Allowed : 11.52 % Favored : 85.86 % 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: 1.50 (0.37), residues: 511 helix: 1.91 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -1.00 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 355 HIS 0.008 0.001 HIS A 368 PHE 0.009 0.001 PHE A 447 TYR 0.009 0.001 TYR A 73 ARG 0.003 0.000 ARG A 173 *********************** 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 111 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 0.2671 time to fit residues: 36.4901 Evaluate side-chains 95 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.632 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0964 time to fit residues: 1.7939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 31 optimal weight: 0.0970 chunk 12 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.6725 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3994 Z= 0.154 Angle : 0.500 4.543 5456 Z= 0.258 Chirality : 0.034 0.130 634 Planarity : 0.003 0.028 678 Dihedral : 3.798 16.022 550 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.83 % Allowed : 14.40 % Favored : 83.77 % 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: 1.48 (0.37), residues: 511 helix: 1.86 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -0.95 (0.43), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 202 HIS 0.002 0.000 HIS A 368 PHE 0.020 0.001 PHE A 276 TYR 0.012 0.001 TYR A 353 ARG 0.002 0.000 ARG A 173 *********************** 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 102 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 99 average time/residue: 0.2312 time to fit residues: 30.6386 Evaluate side-chains 93 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0861 time to fit residues: 1.2052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3994 Z= 0.225 Angle : 0.527 4.943 5456 Z= 0.279 Chirality : 0.035 0.136 634 Planarity : 0.004 0.029 678 Dihedral : 3.909 16.060 550 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.88 % Allowed : 15.71 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.36), residues: 511 helix: 1.63 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -1.32 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 264 HIS 0.004 0.001 HIS A 368 PHE 0.033 0.002 PHE A 276 TYR 0.027 0.002 TYR A 353 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 103 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 99 average time/residue: 0.2583 time to fit residues: 33.4751 Evaluate side-chains 95 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.595 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3321 time to fit residues: 2.7689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 25 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 50.0000 chunk 28 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.6780 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3994 Z= 0.207 Angle : 0.516 4.693 5456 Z= 0.272 Chirality : 0.035 0.134 634 Planarity : 0.004 0.029 678 Dihedral : 3.889 15.799 550 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.57 % Allowed : 15.97 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.36), residues: 511 helix: 1.52 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -1.31 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 355 HIS 0.004 0.001 HIS A 368 PHE 0.036 0.001 PHE A 276 TYR 0.009 0.001 TYR A 353 ARG 0.002 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 99 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 95 average time/residue: 0.2011 time to fit residues: 25.4787 Evaluate side-chains 95 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.497 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0734 time to fit residues: 1.1383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.3853 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= 0.178 Angle : 0.503 4.633 5456 Z= 0.261 Chirality : 0.034 0.130 634 Planarity : 0.004 0.029 678 Dihedral : 3.831 16.605 550 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.05 % Allowed : 17.02 % Favored : 81.94 % 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 (0.36), residues: 511 helix: 1.53 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -1.24 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 355 HIS 0.004 0.001 HIS A 368 PHE 0.028 0.001 PHE A 276 TYR 0.007 0.001 TYR A 73 ARG 0.002 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 95 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 93 average time/residue: 0.2298 time to fit residues: 28.3617 Evaluate side-chains 91 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0928 time to fit residues: 1.0919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 40.0000 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3994 Z= 0.263 Angle : 0.548 5.130 5456 Z= 0.293 Chirality : 0.036 0.127 634 Planarity : 0.004 0.030 678 Dihedral : 4.035 16.419 550 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.88 % Allowed : 17.80 % Favored : 79.32 % 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: 1.33 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -1.29 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.004 0.001 HIS A 49 PHE 0.023 0.001 PHE A 276 TYR 0.008 0.001 TYR A 200 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 102 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 98 average time/residue: 0.2431 time to fit residues: 31.6669 Evaluate side-chains 94 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.601 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0976 time to fit residues: 1.9467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.4156 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= 0.166 Angle : 0.510 4.696 5456 Z= 0.262 Chirality : 0.034 0.131 634 Planarity : 0.004 0.030 678 Dihedral : 3.883 16.310 550 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.52 % Allowed : 18.59 % 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: 1.01 (0.37), residues: 511 helix: 1.55 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -1.19 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 HIS 0.002 0.001 HIS A 11 PHE 0.021 0.001 PHE A 276 TYR 0.008 0.001 TYR A 200 ARG 0.002 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 88 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 87 average time/residue: 0.2547 time to fit residues: 29.2987 Evaluate side-chains 85 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.544 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0902 time to fit residues: 1.0423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.0570 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 0.0170 chunk 40 optimal weight: 0.9980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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: 0.6740 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3994 Z= 0.151 Angle : 0.507 4.643 5456 Z= 0.259 Chirality : 0.034 0.133 634 Planarity : 0.003 0.030 678 Dihedral : 3.786 14.960 550 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.26 % Allowed : 20.68 % Favored : 79.06 % 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: 1.18 (0.37), residues: 511 helix: 1.67 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -1.10 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 355 HIS 0.002 0.001 HIS A 368 PHE 0.020 0.001 PHE A 276 TYR 0.009 0.001 TYR A 200 ARG 0.002 0.000 ARG A 50 *********************** 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 89 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.2684 time to fit residues: 30.8295 Evaluate side-chains 84 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.593 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.6763 moved from start: 0.4369 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= 0.180 Angle : 0.518 4.816 5456 Z= 0.268 Chirality : 0.034 0.131 634 Planarity : 0.004 0.047 678 Dihedral : 3.834 14.788 550 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.52 % Allowed : 20.68 % 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: 1.14 (0.37), residues: 511 helix: 1.65 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -1.13 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 289 HIS 0.002 0.001 HIS A 368 PHE 0.019 0.001 PHE A 276 TYR 0.009 0.001 TYR A 233 ARG 0.006 0.000 ARG A 173 ********************** 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 84 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 0.2642 time to fit residues: 29.0097 Evaluate side-chains 81 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.611 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.175224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141561 restraints weight = 14795.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147600 restraints weight = 6064.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.151485 restraints weight = 3448.562| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4435 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= 0.186 Angle : 0.521 4.798 5456 Z= 0.271 Chirality : 0.034 0.132 634 Planarity : 0.004 0.044 678 Dihedral : 3.843 14.639 550 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.26 % Allowed : 21.20 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.37), residues: 511 helix: 1.63 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -1.16 (0.44), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 289 HIS 0.002 0.001 HIS A 368 PHE 0.019 0.001 PHE A 276 TYR 0.009 0.001 TYR A 353 ARG 0.006 0.000 ARG A 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2522.99 seconds wall clock time: 48 minutes 6.60 seconds (2886.60 seconds total)