Starting phenix.real_space_refine on Fri Aug 2 18:36:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/08_2024/8wfk_37494.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/08_2024/8wfk_37494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/08_2024/8wfk_37494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/08_2024/8wfk_37494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/08_2024/8wfk_37494.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/08_2024/8wfk_37494.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 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: 7 Type Number sf(0) Gaussians S 35 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 2918 2.51 5 N 683 2.21 5 O 728 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4371 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4341 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 25, 'TRANS': 520} Chain breaks: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CL': 1, ' NA': 2, 'W5O': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.03, per 1000 atoms: 0.69 Number of scatterers: 4371 At special positions: 0 Unit cell: (84.15, 73.1, 86.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 35 16.00 Na 2 11.00 F 3 9.00 O 728 8.00 N 683 7.00 C 2918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 239 " distance=1.13 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " distance=1.09 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 765.5 milliseconds 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 994 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 1 sheets defined 70.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.547A pdb=" N PHE A 55 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.928A pdb=" N ASN A 68 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 69 " --> pdb=" O LEU A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 71 through 79 Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.885A pdb=" N ILE A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 110 removed outlier: 4.068A pdb=" N ALA A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 124 Processing helix chain 'A' and resid 125 through 141 removed outlier: 3.800A pdb=" N VAL A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 135 " --> pdb=" O MET A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.034A pdb=" N TYR A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.544A pdb=" N CYS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 267 through 283 removed outlier: 3.525A pdb=" N VAL A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.539A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 302 Processing helix chain 'A' and resid 303 through 318 removed outlier: 4.072A pdb=" N TRP A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.800A pdb=" N SER A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 371 removed outlier: 4.165A pdb=" N TYR A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.631A pdb=" N THR A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 435 removed outlier: 3.820A pdb=" N TRP A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N CYS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 435 " --> pdb=" O VAL A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 removed outlier: 3.768A pdb=" N LYS A 442 " --> pdb=" O TRP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 456 removed outlier: 3.548A pdb=" N ALA A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 463 Proline residue: A 460 - end of helix removed outlier: 3.512A pdb=" N SER A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 463' Processing helix chain 'A' and resid 466 through 474 removed outlier: 3.510A pdb=" N LEU A 472 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET A 473 " --> pdb=" O TRP A 469 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 495 removed outlier: 4.657A pdb=" N PHE A 480 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 removed outlier: 3.840A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 524 through 540 removed outlier: 3.623A pdb=" N ALA A 528 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 564 Processing helix chain 'A' and resid 568 through 579 removed outlier: 3.838A pdb=" N LEU A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 592 Processing sheet with id=AA1, first strand: chain 'A' and resid 545 through 546 207 hydrogen bonds defined for protein. 612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 637 1.31 - 1.44: 1397 1.44 - 1.56: 2421 1.56 - 1.69: 0 1.69 - 1.82: 54 Bond restraints: 4509 Sorted by residual: bond pdb=" C15 W5O A 701 " pdb=" N14 W5O A 701 " ideal model delta sigma weight residual 1.342 1.452 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C18 W5O A 701 " pdb="CL27 W5O A 701 " ideal model delta sigma weight residual 1.727 1.784 -0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" C PRO A 296 " pdb=" O PRO A 296 " ideal model delta sigma weight residual 1.233 1.205 0.028 1.06e-02 8.90e+03 6.89e+00 bond pdb=" N ASP A 474 " pdb=" CA ASP A 474 " ideal model delta sigma weight residual 1.456 1.485 -0.030 1.35e-02 5.49e+03 4.89e+00 bond pdb=" N PRO A 296 " pdb=" CA PRO A 296 " ideal model delta sigma weight residual 1.470 1.443 0.027 1.23e-02 6.61e+03 4.86e+00 ... (remaining 4504 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.37: 135 106.37 - 113.29: 2303 113.29 - 120.20: 1753 120.20 - 127.12: 1894 127.12 - 134.04: 65 Bond angle restraints: 6150 Sorted by residual: angle pdb=" N PRO A 296 " pdb=" CA PRO A 296 " pdb=" C PRO A 296 " ideal model delta sigma weight residual 110.55 117.00 -6.45 1.63e+00 3.76e-01 1.57e+01 angle pdb=" CA CYS A 147 " pdb=" C CYS A 147 " pdb=" N ILE A 148 " ideal model delta sigma weight residual 117.17 121.08 -3.91 1.18e+00 7.18e-01 1.10e+01 angle pdb=" CA CYS A 147 " pdb=" C CYS A 147 " pdb=" O CYS A 147 " ideal model delta sigma weight residual 120.70 117.40 3.30 1.03e+00 9.43e-01 1.03e+01 angle pdb=" CA CYS A 239 " pdb=" C CYS A 239 " pdb=" O CYS A 239 " ideal model delta sigma weight residual 120.55 117.22 3.33 1.06e+00 8.90e-01 9.88e+00 angle pdb=" N CYS A 239 " pdb=" CA CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sigma weight residual 110.12 114.69 -4.57 1.47e+00 4.63e-01 9.66e+00 ... (remaining 6145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 2190 17.64 - 35.28: 283 35.28 - 52.92: 66 52.92 - 70.55: 13 70.55 - 88.19: 7 Dihedral angle restraints: 2559 sinusoidal: 987 harmonic: 1572 Sorted by residual: dihedral pdb=" CB CYS A 147 " pdb=" SG CYS A 147 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 6.64 86.36 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " pdb=" SG CYS A 175 " pdb=" CB CYS A 175 " ideal model delta sinusoidal sigma weight residual 93.00 159.25 -66.25 1 1.00e+01 1.00e-02 5.73e+01 dihedral pdb=" CA TRP A 322 " pdb=" C TRP A 322 " pdb=" N GLY A 323 " pdb=" CA GLY A 323 " ideal model delta harmonic sigma weight residual -180.00 -162.74 -17.26 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 2556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 520 0.047 - 0.093: 132 0.093 - 0.139: 20 0.139 - 0.186: 2 0.186 - 0.232: 2 Chirality restraints: 676 Sorted by residual: chirality pdb=" C07 W5O A 701 " pdb=" C05 W5O A 701 " pdb=" C08 W5O A 701 " pdb=" N14 W5O A 701 " both_signs ideal model delta sigma weight residual False -2.35 -2.58 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA CYS A 147 " pdb=" N CYS A 147 " pdb=" C CYS A 147 " pdb=" CB CYS A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA PRO A 296 " pdb=" N PRO A 296 " pdb=" C PRO A 296 " pdb=" CB PRO A 296 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.66e-01 ... (remaining 673 not shown) Planarity restraints: 753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 209 " 0.040 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO A 210 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 146 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.77e+00 pdb=" C ILE A 146 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 146 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS A 147 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 238 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C GLY A 238 " 0.033 2.00e-02 2.50e+03 pdb=" O GLY A 238 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 239 " -0.011 2.00e-02 2.50e+03 ... (remaining 750 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 82 2.69 - 3.24: 4060 3.24 - 3.79: 6402 3.79 - 4.35: 8450 4.35 - 4.90: 14419 Nonbonded interactions: 33413 Sorted by model distance: nonbonded pdb=" O VAL A 64 " pdb="NA NA A 704 " model vdw 2.137 2.470 nonbonded pdb=" OH TYR A 316 " pdb=" O SER A 479 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR A 172 " pdb=" OE2 GLU A 213 " model vdw 2.262 3.040 nonbonded pdb=" O LEU A 414 " pdb="NA NA A 704 " model vdw 2.297 2.470 nonbonded pdb=" O TYR A 218 " pdb=" NH1 ARG A 233 " model vdw 2.312 3.120 ... (remaining 33408 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 individual isotropic 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.840 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.004 0.110 4509 Z= 0.220 Angle : 0.624 7.229 6150 Z= 0.343 Chirality : 0.041 0.232 676 Planarity : 0.005 0.059 753 Dihedral : 16.764 88.191 1559 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 26.90 % Favored : 73.10 % 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: -1.97 (0.35), residues: 542 helix: -0.85 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -2.01 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 554 HIS 0.005 0.001 HIS A 381 PHE 0.014 0.001 PHE A 366 TYR 0.016 0.001 TYR A 77 ARG 0.001 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8355 (mttt) cc_final: 0.7203 (tttt) REVERT: A 367 MET cc_start: 0.7052 (tpt) cc_final: 0.6670 (tpt) REVERT: A 452 VAL cc_start: 0.8345 (p) cc_final: 0.8096 (t) REVERT: A 475 ASN cc_start: 0.8647 (m-40) cc_final: 0.8325 (t0) REVERT: A 531 PHE cc_start: 0.7916 (t80) cc_final: 0.7625 (t80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1646 time to fit residues: 15.0477 Evaluate side-chains 61 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.8123 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4509 Z= 0.164 Angle : 0.573 7.318 6150 Z= 0.292 Chirality : 0.040 0.111 676 Planarity : 0.005 0.049 753 Dihedral : 5.278 46.243 625 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.04 % Allowed : 25.60 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.36), residues: 542 helix: -0.19 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -2.14 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 554 HIS 0.005 0.001 HIS A 381 PHE 0.011 0.001 PHE A 366 TYR 0.014 0.001 TYR A 141 ARG 0.001 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.473 Fit side-chains REVERT: A 165 TYR cc_start: 0.8454 (m-80) cc_final: 0.8238 (m-80) REVERT: A 350 CYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8052 (m) REVERT: A 399 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6821 (mt) REVERT: A 452 VAL cc_start: 0.7873 (p) cc_final: 0.7624 (t) REVERT: A 475 ASN cc_start: 0.8678 (m-40) cc_final: 0.8212 (t0) REVERT: A 531 PHE cc_start: 0.7952 (t80) cc_final: 0.7654 (t80) outliers start: 14 outliers final: 3 residues processed: 70 average time/residue: 0.1354 time to fit residues: 12.7415 Evaluate side-chains 62 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 399 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4509 Z= 0.183 Angle : 0.558 13.170 6150 Z= 0.280 Chirality : 0.040 0.111 676 Planarity : 0.005 0.049 753 Dihedral : 4.737 38.466 625 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.82 % Allowed : 24.95 % Favored : 72.23 % 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: -0.97 (0.36), residues: 542 helix: 0.12 (0.29), residues: 362 sheet: None (None), residues: 0 loop : -2.15 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 554 HIS 0.004 0.001 HIS A 381 PHE 0.008 0.001 PHE A 361 TYR 0.014 0.001 TYR A 141 ARG 0.003 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.487 Fit side-chains REVERT: A 399 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6927 (mt) REVERT: A 475 ASN cc_start: 0.8637 (m-40) cc_final: 0.8126 (t0) REVERT: A 531 PHE cc_start: 0.8013 (t80) cc_final: 0.7671 (t80) outliers start: 13 outliers final: 5 residues processed: 63 average time/residue: 0.1314 time to fit residues: 11.3080 Evaluate side-chains 60 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8154 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4509 Z= 0.185 Angle : 0.545 11.824 6150 Z= 0.273 Chirality : 0.040 0.117 676 Planarity : 0.005 0.045 753 Dihedral : 4.561 34.177 625 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.47 % Allowed : 25.38 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.37), residues: 542 helix: 0.34 (0.29), residues: 362 sheet: None (None), residues: 0 loop : -2.08 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 554 HIS 0.004 0.001 HIS A 370 PHE 0.009 0.001 PHE A 150 TYR 0.013 0.001 TYR A 141 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.585 Fit side-chains REVERT: A 399 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6902 (mt) REVERT: A 475 ASN cc_start: 0.8622 (m-40) cc_final: 0.8109 (t0) REVERT: A 531 PHE cc_start: 0.8055 (t80) cc_final: 0.7724 (t80) outliers start: 16 outliers final: 5 residues processed: 65 average time/residue: 0.1336 time to fit residues: 12.0452 Evaluate side-chains 61 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 432 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.8161 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4509 Z= 0.184 Angle : 0.532 8.508 6150 Z= 0.267 Chirality : 0.041 0.189 676 Planarity : 0.005 0.042 753 Dihedral : 4.433 31.846 625 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.47 % Allowed : 24.95 % Favored : 71.58 % 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: -0.56 (0.37), residues: 542 helix: 0.46 (0.29), residues: 360 sheet: None (None), residues: 0 loop : -2.04 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 215 HIS 0.003 0.001 HIS A 381 PHE 0.009 0.001 PHE A 361 TYR 0.014 0.001 TYR A 141 ARG 0.001 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.423 Fit side-chains REVERT: A 399 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6983 (mt) REVERT: A 475 ASN cc_start: 0.8623 (m-40) cc_final: 0.8111 (t0) REVERT: A 531 PHE cc_start: 0.8090 (t80) cc_final: 0.7767 (t80) outliers start: 16 outliers final: 12 residues processed: 67 average time/residue: 0.1278 time to fit residues: 11.6865 Evaluate side-chains 68 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8158 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4509 Z= 0.186 Angle : 0.529 6.213 6150 Z= 0.267 Chirality : 0.040 0.115 676 Planarity : 0.005 0.042 753 Dihedral : 4.391 30.708 625 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.69 % Allowed : 23.86 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.37), residues: 542 helix: 0.57 (0.29), residues: 360 sheet: None (None), residues: 0 loop : -2.00 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 215 HIS 0.003 0.001 HIS A 381 PHE 0.009 0.001 PHE A 150 TYR 0.015 0.001 TYR A 77 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.490 Fit side-chains REVERT: A 399 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6944 (mt) REVERT: A 475 ASN cc_start: 0.8607 (m-40) cc_final: 0.8094 (t0) REVERT: A 531 PHE cc_start: 0.8107 (t80) cc_final: 0.7777 (t80) outliers start: 17 outliers final: 13 residues processed: 64 average time/residue: 0.1401 time to fit residues: 12.4317 Evaluate side-chains 69 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.8171 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 4509 Z= 0.201 Angle : 0.534 6.257 6150 Z= 0.269 Chirality : 0.041 0.125 676 Planarity : 0.005 0.042 753 Dihedral : 4.363 29.460 625 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.47 % Allowed : 24.73 % Favored : 71.80 % 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: -0.42 (0.37), residues: 542 helix: 0.55 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.03 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 215 HIS 0.003 0.001 HIS A 381 PHE 0.009 0.001 PHE A 361 TYR 0.015 0.001 TYR A 77 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 0.494 Fit side-chains REVERT: A 399 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.7058 (mt) REVERT: A 475 ASN cc_start: 0.8613 (m-40) cc_final: 0.8089 (t0) REVERT: A 531 PHE cc_start: 0.8138 (t80) cc_final: 0.7828 (t80) outliers start: 16 outliers final: 13 residues processed: 63 average time/residue: 0.1329 time to fit residues: 11.4581 Evaluate side-chains 66 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8150 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4509 Z= 0.166 Angle : 0.532 7.264 6150 Z= 0.269 Chirality : 0.040 0.115 676 Planarity : 0.004 0.042 753 Dihedral : 4.337 28.855 625 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.69 % Allowed : 25.38 % Favored : 70.93 % 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: -0.31 (0.37), residues: 542 helix: 0.66 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.04 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 215 HIS 0.003 0.001 HIS A 381 PHE 0.013 0.001 PHE A 229 TYR 0.016 0.001 TYR A 77 ARG 0.001 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.417 Fit side-chains REVERT: A 104 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7698 (mp) REVERT: A 174 ASP cc_start: 0.6436 (m-30) cc_final: 0.6060 (t0) REVERT: A 399 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.7056 (mt) REVERT: A 475 ASN cc_start: 0.8585 (m-40) cc_final: 0.8082 (t0) REVERT: A 531 PHE cc_start: 0.8134 (t80) cc_final: 0.7819 (t80) outliers start: 17 outliers final: 12 residues processed: 66 average time/residue: 0.1289 time to fit residues: 11.6855 Evaluate side-chains 67 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8148 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 4509 Z= 0.180 Angle : 0.546 6.406 6150 Z= 0.278 Chirality : 0.041 0.146 676 Planarity : 0.004 0.042 753 Dihedral : 4.392 28.208 625 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.04 % Allowed : 27.11 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.37), residues: 542 helix: 0.72 (0.29), residues: 364 sheet: None (None), residues: 0 loop : -1.99 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 215 HIS 0.003 0.001 HIS A 381 PHE 0.012 0.001 PHE A 229 TYR 0.016 0.001 TYR A 77 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.440 Fit side-chains REVERT: A 104 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 399 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.7075 (mt) REVERT: A 475 ASN cc_start: 0.8586 (m-40) cc_final: 0.8077 (t0) REVERT: A 531 PHE cc_start: 0.8132 (t80) cc_final: 0.7820 (t80) outliers start: 14 outliers final: 11 residues processed: 62 average time/residue: 0.1316 time to fit residues: 11.1117 Evaluate side-chains 66 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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: 0.8253 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 4509 Z= 0.418 Angle : 0.682 7.183 6150 Z= 0.351 Chirality : 0.047 0.165 676 Planarity : 0.005 0.042 753 Dihedral : 4.819 29.062 625 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.39 % Allowed : 27.33 % Favored : 70.28 % 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: 542 helix: 0.10 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -2.16 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 215 HIS 0.006 0.001 HIS A 370 PHE 0.016 0.002 PHE A 150 TYR 0.023 0.002 TYR A 141 ARG 0.003 0.001 ARG A 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.468 Fit side-chains REVERT: A 104 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7790 (mp) outliers start: 11 outliers final: 9 residues processed: 59 average time/residue: 0.1198 time to fit residues: 9.9839 Evaluate side-chains 60 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0470 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.0170 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 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 = 0.3553 r_free = 0.3553 target = 0.133496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115616 restraints weight = 5532.984| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.83 r_work: 0.3235 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4509 Z= 0.155 Angle : 0.542 6.576 6150 Z= 0.274 Chirality : 0.040 0.122 676 Planarity : 0.005 0.042 753 Dihedral : 4.588 28.368 625 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.60 % Allowed : 27.55 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.37), residues: 542 helix: 0.61 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.01 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 215 HIS 0.006 0.001 HIS A 173 PHE 0.012 0.001 PHE A 229 TYR 0.018 0.001 TYR A 77 ARG 0.001 0.000 ARG A 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1222.30 seconds wall clock time: 22 minutes 32.85 seconds (1352.85 seconds total)