Starting phenix.real_space_refine on Wed Jun 4 22:38:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfk_37494/06_2025/8wfk_37494.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfk_37494/06_2025/8wfk_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/cci-nas-00/data/ceres_data/8wfk_37494/06_2025/8wfk_37494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfk_37494/06_2025/8wfk_37494.map" model { file = "/net/cci-nas-00/data/ceres_data/8wfk_37494/06_2025/8wfk_37494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfk_37494/06_2025/8wfk_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. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 3.22, per 1000 atoms: 0.74 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 - 3.00 Amino acid : True - 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: 1.24 Conformation dependent library (CDL) restraints added in 476.4 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: 0.41 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: 1.04 Time building geometry restraints manager: 1.24 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: 0.00 - 1.45: 5940 1.45 - 2.89: 158 2.89 - 4.34: 34 4.34 - 5.78: 16 5.78 - 7.23: 2 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: 1.520 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: 0.040 Process input model: 14.100 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.720 ------------------------------------------------------------------------------- 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 : 0.020 0.945 4511 Z= 0.989 Angle : 1.282 62.837 6154 Z= 0.634 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 Details of bonding type rmsd hydrogen bonds : bond 0.23711 ( 207) hydrogen bonds : angle 7.53663 ( 612) SS BOND : bond 0.92245 ( 2) SS BOND : angle 43.91987 ( 4) covalent geometry : bond 0.00356 ( 4509) covalent geometry : angle 0.62360 ( 6150) *********************** 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 to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.424 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: 0.1650 time to fit residues: 15.1001 Evaluate side-chains 61 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.137435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118484 restraints weight = 5614.703| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.00 r_work: 0.3261 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4511 Z= 0.128 Angle : 0.584 7.316 6154 Z= 0.297 Chirality : 0.041 0.117 676 Planarity : 0.005 0.050 753 Dihedral : 5.304 46.440 625 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.82 % Allowed : 26.03 % 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: -1.33 (0.36), residues: 542 helix: -0.21 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -2.16 (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 0.002 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.05415 ( 207) hydrogen bonds : angle 4.74465 ( 612) SS BOND : bond 0.01308 ( 2) SS BOND : angle 3.19887 ( 4) covalent geometry : bond 0.00274 ( 4509) covalent geometry : angle 0.57878 ( 6150) *********************** 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 72 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.428 Fit side-chains REVERT: A 399 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.7135 (mt) REVERT: A 452 VAL cc_start: 0.8250 (p) cc_final: 0.7908 (t) REVERT: A 475 ASN cc_start: 0.8795 (m-40) cc_final: 0.8369 (t0) REVERT: A 531 PHE cc_start: 0.8231 (t80) cc_final: 0.7961 (t80) outliers start: 13 outliers final: 3 residues processed: 70 average time/residue: 0.1414 time to fit residues: 13.2846 Evaluate side-chains 63 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 399 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.132328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114066 restraints weight = 5513.735| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.85 r_work: 0.3213 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4511 Z= 0.149 Angle : 0.604 14.031 6154 Z= 0.303 Chirality : 0.041 0.117 676 Planarity : 0.005 0.048 753 Dihedral : 4.844 38.888 625 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.25 % Allowed : 25.16 % 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: -1.05 (0.36), residues: 542 helix: 0.06 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -2.19 (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 0.010 0.001 PHE A 361 TYR 0.016 0.001 TYR A 141 ARG 0.003 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.05134 ( 207) hydrogen bonds : angle 4.26437 ( 612) SS BOND : bond 0.01279 ( 2) SS BOND : angle 5.60458 ( 4) covalent geometry : bond 0.00364 ( 4509) covalent geometry : angle 0.58698 ( 6150) *********************** 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 70 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.457 Fit side-chains REVERT: A 399 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7288 (mt) REVERT: A 475 ASN cc_start: 0.8754 (m-40) cc_final: 0.8282 (t0) REVERT: A 531 PHE cc_start: 0.8278 (t80) cc_final: 0.7967 (t80) outliers start: 15 outliers final: 6 residues processed: 64 average time/residue: 0.1317 time to fit residues: 11.5413 Evaluate side-chains 61 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 363 ILE 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 28 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.137199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.116672 restraints weight = 5769.468| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.22 r_work: 0.3185 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4511 Z= 0.132 Angle : 0.560 11.044 6154 Z= 0.280 Chirality : 0.040 0.118 676 Planarity : 0.005 0.046 753 Dihedral : 4.617 34.299 625 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.69 % Allowed : 24.73 % 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: -0.82 (0.36), residues: 542 helix: 0.22 (0.29), residues: 363 sheet: None (None), residues: 0 loop : -2.06 (0.42), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 215 HIS 0.004 0.001 HIS A 370 PHE 0.010 0.001 PHE A 361 TYR 0.014 0.001 TYR A 141 ARG 0.002 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 207) hydrogen bonds : angle 4.06276 ( 612) SS BOND : bond 0.00401 ( 2) SS BOND : angle 4.23365 ( 4) covalent geometry : bond 0.00325 ( 4509) covalent geometry : angle 0.54920 ( 6150) *********************** 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 to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.455 Fit side-chains REVERT: A 399 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.7115 (mt) REVERT: A 475 ASN cc_start: 0.8772 (m-40) cc_final: 0.8313 (t0) REVERT: A 531 PHE cc_start: 0.8237 (t80) cc_final: 0.7931 (t80) outliers start: 17 outliers final: 7 residues processed: 65 average time/residue: 0.1422 time to fit residues: 12.7476 Evaluate side-chains 63 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 548 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 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 = 0.3526 r_free = 0.3526 target = 0.131854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113977 restraints weight = 5659.223| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.80 r_work: 0.3220 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4511 Z= 0.119 Angle : 0.544 8.933 6154 Z= 0.273 Chirality : 0.040 0.154 676 Planarity : 0.005 0.043 753 Dihedral : 4.488 32.184 625 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.25 % Allowed : 24.51 % 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: -0.55 (0.37), residues: 542 helix: 0.45 (0.29), residues: 360 sheet: None (None), residues: 0 loop : -1.98 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 215 HIS 0.004 0.001 HIS A 381 PHE 0.008 0.001 PHE A 229 TYR 0.014 0.001 TYR A 77 ARG 0.002 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 207) hydrogen bonds : angle 3.93392 ( 612) SS BOND : bond 0.00644 ( 2) SS BOND : angle 3.90502 ( 4) covalent geometry : bond 0.00287 ( 4509) covalent geometry : angle 0.53525 ( 6150) *********************** 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 70 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.480 Fit side-chains REVERT: A 399 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7305 (mt) REVERT: A 475 ASN cc_start: 0.8741 (m-40) cc_final: 0.8281 (t0) REVERT: A 531 PHE cc_start: 0.8351 (t80) cc_final: 0.8036 (t80) outliers start: 15 outliers final: 9 residues processed: 64 average time/residue: 0.1253 time to fit residues: 11.0042 Evaluate side-chains 63 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 432 ASP 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 7 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.133784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115044 restraints weight = 5631.123| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.89 r_work: 0.3214 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 4511 Z= 0.126 Angle : 0.555 8.325 6154 Z= 0.279 Chirality : 0.040 0.119 676 Planarity : 0.005 0.043 753 Dihedral : 4.433 30.963 625 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.04 % Allowed : 25.38 % 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: -0.44 (0.37), residues: 542 helix: 0.52 (0.29), residues: 366 sheet: None (None), residues: 0 loop : -1.98 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 215 HIS 0.004 0.001 HIS A 381 PHE 0.008 0.001 PHE A 361 TYR 0.015 0.001 TYR A 77 ARG 0.002 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 207) hydrogen bonds : angle 3.88727 ( 612) SS BOND : bond 0.00884 ( 2) SS BOND : angle 5.00987 ( 4) covalent geometry : bond 0.00309 ( 4509) covalent geometry : angle 0.54074 ( 6150) *********************** 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 70 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.424 Fit side-chains REVERT: A 104 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8037 (mp) REVERT: A 399 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7322 (mt) REVERT: A 436 ASN cc_start: 0.6756 (m110) cc_final: 0.6513 (m110) REVERT: A 475 ASN cc_start: 0.8729 (m-40) cc_final: 0.8264 (t0) REVERT: A 531 PHE cc_start: 0.8385 (t80) cc_final: 0.8083 (t80) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 0.1262 time to fit residues: 11.1754 Evaluate side-chains 67 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU 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 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 432 ASP 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: 0.9980 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.134053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115408 restraints weight = 5654.504| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.89 r_work: 0.3230 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4511 Z= 0.116 Angle : 0.534 7.677 6154 Z= 0.266 Chirality : 0.040 0.121 676 Planarity : 0.005 0.042 753 Dihedral : 4.356 29.843 625 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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: -0.30 (0.37), residues: 542 helix: 0.63 (0.29), residues: 366 sheet: None (None), residues: 0 loop : -1.93 (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 0.008 0.001 PHE A 229 TYR 0.015 0.001 TYR A 77 ARG 0.002 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 207) hydrogen bonds : angle 3.81371 ( 612) SS BOND : bond 0.00542 ( 2) SS BOND : angle 3.50963 ( 4) covalent geometry : bond 0.00277 ( 4509) covalent geometry : angle 0.52678 ( 6150) *********************** 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 71 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.550 Fit side-chains REVERT: A 399 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7355 (mt) REVERT: A 436 ASN cc_start: 0.6757 (m110) cc_final: 0.6469 (m110) REVERT: A 475 ASN cc_start: 0.8741 (m-40) cc_final: 0.8280 (t0) REVERT: A 531 PHE cc_start: 0.8358 (t80) cc_final: 0.8078 (t80) outliers start: 14 outliers final: 12 residues processed: 66 average time/residue: 0.1276 time to fit residues: 11.5428 Evaluate side-chains 67 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 355 TYR 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 459 ILE 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 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.137051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117446 restraints weight = 5537.334| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.11 r_work: 0.3208 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4511 Z= 0.112 Angle : 0.525 7.549 6154 Z= 0.262 Chirality : 0.040 0.116 676 Planarity : 0.004 0.042 753 Dihedral : 4.324 29.304 625 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.47 % Allowed : 25.16 % 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: -0.23 (0.37), residues: 542 helix: 0.67 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -1.89 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 215 HIS 0.004 0.001 HIS A 381 PHE 0.008 0.001 PHE A 229 TYR 0.017 0.001 TYR A 77 ARG 0.001 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 207) hydrogen bonds : angle 3.76867 ( 612) SS BOND : bond 0.00496 ( 2) SS BOND : angle 2.81711 ( 4) covalent geometry : bond 0.00266 ( 4509) covalent geometry : angle 0.52043 ( 6150) *********************** 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 71 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.395 Fit side-chains REVERT: A 104 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7862 (mp) REVERT: A 399 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7225 (mt) REVERT: A 436 ASN cc_start: 0.6643 (m110) cc_final: 0.6342 (m110) REVERT: A 475 ASN cc_start: 0.8735 (m-40) cc_final: 0.8266 (t0) REVERT: A 531 PHE cc_start: 0.8228 (t80) cc_final: 0.7945 (t80) outliers start: 16 outliers final: 11 residues processed: 65 average time/residue: 0.1294 time to fit residues: 11.5069 Evaluate side-chains 68 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU 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 355 TYR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 459 ILE 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 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.134521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115032 restraints weight = 5689.040| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.08 r_work: 0.3216 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 4511 Z= 0.125 Angle : 0.565 10.407 6154 Z= 0.283 Chirality : 0.041 0.147 676 Planarity : 0.004 0.042 753 Dihedral : 4.353 28.795 625 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.04 % Allowed : 25.81 % 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: -0.21 (0.37), residues: 542 helix: 0.69 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.87 (0.45), residues: 177 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 0.002 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 207) hydrogen bonds : angle 3.75045 ( 612) SS BOND : bond 0.00569 ( 2) SS BOND : angle 5.76819 ( 4) covalent geometry : bond 0.00305 ( 4509) covalent geometry : angle 0.54576 ( 6150) *********************** 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 68 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.435 Fit side-chains REVERT: A 104 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7854 (mp) REVERT: A 399 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7273 (mt) REVERT: A 436 ASN cc_start: 0.6605 (m110) cc_final: 0.6306 (m110) REVERT: A 475 ASN cc_start: 0.8734 (m-40) cc_final: 0.8267 (t0) REVERT: A 531 PHE cc_start: 0.8218 (t80) cc_final: 0.7935 (t80) outliers start: 14 outliers final: 12 residues processed: 63 average time/residue: 0.1307 time to fit residues: 11.3049 Evaluate side-chains 67 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU 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 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 459 ILE 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 28 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.137316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.117870 restraints weight = 5500.577| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.09 r_work: 0.3210 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 4511 Z= 0.122 Angle : 0.553 9.531 6154 Z= 0.278 Chirality : 0.040 0.122 676 Planarity : 0.004 0.042 753 Dihedral : 4.342 28.340 625 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.04 % Allowed : 26.03 % 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: -0.17 (0.37), residues: 542 helix: 0.72 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.84 (0.45), residues: 177 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 0.012 0.001 PHE A 229 TYR 0.017 0.001 TYR A 77 ARG 0.001 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 207) hydrogen bonds : angle 3.71540 ( 612) SS BOND : bond 0.00446 ( 2) SS BOND : angle 5.31922 ( 4) covalent geometry : bond 0.00296 ( 4509) covalent geometry : angle 0.53651 ( 6150) ********************** 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 69 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.448 Fit side-chains REVERT: A 104 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7832 (mp) REVERT: A 399 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7263 (mt) REVERT: A 436 ASN cc_start: 0.6567 (m110) cc_final: 0.6283 (m110) REVERT: A 475 ASN cc_start: 0.8732 (m-40) cc_final: 0.8270 (t0) REVERT: A 531 PHE cc_start: 0.8238 (t80) cc_final: 0.7948 (t80) outliers start: 14 outliers final: 12 residues processed: 64 average time/residue: 0.1351 time to fit residues: 12.0230 Evaluate side-chains 66 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU 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 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 459 ILE 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 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 7 optimal weight: 0.0770 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.135661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116779 restraints weight = 5716.932| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.96 r_work: 0.3241 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4511 Z= 0.112 Angle : 0.541 8.310 6154 Z= 0.272 Chirality : 0.040 0.203 676 Planarity : 0.004 0.042 753 Dihedral : 4.271 27.901 625 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.25 % Allowed : 25.81 % 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: -0.09 (0.37), residues: 542 helix: 0.77 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.80 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 215 HIS 0.004 0.001 HIS A 381 PHE 0.014 0.001 PHE A 109 TYR 0.017 0.001 TYR A 77 ARG 0.001 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 207) hydrogen bonds : angle 3.71286 ( 612) SS BOND : bond 0.00301 ( 2) SS BOND : angle 4.72008 ( 4) covalent geometry : bond 0.00262 ( 4509) covalent geometry : angle 0.52756 ( 6150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2852.39 seconds wall clock time: 50 minutes 13.21 seconds (3013.21 seconds total)