Starting phenix.real_space_refine on Mon Sep 23 17:15:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1l_44083/09_2024/9b1l_44083.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1l_44083/09_2024/9b1l_44083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1l_44083/09_2024/9b1l_44083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1l_44083/09_2024/9b1l_44083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1l_44083/09_2024/9b1l_44083.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1l_44083/09_2024/9b1l_44083.cif" } resolution = 3.1 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= 0.001 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2628 2.51 5 N 683 2.21 5 O 700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4041 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 31, 'TRANS': 497} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.39, per 1000 atoms: 0.84 Number of scatterers: 4041 At special positions: 0 Unit cell: (59.708, 90.86, 101.893, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 700 8.00 N 683 7.00 C 2628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " distance=2.03 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: 1.06 Conformation dependent library (CDL) restraints added in 510.5 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 82.8% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.601A pdb=" N LEU A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 37 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.520A pdb=" N SER A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.955A pdb=" N ASP A 97 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.766A pdb=" N TRP A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.895A pdb=" N GLN A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 168 through 189 removed outlier: 4.155A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 220 removed outlier: 3.611A pdb=" N ALA A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 252 removed outlier: 4.336A pdb=" N PHE A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 264 through 274 removed outlier: 4.061A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TRP A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 304 removed outlier: 4.198A pdb=" N GLN A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 removed outlier: 3.594A pdb=" N ALA A 308 " --> pdb=" O HIS A 305 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS A 309 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 325 removed outlier: 6.245A pdb=" N GLU A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 339 through 367 removed outlier: 4.528A pdb=" N PHE A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLY A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 371 removed outlier: 4.104A pdb=" N GLY A 371 " --> pdb=" O GLN A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.895A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.906A pdb=" N ALA A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 419 removed outlier: 3.817A pdb=" N THR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 426 through 455 removed outlier: 3.672A pdb=" N SER A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 483 Proline residue: A 480 - end of helix removed outlier: 3.610A pdb=" N ARG A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.648A pdb=" N VAL A 487 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 removed outlier: 4.506A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Proline residue: A 501 - end of helix removed outlier: 3.758A pdb=" N LEU A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.521A pdb=" N VAL A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 530 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 271 hydrogen bonds defined for protein. 780 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: 1.08 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1278 1.34 - 1.46: 964 1.46 - 1.58: 1854 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4143 Sorted by residual: bond pdb=" C2 URC A 901 " pdb=" O11 URC A 901 " ideal model delta sigma weight residual 1.213 1.365 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C8 URC A 901 " pdb=" O24 URC A 901 " ideal model delta sigma weight residual 1.215 1.352 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C6 URC A 901 " pdb=" O13 URC A 901 " ideal model delta sigma weight residual 1.218 1.354 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" C4 URC A 901 " pdb=" C5 URC A 901 " ideal model delta sigma weight residual 1.358 1.487 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C8 URC A 901 " pdb=" N7 URC A 901 " ideal model delta sigma weight residual 1.360 1.430 -0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 4138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 5583 2.66 - 5.32: 61 5.32 - 7.99: 5 7.99 - 10.65: 4 10.65 - 13.31: 3 Bond angle restraints: 5656 Sorted by residual: angle pdb=" N1 URC A 901 " pdb=" C2 URC A 901 " pdb=" N3 URC A 901 " ideal model delta sigma weight residual 114.62 127.93 -13.31 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C2 URC A 901 " pdb=" N1 URC A 901 " pdb=" C6 URC A 901 " ideal model delta sigma weight residual 129.31 117.43 11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N7 URC A 901 " pdb=" C8 URC A 901 " pdb=" N9 URC A 901 " ideal model delta sigma weight residual 104.73 116.29 -11.56 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C5 URC A 901 " pdb=" C6 URC A 901 " pdb=" N1 URC A 901 " ideal model delta sigma weight residual 111.19 121.50 -10.31 3.00e+00 1.11e-01 1.18e+01 angle pdb=" N7 URC A 901 " pdb=" C8 URC A 901 " pdb=" O24 URC A 901 " ideal model delta sigma weight residual 129.09 119.59 9.50 3.00e+00 1.11e-01 1.00e+01 ... (remaining 5651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 2292 17.32 - 34.65: 123 34.65 - 51.97: 19 51.97 - 69.29: 4 69.29 - 86.62: 2 Dihedral angle restraints: 2440 sinusoidal: 926 harmonic: 1514 Sorted by residual: dihedral pdb=" CG ARG A 401 " pdb=" CD ARG A 401 " pdb=" NE ARG A 401 " pdb=" CZ ARG A 401 " ideal model delta sinusoidal sigma weight residual -180.00 -137.90 -42.10 2 1.50e+01 4.44e-03 9.59e+00 dihedral pdb=" CB GLU A 278 " pdb=" CG GLU A 278 " pdb=" CD GLU A 278 " pdb=" OE1 GLU A 278 " ideal model delta sinusoidal sigma weight residual 0.00 -83.65 83.65 1 3.00e+01 1.11e-03 9.49e+00 dihedral pdb=" CA ASP A 335 " pdb=" C ASP A 335 " pdb=" N LEU A 336 " pdb=" CA LEU A 336 " ideal model delta harmonic sigma weight residual 180.00 165.35 14.65 0 5.00e+00 4.00e-02 8.59e+00 ... (remaining 2437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 362 0.026 - 0.052: 204 0.052 - 0.078: 63 0.078 - 0.104: 27 0.104 - 0.130: 9 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA PRO A 52 " pdb=" N PRO A 52 " pdb=" C PRO A 52 " pdb=" CB PRO A 52 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA TYR A 272 " pdb=" N TYR A 272 " pdb=" C TYR A 272 " pdb=" CB TYR A 272 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA PRO A 501 " pdb=" N PRO A 501 " pdb=" C PRO A 501 " pdb=" CB PRO A 501 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 662 not shown) Planarity restraints: 706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 479 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO A 480 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 297 " 0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C ARG A 297 " -0.021 2.00e-02 2.50e+03 pdb=" O ARG A 297 " 0.008 2.00e-02 2.50e+03 pdb=" N LYS A 298 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 272 " 0.010 2.00e-02 2.50e+03 8.56e-03 1.46e+00 pdb=" CG TYR A 272 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 272 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 272 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 272 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 272 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 272 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 272 " 0.002 2.00e-02 2.50e+03 ... (remaining 703 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1427 2.86 - 3.37: 4071 3.37 - 3.88: 6706 3.88 - 4.39: 7810 4.39 - 4.90: 12957 Nonbonded interactions: 32971 Sorted by model distance: nonbonded pdb=" OG SER A 239 " pdb=" OD2 ASP A 385 " model vdw 2.349 3.040 nonbonded pdb=" OE1 GLU A 220 " pdb=" OG SER A 279 " model vdw 2.398 3.040 nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.408 3.040 nonbonded pdb=" OH TYR A 451 " pdb=" O PRO A 512 " model vdw 2.439 3.040 nonbonded pdb=" OD2 ASP A 385 " pdb=" NZ LYS A 389 " model vdw 2.489 3.120 ... (remaining 32966 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: 2.910 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.006 0.152 4143 Z= 0.357 Angle : 0.788 13.310 5656 Z= 0.388 Chirality : 0.038 0.130 665 Planarity : 0.005 0.032 706 Dihedral : 11.089 86.615 1456 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 0.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 0.53 (0.37), residues: 527 helix: 0.17 (0.27), residues: 366 sheet: None (None), residues: 0 loop : 1.27 (0.53), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.003 0.001 HIS A 83 PHE 0.013 0.002 PHE A 358 TYR 0.021 0.002 TYR A 272 ARG 0.005 0.001 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 166 ARG cc_start: 0.7530 (ttt180) cc_final: 0.7323 (ttt90) REVERT: A 332 SER cc_start: 0.7736 (t) cc_final: 0.7193 (p) REVERT: A 335 ASP cc_start: 0.5566 (m-30) cc_final: 0.5218 (m-30) REVERT: A 340 PRO cc_start: 0.8075 (Cg_exo) cc_final: 0.7812 (Cg_endo) REVERT: A 349 SER cc_start: 0.7614 (t) cc_final: 0.7403 (p) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1564 time to fit residues: 15.7167 Evaluate side-chains 52 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.0770 chunk 40 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 30 optimal weight: 0.0060 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4143 Z= 0.177 Angle : 0.524 5.159 5656 Z= 0.267 Chirality : 0.039 0.123 665 Planarity : 0.004 0.034 706 Dihedral : 4.078 13.386 562 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.40 % Allowed : 8.62 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.37), residues: 527 helix: 0.90 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 1.34 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.011 0.001 PHE A 16 TYR 0.020 0.002 TYR A 272 ARG 0.003 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.397 Fit side-chains REVERT: A 146 GLN cc_start: 0.7310 (mt0) cc_final: 0.6377 (tp-100) REVERT: A 332 SER cc_start: 0.7515 (t) cc_final: 0.6798 (p) REVERT: A 335 ASP cc_start: 0.5200 (m-30) cc_final: 0.4821 (m-30) REVERT: A 513 GLU cc_start: 0.8106 (tp30) cc_final: 0.7844 (tp30) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 0.1409 time to fit residues: 11.9918 Evaluate side-chains 52 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.7494 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4143 Z= 0.181 Angle : 0.499 5.460 5656 Z= 0.251 Chirality : 0.038 0.120 665 Planarity : 0.004 0.035 706 Dihedral : 3.860 12.487 562 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.86 % Allowed : 10.02 % Favored : 88.11 % 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: 1.67 (0.37), residues: 527 helix: 1.26 (0.27), residues: 380 sheet: -1.54 (1.55), residues: 10 loop : 1.24 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 83 PHE 0.010 0.001 PHE A 358 TYR 0.020 0.002 TYR A 272 ARG 0.002 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7311 (mt0) cc_final: 0.6320 (tp-100) REVERT: A 332 SER cc_start: 0.7527 (t) cc_final: 0.6872 (p) REVERT: A 335 ASP cc_start: 0.5049 (m-30) cc_final: 0.4819 (m-30) outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 0.1314 time to fit residues: 10.3598 Evaluate side-chains 55 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 28 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7489 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4143 Z= 0.175 Angle : 0.476 5.227 5656 Z= 0.240 Chirality : 0.037 0.117 665 Planarity : 0.004 0.035 706 Dihedral : 3.731 11.928 562 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.33 % Allowed : 9.79 % Favored : 87.88 % 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: 1.84 (0.38), residues: 527 helix: 1.40 (0.27), residues: 381 sheet: -1.83 (1.61), residues: 10 loop : 1.29 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.000 HIS A 47 PHE 0.010 0.001 PHE A 358 TYR 0.019 0.002 TYR A 272 ARG 0.001 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 438 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.7021 (tt) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.1316 time to fit residues: 9.3471 Evaluate side-chains 53 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.0030 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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: 0.7501 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4143 Z= 0.188 Angle : 0.482 5.378 5656 Z= 0.240 Chirality : 0.037 0.118 665 Planarity : 0.004 0.035 706 Dihedral : 3.682 11.874 562 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.80 % Allowed : 9.79 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.38), residues: 527 helix: 1.48 (0.27), residues: 380 sheet: -1.66 (1.79), residues: 10 loop : 1.24 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 47 PHE 0.010 0.001 PHE A 358 TYR 0.020 0.002 TYR A 272 ARG 0.001 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.389 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 52 average time/residue: 0.1293 time to fit residues: 9.1104 Evaluate side-chains 51 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 48 optimal weight: 0.0670 chunk 5 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 378 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4143 Z= 0.130 Angle : 0.448 5.407 5656 Z= 0.223 Chirality : 0.035 0.121 665 Planarity : 0.004 0.036 706 Dihedral : 3.474 11.331 562 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.40 % Allowed : 12.12 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.38), residues: 527 helix: 1.73 (0.27), residues: 378 sheet: -1.60 (1.87), residues: 10 loop : 1.22 (0.56), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.000 HIS A 139 PHE 0.010 0.001 PHE A 201 TYR 0.017 0.001 TYR A 272 ARG 0.001 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 332 SER cc_start: 0.7325 (t) cc_final: 0.6711 (p) REVERT: A 335 ASP cc_start: 0.3946 (m-30) cc_final: 0.3635 (m-30) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.1397 time to fit residues: 9.3131 Evaluate side-chains 50 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 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: 0.7514 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4143 Z= 0.215 Angle : 0.502 5.939 5656 Z= 0.246 Chirality : 0.038 0.117 665 Planarity : 0.004 0.036 706 Dihedral : 3.652 11.943 562 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.86 % Allowed : 12.12 % Favored : 86.01 % 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: 1.96 (0.38), residues: 527 helix: 1.52 (0.27), residues: 380 sheet: -1.74 (1.80), residues: 10 loop : 1.24 (0.58), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.003 0.001 HIS A 47 PHE 0.012 0.001 PHE A 361 TYR 0.021 0.002 TYR A 272 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.412 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.1351 time to fit residues: 8.8046 Evaluate side-chains 48 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.0000 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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: 0.7502 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4143 Z= 0.189 Angle : 0.492 8.528 5656 Z= 0.240 Chirality : 0.037 0.119 665 Planarity : 0.004 0.035 706 Dihedral : 3.612 11.988 562 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.86 % Allowed : 12.12 % Favored : 86.01 % 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: 1.98 (0.38), residues: 527 helix: 1.54 (0.27), residues: 380 sheet: -1.93 (1.73), residues: 10 loop : 1.23 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 47 PHE 0.011 0.001 PHE A 361 TYR 0.019 0.002 TYR A 272 ARG 0.001 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.435 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 0.1361 time to fit residues: 9.0279 Evaluate side-chains 48 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.0000 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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: 0.7487 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4143 Z= 0.168 Angle : 0.475 5.490 5656 Z= 0.232 Chirality : 0.036 0.120 665 Planarity : 0.004 0.035 706 Dihedral : 3.540 11.702 562 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.10 % Allowed : 11.89 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.38), residues: 527 helix: 1.62 (0.27), residues: 380 sheet: -1.89 (1.74), residues: 10 loop : 1.24 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.000 HIS A 47 PHE 0.010 0.001 PHE A 361 TYR 0.018 0.001 TYR A 272 ARG 0.001 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7838 (t70) cc_final: 0.7220 (t0) outliers start: 9 outliers final: 9 residues processed: 50 average time/residue: 0.1382 time to fit residues: 9.4494 Evaluate side-chains 51 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 30.0000 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 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: 0.7511 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4143 Z= 0.205 Angle : 0.498 5.682 5656 Z= 0.243 Chirality : 0.037 0.119 665 Planarity : 0.004 0.035 706 Dihedral : 3.632 12.150 562 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.86 % Allowed : 12.35 % Favored : 85.78 % 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 (0.38), residues: 527 helix: 1.53 (0.27), residues: 380 sheet: -1.94 (1.74), residues: 10 loop : 1.24 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS A 47 PHE 0.011 0.001 PHE A 361 TYR 0.020 0.002 TYR A 272 ARG 0.001 0.000 ARG A 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7873 (t70) cc_final: 0.7258 (t0) outliers start: 8 outliers final: 8 residues processed: 47 average time/residue: 0.1596 time to fit residues: 10.2318 Evaluate side-chains 49 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.172245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.134121 restraints weight = 4407.629| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.01 r_work: 0.3415 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4143 Z= 0.188 Angle : 0.486 5.671 5656 Z= 0.237 Chirality : 0.037 0.120 665 Planarity : 0.004 0.035 706 Dihedral : 3.587 11.893 562 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.10 % Allowed : 12.12 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.38), residues: 527 helix: 1.58 (0.27), residues: 380 sheet: -1.90 (1.74), residues: 10 loop : 1.23 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 47 PHE 0.011 0.001 PHE A 361 TYR 0.019 0.002 TYR A 272 ARG 0.001 0.000 ARG A 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1424.86 seconds wall clock time: 25 minutes 48.42 seconds (1548.42 seconds total)