Starting phenix.real_space_refine on Fri Apr 5 15:55:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc2_40335/04_2024/8sc2_40335_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc2_40335/04_2024/8sc2_40335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc2_40335/04_2024/8sc2_40335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc2_40335/04_2024/8sc2_40335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc2_40335/04_2024/8sc2_40335_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc2_40335/04_2024/8sc2_40335_updated.pdb" } resolution = 3.36 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= 0.018 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 32 5.16 5 C 2330 2.51 5 N 572 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3534 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3505 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 24, 'TRANS': 428} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'C9F': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.72 Number of scatterers: 3534 At special positions: 0 Unit cell: (88.2, 82.32, 66.36, 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 32 16.00 O 600 8.00 N 572 7.00 C 2330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 711.4 milliseconds 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 1 sheets defined 74.6% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.631A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 38 through 42 removed outlier: 3.608A pdb=" N LEU A 42 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.786A pdb=" N ASN A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 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 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 142 through 172 removed outlier: 4.383A pdb=" N TRP A 146 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 149 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS A 154 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A 165 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL A 166 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 195 removed outlier: 3.848A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 227 removed outlier: 3.712A pdb=" N VAL A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 257 removed outlier: 3.925A pdb=" N ARG A 233 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 235 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 278 Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.575A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 339 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 371 Processing helix chain 'A' and resid 375 through 400 removed outlier: 3.503A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix removed outlier: 4.025A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.919A pdb=" N ILE A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 456 removed outlier: 3.668A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 490 removed outlier: 3.962A pdb=" N LEU A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N CYS A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 3.552A pdb=" N LEU A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 4.271A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 48 through 50 214 hydrogen bonds defined for protein. 498 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: 0.91 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 637 1.33 - 1.45: 975 1.45 - 1.58: 1970 1.58 - 1.71: 0 1.71 - 1.83: 48 Bond restraints: 3630 Sorted by residual: bond pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta sigma weight residual 1.461 1.498 -0.038 1.19e-02 7.06e+03 9.96e+00 bond pdb=" N VAL A 37 " pdb=" CA VAL A 37 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.19e+00 bond pdb=" N LEU A 248 " pdb=" CA LEU A 248 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 7.04e+00 bond pdb=" N LEU A 251 " pdb=" CA LEU A 251 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.63e+00 bond pdb=" N TRP A 64 " pdb=" CA TRP A 64 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.24e-02 6.50e+03 5.82e+00 ... (remaining 3625 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.92: 129 106.92 - 113.75: 1991 113.75 - 120.58: 1561 120.58 - 127.41: 1224 127.41 - 134.23: 46 Bond angle restraints: 4951 Sorted by residual: angle pdb=" CA ILE A 365 " pdb=" C ILE A 365 " pdb=" O ILE A 365 " ideal model delta sigma weight residual 120.95 117.51 3.44 1.04e+00 9.25e-01 1.10e+01 angle pdb=" CA CYS A 36 " pdb=" C CYS A 36 " pdb=" O CYS A 36 " ideal model delta sigma weight residual 120.70 117.45 3.25 1.03e+00 9.43e-01 9.93e+00 angle pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" O VAL A 40 " ideal model delta sigma weight residual 120.57 117.59 2.98 1.07e+00 8.73e-01 7.78e+00 angle pdb=" C GLU A 386 " pdb=" N ILE A 387 " pdb=" CA ILE A 387 " ideal model delta sigma weight residual 120.33 122.52 -2.19 8.00e-01 1.56e+00 7.49e+00 angle pdb=" N ASP A 149 " pdb=" CA ASP A 149 " pdb=" C ASP A 149 " ideal model delta sigma weight residual 111.71 108.79 2.92 1.15e+00 7.56e-01 6.43e+00 ... (remaining 4946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.24: 1889 9.24 - 18.49: 164 18.49 - 27.73: 47 27.73 - 36.98: 17 36.98 - 46.22: 6 Dihedral angle restraints: 2123 sinusoidal: 826 harmonic: 1297 Sorted by residual: dihedral pdb=" N LEU A 192 " pdb=" CA LEU A 192 " pdb=" CB LEU A 192 " pdb=" CG LEU A 192 " ideal model delta sinusoidal sigma weight residual -60.00 -101.37 41.37 3 1.50e+01 4.44e-03 7.40e+00 dihedral pdb=" N GLN A 241 " pdb=" CA GLN A 241 " pdb=" CB GLN A 241 " pdb=" CG GLN A 241 " ideal model delta sinusoidal sigma weight residual -180.00 -140.11 -39.89 3 1.50e+01 4.44e-03 7.09e+00 dihedral pdb=" C ILE A 365 " pdb=" N ILE A 365 " pdb=" CA ILE A 365 " pdb=" CB ILE A 365 " ideal model delta harmonic sigma weight residual -122.00 -128.63 6.63 0 2.50e+00 1.60e-01 7.04e+00 ... (remaining 2120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 447 0.044 - 0.087: 93 0.087 - 0.130: 26 0.130 - 0.174: 3 0.174 - 0.217: 2 Chirality restraints: 571 Sorted by residual: chirality pdb=" CA ILE A 35 " pdb=" N ILE A 35 " pdb=" C ILE A 35 " pdb=" CB ILE A 35 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA LEU A 248 " pdb=" N LEU A 248 " pdb=" C LEU A 248 " pdb=" CB LEU A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CB ILE A 35 " pdb=" CA ILE A 35 " pdb=" CG1 ILE A 35 " pdb=" CG2 ILE A 35 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 568 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 40 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C VAL A 40 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL A 40 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 41 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 196 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 197 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 258 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 259 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.016 5.00e-02 4.00e+02 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 843 2.79 - 3.31: 3523 3.31 - 3.84: 5619 3.84 - 4.37: 6440 4.37 - 4.90: 11287 Nonbonded interactions: 27712 Sorted by model distance: nonbonded pdb=" OD1 ASN A 198 " pdb=" OG SER A 201 " model vdw 2.258 2.440 nonbonded pdb=" O ILE A 392 " pdb=" OG1 THR A 396 " model vdw 2.265 2.440 nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.297 2.440 nonbonded pdb=" O GLN A 209 " pdb=" OG SER A 213 " model vdw 2.317 2.440 nonbonded pdb=" O CYS A 142 " pdb=" OG SER A 145 " model vdw 2.360 2.440 ... (remaining 27707 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 3.690 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.140 Find NCS groups from input model: 0.090 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:2.910 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.003 0.038 3630 Z= 0.208 Angle : 0.551 5.341 4951 Z= 0.345 Chirality : 0.041 0.217 571 Planarity : 0.004 0.036 612 Dihedral : 8.521 46.221 1284 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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: 2.79 (0.42), residues: 449 helix: 2.07 (0.31), residues: 311 sheet: None (None), residues: 0 loop : 1.57 (0.60), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.007 0.001 TYR A 168 ARG 0.002 0.000 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8480 (tpt) cc_final: 0.8139 (tpt) REVERT: A 431 ASN cc_start: 0.8059 (t0) cc_final: 0.7805 (t0) REVERT: A 435 MET cc_start: 0.8132 (tpp) cc_final: 0.7737 (tpp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1804 time to fit residues: 24.0991 Evaluate side-chains 83 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 156 ASN A 367 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3630 Z= 0.179 Angle : 0.543 7.481 4951 Z= 0.276 Chirality : 0.039 0.213 571 Planarity : 0.005 0.032 612 Dihedral : 4.221 30.759 516 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.12 % Allowed : 9.55 % Favored : 88.33 % 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: 2.60 (0.41), residues: 449 helix: 2.03 (0.31), residues: 305 sheet: None (None), residues: 0 loop : 1.25 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.001 0.000 HIS A 367 PHE 0.014 0.001 PHE A 334 TYR 0.012 0.001 TYR A 72 ARG 0.004 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8103 (t0) REVERT: A 431 ASN cc_start: 0.7996 (t0) cc_final: 0.7592 (t0) REVERT: A 435 MET cc_start: 0.8058 (tpp) cc_final: 0.7733 (tpp) outliers start: 8 outliers final: 3 residues processed: 88 average time/residue: 0.1242 time to fit residues: 13.8717 Evaluate side-chains 81 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 396 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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: 0.8040 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3630 Z= 0.175 Angle : 0.536 8.452 4951 Z= 0.267 Chirality : 0.038 0.184 571 Planarity : 0.004 0.034 612 Dihedral : 4.254 31.210 516 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.65 % Allowed : 11.14 % Favored : 86.21 % 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: 2.17 (0.41), residues: 449 helix: 1.73 (0.31), residues: 305 sheet: None (None), residues: 0 loop : 1.03 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.016 0.001 PHE A 334 TYR 0.014 0.001 TYR A 72 ARG 0.004 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8207 (tm-30) REVERT: A 431 ASN cc_start: 0.8009 (t0) cc_final: 0.7641 (t0) REVERT: A 435 MET cc_start: 0.8075 (tpp) cc_final: 0.7746 (tpp) REVERT: A 479 ILE cc_start: 0.6982 (mm) cc_final: 0.6764 (mt) REVERT: A 504 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7581 (mm) outliers start: 10 outliers final: 6 residues processed: 90 average time/residue: 0.1346 time to fit residues: 15.4013 Evaluate side-chains 86 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3630 Z= 0.257 Angle : 0.573 8.350 4951 Z= 0.286 Chirality : 0.040 0.189 571 Planarity : 0.005 0.038 612 Dihedral : 4.340 23.482 516 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.71 % Allowed : 11.67 % Favored : 84.62 % 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: 1.83 (0.41), residues: 449 helix: 1.43 (0.31), residues: 306 sheet: None (None), residues: 0 loop : 1.02 (0.56), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.011 0.001 PHE A 32 TYR 0.010 0.001 TYR A 72 ARG 0.002 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7576 (ptt180) cc_final: 0.7289 (ptt90) REVERT: A 122 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8250 (tm-30) REVERT: A 357 ASP cc_start: 0.8274 (m-30) cc_final: 0.7942 (m-30) REVERT: A 435 MET cc_start: 0.8129 (tpp) cc_final: 0.7822 (tpp) REVERT: A 448 MET cc_start: 0.8373 (mmm) cc_final: 0.8085 (mmm) outliers start: 14 outliers final: 9 residues processed: 91 average time/residue: 0.1274 time to fit residues: 14.7587 Evaluate side-chains 82 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 511 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.0050 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- 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: 0.8086 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3630 Z= 0.203 Angle : 0.567 8.961 4951 Z= 0.274 Chirality : 0.039 0.155 571 Planarity : 0.004 0.034 612 Dihedral : 4.299 25.438 516 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.71 % Allowed : 11.41 % Favored : 84.88 % 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: 1.92 (0.42), residues: 449 helix: 1.48 (0.31), residues: 306 sheet: None (None), residues: 0 loop : 1.08 (0.57), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.010 0.001 PHE A 355 TYR 0.010 0.001 TYR A 72 ARG 0.002 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8341 (tm-30) REVERT: A 123 ASP cc_start: 0.8242 (m-30) cc_final: 0.7656 (m-30) REVERT: A 435 MET cc_start: 0.8132 (tpp) cc_final: 0.7826 (tpp) REVERT: A 448 MET cc_start: 0.8367 (mmm) cc_final: 0.8065 (mmm) REVERT: A 472 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8042 (mm) REVERT: A 498 LEU cc_start: 0.7981 (tt) cc_final: 0.7454 (mm) outliers start: 14 outliers final: 9 residues processed: 89 average time/residue: 0.1313 time to fit residues: 14.9118 Evaluate side-chains 86 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3630 Z= 0.275 Angle : 0.605 8.667 4951 Z= 0.296 Chirality : 0.042 0.277 571 Planarity : 0.005 0.038 612 Dihedral : 4.414 21.273 516 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.71 % Allowed : 13.26 % Favored : 83.02 % 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: 1.70 (0.42), residues: 449 helix: 1.32 (0.31), residues: 305 sheet: None (None), residues: 0 loop : 0.99 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.011 0.001 PHE A 32 TYR 0.010 0.001 TYR A 72 ARG 0.004 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8357 (tm-30) REVERT: A 123 ASP cc_start: 0.8088 (m-30) cc_final: 0.7719 (m-30) REVERT: A 435 MET cc_start: 0.8143 (tpp) cc_final: 0.7852 (tpp) REVERT: A 472 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8101 (mm) REVERT: A 498 LEU cc_start: 0.8051 (tt) cc_final: 0.7498 (mm) outliers start: 14 outliers final: 11 residues processed: 86 average time/residue: 0.1424 time to fit residues: 15.5405 Evaluate side-chains 85 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 511 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.0020 chunk 29 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3630 Z= 0.182 Angle : 0.567 8.951 4951 Z= 0.276 Chirality : 0.040 0.239 571 Planarity : 0.004 0.032 612 Dihedral : 4.342 27.205 516 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.45 % Allowed : 14.32 % Favored : 82.23 % 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: 1.85 (0.42), residues: 449 helix: 1.46 (0.31), residues: 305 sheet: None (None), residues: 0 loop : 0.98 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 355 TYR 0.011 0.001 TYR A 72 ARG 0.005 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8292 (tm-30) REVERT: A 123 ASP cc_start: 0.8049 (m-30) cc_final: 0.7623 (m-30) REVERT: A 435 MET cc_start: 0.8110 (tpp) cc_final: 0.7810 (tpp) REVERT: A 448 MET cc_start: 0.8331 (mmm) cc_final: 0.8003 (mmm) REVERT: A 472 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8032 (mm) REVERT: A 498 LEU cc_start: 0.8065 (tt) cc_final: 0.7530 (mm) outliers start: 13 outliers final: 10 residues processed: 86 average time/residue: 0.1468 time to fit residues: 15.9116 Evaluate side-chains 89 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.9520 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3630 Z= 0.218 Angle : 0.584 9.194 4951 Z= 0.284 Chirality : 0.041 0.220 571 Planarity : 0.004 0.035 612 Dihedral : 4.375 25.881 516 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.92 % Allowed : 14.59 % Favored : 82.49 % 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: 1.69 (0.42), residues: 449 helix: 1.35 (0.31), residues: 305 sheet: -0.73 (1.49), residues: 10 loop : 1.01 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.011 0.001 PHE A 355 TYR 0.011 0.001 TYR A 72 ARG 0.005 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7799 (m-10) cc_final: 0.7546 (m-10) REVERT: A 122 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8300 (tm-30) REVERT: A 123 ASP cc_start: 0.8107 (m-30) cc_final: 0.7657 (m-30) REVERT: A 435 MET cc_start: 0.8129 (tpp) cc_final: 0.7826 (tpp) REVERT: A 448 MET cc_start: 0.8350 (mmm) cc_final: 0.8025 (mmm) REVERT: A 472 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8034 (mm) REVERT: A 498 LEU cc_start: 0.8058 (tt) cc_final: 0.7517 (mm) outliers start: 11 outliers final: 10 residues processed: 82 average time/residue: 0.1283 time to fit residues: 13.4605 Evaluate side-chains 85 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.0060 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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: 0.8066 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3630 Z= 0.160 Angle : 0.577 9.363 4951 Z= 0.279 Chirality : 0.040 0.214 571 Planarity : 0.004 0.031 612 Dihedral : 4.298 30.722 516 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.65 % Allowed : 15.65 % Favored : 81.70 % 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: 1.73 (0.42), residues: 449 helix: 1.39 (0.31), residues: 305 sheet: -0.71 (1.53), residues: 10 loop : 1.00 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.010 0.001 TYR A 72 ARG 0.005 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7765 (m-10) cc_final: 0.7508 (m-10) REVERT: A 122 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 123 ASP cc_start: 0.8044 (m-30) cc_final: 0.7585 (m-30) REVERT: A 233 ARG cc_start: 0.7316 (mtt180) cc_final: 0.6368 (ttt180) REVERT: A 435 MET cc_start: 0.8104 (tpp) cc_final: 0.7803 (tpp) REVERT: A 448 MET cc_start: 0.8310 (mmm) cc_final: 0.7949 (mmm) REVERT: A 472 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8031 (mm) REVERT: A 479 ILE cc_start: 0.6958 (mm) cc_final: 0.6741 (mt) REVERT: A 498 LEU cc_start: 0.8041 (tt) cc_final: 0.7500 (mm) outliers start: 10 outliers final: 8 residues processed: 85 average time/residue: 0.1380 time to fit residues: 14.7908 Evaluate side-chains 89 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 0.0270 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.0270 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 overall best weight: 0.3854 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3630 Z= 0.145 Angle : 0.577 9.651 4951 Z= 0.281 Chirality : 0.041 0.323 571 Planarity : 0.004 0.029 612 Dihedral : 4.278 35.757 516 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.12 % Allowed : 16.71 % Favored : 81.17 % 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: 1.81 (0.42), residues: 449 helix: 1.41 (0.31), residues: 306 sheet: None (None), residues: 0 loop : 1.01 (0.57), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 354 HIS 0.002 0.001 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.010 0.001 TYR A 72 ARG 0.005 0.000 ARG A 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7709 (m-10) cc_final: 0.7493 (m-10) REVERT: A 122 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8316 (tm-30) REVERT: A 123 ASP cc_start: 0.8010 (m-30) cc_final: 0.7582 (m-30) REVERT: A 233 ARG cc_start: 0.7265 (mtt180) cc_final: 0.6375 (ttt180) REVERT: A 435 MET cc_start: 0.8125 (tpp) cc_final: 0.7811 (tpp) REVERT: A 448 MET cc_start: 0.8276 (mmm) cc_final: 0.7942 (mmm) REVERT: A 472 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8044 (mm) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.1436 time to fit residues: 15.4147 Evaluate side-chains 90 residues out of total 377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.187748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.146269 restraints weight = 4770.622| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.65 r_work: 0.3466 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3630 Z= 0.191 Angle : 0.587 9.433 4951 Z= 0.287 Chirality : 0.042 0.306 571 Planarity : 0.004 0.031 612 Dihedral : 4.272 32.830 516 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.92 % Allowed : 16.71 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.42), residues: 449 helix: 1.36 (0.31), residues: 306 sheet: None (None), residues: 0 loop : 0.97 (0.57), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.010 0.001 PHE A 355 TYR 0.010 0.001 TYR A 72 ARG 0.006 0.000 ARG A 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1265.57 seconds wall clock time: 23 minutes 31.50 seconds (1411.50 seconds total)