Starting phenix.real_space_refine on Sun Mar 10 18:31:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/03_2024/7fil_31602.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/03_2024/7fil_31602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/03_2024/7fil_31602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/03_2024/7fil_31602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/03_2024/7fil_31602.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fil_31602/03_2024/7fil_31602.pdb" } resolution = 3.0 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= 0.006 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 22 5.16 5 C 2551 2.51 5 N 673 2.21 5 O 747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 501": "OD1" <-> "OD2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A ASP 532": "OD1" <-> "OD2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A ARG 562": "NH1" <-> "NH2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 626": "OD1" <-> "OD2" Residue "A PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 636": "OD1" <-> "OD2" Residue "A ASP 644": "OD1" <-> "OD2" Residue "A GLU 646": "OE1" <-> "OE2" Residue "A ASP 660": "OD1" <-> "OD2" Residue "A ASP 665": "OD1" <-> "OD2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A ASP 696": "OD1" <-> "OD2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A ASP 722": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3993 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3993 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 22, 'TRANS': 481} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 2.74, per 1000 atoms: 0.69 Number of scatterers: 3993 At special positions: 0 Unit cell: (76.285, 77.672, 102.638, 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 22 16.00 O 747 8.00 N 673 7.00 C 2551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.71 Conformation dependent library (CDL) restraints added in 792.2 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 67.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 222 through 243 removed outlier: 4.095A pdb=" N LYS A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 removed outlier: 3.565A pdb=" N LYS A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.452A pdb=" N VAL A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 325 removed outlier: 3.654A pdb=" N ALA A 322 " --> pdb=" O CYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 362 Processing helix chain 'A' and resid 366 through 375 removed outlier: 3.800A pdb=" N SER A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 390 removed outlier: 4.342A pdb=" N PHE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 427 removed outlier: 3.880A pdb=" N SER A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.683A pdb=" N TRP A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 502 removed outlier: 3.536A pdb=" N LEU A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 539 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.940A pdb=" N LEU A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 588 " --> pdb=" O THR A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 614 removed outlier: 4.195A pdb=" N GLU A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) Proline residue: A 610 - end of helix removed outlier: 3.555A pdb=" N LEU A 614 " --> pdb=" O PRO A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 659 Processing helix chain 'A' and resid 662 through 671 removed outlier: 3.511A pdb=" N ILE A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 690 removed outlier: 3.508A pdb=" N TYR A 679 " --> pdb=" O ASN A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 713 removed outlier: 3.824A pdb=" N GLU A 701 " --> pdb=" O CYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 3.683A pdb=" N ALA A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) Proline residue: A 728 - end of helix 235 hydrogen bonds defined for protein. 705 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: 0.99 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1056 1.33 - 1.45: 701 1.45 - 1.57: 2286 1.57 - 1.69: 1 1.69 - 1.82: 31 Bond restraints: 4075 Sorted by residual: bond pdb=" N PRO A 314 " pdb=" CA PRO A 314 " ideal model delta sigma weight residual 1.469 1.692 -0.223 1.28e-02 6.10e+03 3.05e+02 bond pdb=" C LYS A 327 " pdb=" N PRO A 328 " ideal model delta sigma weight residual 1.333 1.499 -0.167 1.17e-02 7.31e+03 2.03e+02 bond pdb=" C VAL A 325 " pdb=" N PRO A 326 " ideal model delta sigma weight residual 1.332 1.509 -0.177 1.32e-02 5.74e+03 1.80e+02 bond pdb=" C GLU A 313 " pdb=" N PRO A 314 " ideal model delta sigma weight residual 1.334 1.450 -0.116 2.34e-02 1.83e+03 2.48e+01 bond pdb=" N LYS A 365 " pdb=" CA LYS A 365 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 9.02e+00 ... (remaining 4070 not shown) Histogram of bond angle deviations from ideal: 97.38 - 105.30: 71 105.30 - 113.22: 2301 113.22 - 121.14: 2168 121.14 - 129.06: 943 129.06 - 136.98: 38 Bond angle restraints: 5521 Sorted by residual: angle pdb=" C LYS A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta sigma weight residual 119.90 136.48 -16.58 1.05e+00 9.07e-01 2.49e+02 angle pdb=" C VAL A 325 " pdb=" N PRO A 326 " pdb=" CA PRO A 326 " ideal model delta sigma weight residual 119.76 134.51 -14.75 1.00e+00 1.00e+00 2.18e+02 angle pdb=" C GLU A 313 " pdb=" N PRO A 314 " pdb=" CA PRO A 314 " ideal model delta sigma weight residual 119.84 136.98 -17.14 1.25e+00 6.40e-01 1.88e+02 angle pdb=" N PRO A 314 " pdb=" CA PRO A 314 " pdb=" C PRO A 314 " ideal model delta sigma weight residual 112.47 97.38 15.09 2.06e+00 2.36e-01 5.37e+01 angle pdb=" CA PRO A 314 " pdb=" N PRO A 314 " pdb=" CD PRO A 314 " ideal model delta sigma weight residual 112.00 101.88 10.12 1.40e+00 5.10e-01 5.23e+01 ... (remaining 5516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 2098 17.76 - 35.52: 261 35.52 - 53.28: 80 53.28 - 71.04: 23 71.04 - 88.80: 7 Dihedral angle restraints: 2469 sinusoidal: 982 harmonic: 1487 Sorted by residual: dihedral pdb=" CA GLN A 564 " pdb=" C GLN A 564 " pdb=" N GLU A 565 " pdb=" CA GLU A 565 " ideal model delta harmonic sigma weight residual 180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" C TYR A 597 " pdb=" N TYR A 597 " pdb=" CA TYR A 597 " pdb=" CB TYR A 597 " ideal model delta harmonic sigma weight residual -122.60 -133.07 10.47 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" CA PRO A 462 " pdb=" C PRO A 462 " pdb=" N ARG A 463 " pdb=" CA ARG A 463 " ideal model delta harmonic sigma weight residual 180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 2466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 607 0.128 - 0.257: 15 0.257 - 0.385: 3 0.385 - 0.513: 0 0.513 - 0.641: 1 Chirality restraints: 626 Sorted by residual: chirality pdb=" CA PRO A 314 " pdb=" N PRO A 314 " pdb=" C PRO A 314 " pdb=" CB PRO A 314 " both_signs ideal model delta sigma weight residual False 2.72 3.36 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA TYR A 597 " pdb=" N TYR A 597 " pdb=" C TYR A 597 " pdb=" CB TYR A 597 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA LYS A 327 " pdb=" N LYS A 327 " pdb=" C LYS A 327 " pdb=" CB LYS A 327 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 623 not shown) Planarity restraints: 705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 322 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C ALA A 322 " -0.043 2.00e-02 2.50e+03 pdb=" O ALA A 322 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 323 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 360 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C THR A 360 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 360 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 361 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 314 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C PRO A 314 " 0.037 2.00e-02 2.50e+03 pdb=" O PRO A 314 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 315 " -0.012 2.00e-02 2.50e+03 ... (remaining 702 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 597 2.75 - 3.29: 4096 3.29 - 3.83: 6537 3.83 - 4.36: 7249 4.36 - 4.90: 12045 Nonbonded interactions: 30524 Sorted by model distance: nonbonded pdb=" O PHE A 632 " pdb=" N ASN A 634 " model vdw 2.213 2.520 nonbonded pdb=" O SER A 478 " pdb=" OG SER A 478 " model vdw 2.218 2.440 nonbonded pdb=" OG SER A 352 " pdb=" OD1 ASP A 423 " model vdw 2.224 2.440 nonbonded pdb=" ND2 ASN A 474 " pdb=" OG1 THR A 559 " model vdw 2.237 2.520 nonbonded pdb=" OE1 GLN A 324 " pdb=" NH1 ARG A 412 " model vdw 2.253 2.520 ... (remaining 30519 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: 0.370 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: 1.980 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.590 Find NCS groups from input model: 0.110 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 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 : 0.008 0.223 4075 Z= 0.513 Angle : 1.046 17.138 5521 Z= 0.706 Chirality : 0.062 0.641 626 Planarity : 0.005 0.040 705 Dihedral : 18.460 88.802 1497 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 1.21 % Allowed : 7.66 % Favored : 91.13 % Rotamer: Outliers : 8.76 % Allowed : 25.58 % Favored : 65.67 % Cbeta Deviations : 0.41 % 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: -1.82 (0.36), residues: 496 helix: -0.21 (0.27), residues: 318 sheet: None (None), residues: 0 loop : -3.06 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 439 HIS 0.004 0.001 HIS A 631 PHE 0.025 0.002 PHE A 376 TYR 0.011 0.002 TYR A 597 ARG 0.003 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 70 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6202 (mpp) cc_final: 0.5826 (mpt) REVERT: A 232 LEU cc_start: 0.8611 (tp) cc_final: 0.8389 (tp) REVERT: A 251 LYS cc_start: 0.7725 (tppp) cc_final: 0.7515 (mtmt) REVERT: A 363 HIS cc_start: 0.7800 (OUTLIER) cc_final: 0.7519 (t70) REVERT: A 393 ASN cc_start: 0.7785 (t0) cc_final: 0.7265 (t0) REVERT: A 397 GLN cc_start: 0.8108 (mt0) cc_final: 0.7762 (tm-30) REVERT: A 446 PHE cc_start: 0.7953 (m-80) cc_final: 0.7607 (m-10) REVERT: A 472 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7012 (pp20) REVERT: A 559 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8297 (m) REVERT: A 622 PRO cc_start: 0.6401 (Cg_exo) cc_final: 0.5544 (Cg_endo) REVERT: A 631 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7656 (t70) REVERT: A 632 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: A 716 PHE cc_start: 0.6143 (m-10) cc_final: 0.5756 (m-10) outliers start: 38 outliers final: 15 residues processed: 106 average time/residue: 1.0067 time to fit residues: 110.9106 Evaluate side-chains 78 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 631 HIS Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain A residue 727 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 378 ASN A 397 GLN A 430 HIS A 436 HIS A 466 GLN A 500 GLN A 555 GLN A 556 HIS A 695 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4075 Z= 0.203 Angle : 0.680 10.056 5521 Z= 0.344 Chirality : 0.041 0.180 626 Planarity : 0.005 0.054 705 Dihedral : 10.339 58.896 567 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.06 % Favored : 92.74 % Rotamer: Outliers : 10.37 % Allowed : 25.58 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.39), residues: 496 helix: 1.18 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.37 (0.49), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 530 HIS 0.004 0.001 HIS A 582 PHE 0.023 0.002 PHE A 629 TYR 0.018 0.001 TYR A 323 ARG 0.005 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 66 time to evaluate : 0.523 Fit side-chains REVERT: A 225 MET cc_start: 0.6013 (OUTLIER) cc_final: 0.5459 (mmm) REVERT: A 232 LEU cc_start: 0.8536 (tp) cc_final: 0.8307 (tp) REVERT: A 233 LEU cc_start: 0.4286 (OUTLIER) cc_final: 0.3849 (mp) REVERT: A 285 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6601 (mpt) REVERT: A 291 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6976 (ttm) REVERT: A 393 ASN cc_start: 0.7892 (t0) cc_final: 0.7592 (t0) REVERT: A 397 GLN cc_start: 0.8065 (mt0) cc_final: 0.7827 (tm-30) REVERT: A 448 SER cc_start: 0.7723 (OUTLIER) cc_final: 0.7217 (p) REVERT: A 466 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.6817 (tm-30) REVERT: A 569 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7600 (mp) REVERT: A 631 HIS cc_start: 0.7640 (OUTLIER) cc_final: 0.6515 (m90) REVERT: A 632 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6630 (m-80) REVERT: A 648 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7102 (mm-30) REVERT: A 716 PHE cc_start: 0.6427 (m-10) cc_final: 0.5917 (m-10) outliers start: 45 outliers final: 13 residues processed: 97 average time/residue: 0.8791 time to fit residues: 89.0918 Evaluate side-chains 83 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 631 HIS Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain A residue 697 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4075 Z= 0.221 Angle : 0.679 10.270 5521 Z= 0.339 Chirality : 0.041 0.193 626 Planarity : 0.005 0.057 705 Dihedral : 8.486 57.692 550 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.66 % Favored : 92.14 % Rotamer: Outliers : 10.37 % Allowed : 27.42 % Favored : 62.21 % 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: 0.42 (0.39), residues: 496 helix: 1.60 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.44 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 530 HIS 0.004 0.001 HIS A 582 PHE 0.017 0.002 PHE A 629 TYR 0.010 0.001 TYR A 289 ARG 0.003 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 62 time to evaluate : 0.470 Fit side-chains REVERT: A 225 MET cc_start: 0.5893 (OUTLIER) cc_final: 0.5516 (mmm) REVERT: A 232 LEU cc_start: 0.8448 (tp) cc_final: 0.8241 (tp) REVERT: A 285 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6842 (mpt) REVERT: A 323 TYR cc_start: 0.6828 (t80) cc_final: 0.6607 (t80) REVERT: A 393 ASN cc_start: 0.8318 (t0) cc_final: 0.7737 (t0) REVERT: A 397 GLN cc_start: 0.8080 (mt0) cc_final: 0.7841 (tm-30) REVERT: A 466 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: A 512 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7181 (mtp180) REVERT: A 569 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7886 (mp) REVERT: A 632 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.6717 (m-80) REVERT: A 651 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.7011 (tt) REVERT: A 707 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7242 (mt0) outliers start: 45 outliers final: 18 residues processed: 99 average time/residue: 0.8490 time to fit residues: 87.9055 Evaluate side-chains 79 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 54 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 707 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 43 optimal weight: 0.4980 chunk 13 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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: 0.7193 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4075 Z= 0.191 Angle : 0.657 12.584 5521 Z= 0.322 Chirality : 0.040 0.191 626 Planarity : 0.005 0.054 705 Dihedral : 7.464 55.476 546 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.85 % Favored : 92.94 % Rotamer: Outliers : 8.99 % Allowed : 28.34 % Favored : 62.67 % 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: 0.94 (0.39), residues: 496 helix: 2.05 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.36 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 530 HIS 0.004 0.001 HIS A 582 PHE 0.013 0.002 PHE A 629 TYR 0.007 0.001 TYR A 323 ARG 0.003 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 60 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.5856 (OUTLIER) cc_final: 0.5417 (mmm) REVERT: A 232 LEU cc_start: 0.8408 (tp) cc_final: 0.8196 (tp) REVERT: A 233 LEU cc_start: 0.4217 (OUTLIER) cc_final: 0.3764 (mp) REVERT: A 323 TYR cc_start: 0.7169 (t80) cc_final: 0.6923 (t80) REVERT: A 466 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6614 (tm-30) REVERT: A 513 CYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6247 (t) REVERT: A 632 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6468 (m-80) outliers start: 39 outliers final: 13 residues processed: 88 average time/residue: 0.8406 time to fit residues: 77.5144 Evaluate side-chains 75 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 513 CYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 697 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.0570 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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: 0.7201 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4075 Z= 0.200 Angle : 0.639 11.062 5521 Z= 0.314 Chirality : 0.039 0.179 626 Planarity : 0.004 0.053 705 Dihedral : 7.155 57.913 542 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.46 % Favored : 92.34 % Rotamer: Outliers : 7.14 % Allowed : 33.18 % Favored : 59.68 % 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: 1.23 (0.39), residues: 496 helix: 2.32 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.34 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 577 HIS 0.004 0.001 HIS A 582 PHE 0.024 0.002 PHE A 376 TYR 0.008 0.001 TYR A 289 ARG 0.002 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 59 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.5388 (mmm) REVERT: A 233 LEU cc_start: 0.4301 (OUTLIER) cc_final: 0.3814 (mp) REVERT: A 323 TYR cc_start: 0.7126 (t80) cc_final: 0.6888 (t80) REVERT: A 379 GLN cc_start: 0.7116 (mm110) cc_final: 0.6905 (mp10) REVERT: A 512 ARG cc_start: 0.7893 (mpp-170) cc_final: 0.7595 (mpp-170) REVERT: A 520 LYS cc_start: 0.7076 (ttmm) cc_final: 0.6807 (tttp) REVERT: A 600 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6712 (mmt90) REVERT: A 626 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: A 632 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6511 (m-80) REVERT: A 651 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6976 (tt) outliers start: 31 outliers final: 15 residues processed: 83 average time/residue: 0.9739 time to fit residues: 84.4037 Evaluate side-chains 79 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 58 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 709 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.0070 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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: 0.7224 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4075 Z= 0.217 Angle : 0.648 10.554 5521 Z= 0.322 Chirality : 0.040 0.176 626 Planarity : 0.004 0.051 705 Dihedral : 6.460 56.025 538 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.66 % Favored : 92.14 % Rotamer: Outliers : 6.91 % Allowed : 32.95 % Favored : 60.14 % 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: 1.25 (0.39), residues: 496 helix: 2.32 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.28 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 577 HIS 0.004 0.001 HIS A 582 PHE 0.013 0.002 PHE A 629 TYR 0.009 0.001 TYR A 289 ARG 0.005 0.001 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 65 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.5831 (OUTLIER) cc_final: 0.5398 (mmm) REVERT: A 233 LEU cc_start: 0.4285 (OUTLIER) cc_final: 0.3837 (mp) REVERT: A 241 PHE cc_start: 0.5647 (t80) cc_final: 0.5364 (t80) REVERT: A 285 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7560 (mmt) REVERT: A 323 TYR cc_start: 0.7124 (t80) cc_final: 0.6892 (t80) REVERT: A 379 GLN cc_start: 0.7266 (mm110) cc_final: 0.6995 (mp10) REVERT: A 393 ASN cc_start: 0.7445 (t0) cc_final: 0.7239 (t0) REVERT: A 600 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6686 (mmt90) REVERT: A 626 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: A 632 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7072 (m-80) REVERT: A 651 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.7102 (tt) outliers start: 30 outliers final: 14 residues processed: 89 average time/residue: 0.9199 time to fit residues: 85.5034 Evaluate side-chains 83 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 709 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- 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: 0.7252 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4075 Z= 0.245 Angle : 0.664 9.667 5521 Z= 0.333 Chirality : 0.041 0.195 626 Planarity : 0.004 0.050 705 Dihedral : 6.507 55.948 538 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.06 % Favored : 91.73 % Rotamer: Outliers : 7.14 % Allowed : 33.87 % Favored : 58.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.39), residues: 496 helix: 2.23 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.41 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 577 HIS 0.005 0.001 HIS A 582 PHE 0.012 0.002 PHE A 629 TYR 0.009 0.001 TYR A 289 ARG 0.002 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 62 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.5771 (OUTLIER) cc_final: 0.5347 (mmm) REVERT: A 233 LEU cc_start: 0.4348 (OUTLIER) cc_final: 0.3890 (mp) REVERT: A 285 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7153 (mmt) REVERT: A 323 TYR cc_start: 0.7136 (t80) cc_final: 0.6916 (t80) REVERT: A 385 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7781 (tm) REVERT: A 520 LYS cc_start: 0.7150 (ttmm) cc_final: 0.6876 (tttp) REVERT: A 557 ASP cc_start: 0.6274 (m-30) cc_final: 0.5808 (m-30) REVERT: A 600 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6735 (mmt90) REVERT: A 626 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: A 707 GLN cc_start: 0.7582 (mp10) cc_final: 0.7370 (mt0) outliers start: 31 outliers final: 16 residues processed: 86 average time/residue: 0.9703 time to fit residues: 86.9089 Evaluate side-chains 85 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 63 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 709 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.0370 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4075 Z= 0.207 Angle : 0.666 10.281 5521 Z= 0.326 Chirality : 0.040 0.198 626 Planarity : 0.004 0.051 705 Dihedral : 6.296 56.286 538 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.46 % Favored : 92.34 % Rotamer: Outliers : 5.76 % Allowed : 35.71 % Favored : 58.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.39), residues: 496 helix: 2.43 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.36 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 530 HIS 0.004 0.001 HIS A 582 PHE 0.011 0.001 PHE A 629 TYR 0.007 0.001 TYR A 289 ARG 0.002 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 62 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.5493 (mmm) REVERT: A 233 LEU cc_start: 0.4422 (OUTLIER) cc_final: 0.4018 (mp) REVERT: A 241 PHE cc_start: 0.5529 (t80) cc_final: 0.5269 (t80) REVERT: A 285 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7055 (mmt) REVERT: A 323 TYR cc_start: 0.7186 (t80) cc_final: 0.6932 (t80) REVERT: A 385 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7639 (tm) REVERT: A 410 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6818 (mt-10) REVERT: A 520 LYS cc_start: 0.7120 (ttmm) cc_final: 0.6845 (tttp) REVERT: A 557 ASP cc_start: 0.6118 (m-30) cc_final: 0.5525 (m-30) REVERT: A 600 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.6915 (mmt90) REVERT: A 626 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7422 (m-30) outliers start: 25 outliers final: 17 residues processed: 81 average time/residue: 0.9426 time to fit residues: 79.6424 Evaluate side-chains 81 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 58 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 709 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4075 Z= 0.223 Angle : 0.671 9.618 5521 Z= 0.332 Chirality : 0.040 0.196 626 Planarity : 0.004 0.050 705 Dihedral : 6.344 56.394 538 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.86 % Favored : 91.94 % Rotamer: Outliers : 5.99 % Allowed : 35.48 % Favored : 58.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.39), residues: 496 helix: 2.37 (0.27), residues: 324 sheet: None (None), residues: 0 loop : -2.33 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 530 HIS 0.004 0.001 HIS A 582 PHE 0.011 0.001 PHE A 629 TYR 0.009 0.001 TYR A 289 ARG 0.008 0.001 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 62 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.5908 (OUTLIER) cc_final: 0.5476 (mmm) REVERT: A 233 LEU cc_start: 0.4449 (OUTLIER) cc_final: 0.4065 (mp) REVERT: A 285 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6978 (mmt) REVERT: A 323 TYR cc_start: 0.7197 (t80) cc_final: 0.6952 (t80) REVERT: A 385 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7719 (tm) REVERT: A 410 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6801 (mt-10) REVERT: A 520 LYS cc_start: 0.7136 (ttmm) cc_final: 0.6854 (tttp) REVERT: A 557 ASP cc_start: 0.6135 (m-30) cc_final: 0.5769 (m-30) REVERT: A 600 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6692 (mmt90) REVERT: A 626 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7457 (m-30) outliers start: 26 outliers final: 18 residues processed: 81 average time/residue: 0.9703 time to fit residues: 81.8011 Evaluate side-chains 80 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 56 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 709 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.0070 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4075 Z= 0.207 Angle : 0.670 9.452 5521 Z= 0.329 Chirality : 0.040 0.204 626 Planarity : 0.004 0.050 705 Dihedral : 6.235 56.522 538 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.06 % Favored : 92.74 % Rotamer: Outliers : 5.53 % Allowed : 36.41 % Favored : 58.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.39), residues: 496 helix: 2.47 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.29 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 680 HIS 0.003 0.001 HIS A 582 PHE 0.010 0.001 PHE A 629 TYR 0.008 0.001 TYR A 289 ARG 0.002 0.000 ARG A 463 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.5913 (OUTLIER) cc_final: 0.5517 (mmm) REVERT: A 233 LEU cc_start: 0.4429 (OUTLIER) cc_final: 0.4077 (mp) REVERT: A 285 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6999 (mmt) REVERT: A 323 TYR cc_start: 0.7336 (t80) cc_final: 0.7078 (t80) REVERT: A 385 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7673 (tm) REVERT: A 410 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6807 (mt-10) REVERT: A 520 LYS cc_start: 0.7124 (ttmm) cc_final: 0.6853 (tttm) REVERT: A 565 GLU cc_start: 0.7035 (mp0) cc_final: 0.6736 (tm-30) REVERT: A 600 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6651 (mmt90) REVERT: A 632 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6803 (m-80) outliers start: 24 outliers final: 16 residues processed: 79 average time/residue: 1.0081 time to fit residues: 82.8978 Evaluate side-chains 76 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 54 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 709 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.154089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.131894 restraints weight = 6367.191| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 3.04 r_work: 0.3883 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4075 Z= 0.213 Angle : 0.673 9.355 5521 Z= 0.332 Chirality : 0.040 0.200 626 Planarity : 0.004 0.051 705 Dihedral : 6.221 56.523 538 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.06 % Favored : 92.74 % Rotamer: Outliers : 5.76 % Allowed : 36.18 % Favored : 58.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.39), residues: 496 helix: 2.46 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.27 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 680 HIS 0.003 0.001 HIS A 582 PHE 0.008 0.001 PHE A 629 TYR 0.008 0.001 TYR A 289 ARG 0.003 0.000 ARG A 528 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2049.86 seconds wall clock time: 37 minutes 29.61 seconds (2249.61 seconds total)