Starting phenix.real_space_refine on Tue Feb 13 06:19:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dha_27434/02_2024/8dha_27434.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dha_27434/02_2024/8dha_27434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dha_27434/02_2024/8dha_27434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dha_27434/02_2024/8dha_27434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dha_27434/02_2024/8dha_27434.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dha_27434/02_2024/8dha_27434.pdb" } resolution = 3.8 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= 0.014 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 16 5.16 5 C 2234 2.51 5 N 596 2.21 5 O 664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 85": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3510 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 89} Chain: "B" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1622 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 188} Chain: "C" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1087 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.47, per 1000 atoms: 0.70 Number of scatterers: 3510 At special positions: 0 Unit cell: (103.786, 72.7693, 95.4352, 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 16 16.00 O 664 8.00 N 596 7.00 C 2234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 496 " 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 345 " " NAG B 901 " - " ASN B 622 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 523.3 milliseconds 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 844 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 25.7% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.739A pdb=" N VAL B 532 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 533 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 26 Processing helix chain 'C' and resid 50 through 67 Processing helix chain 'C' and resid 70 through 94 Processing helix chain 'C' and resid 107 through 117 removed outlier: 3.554A pdb=" N ASP C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 141 removed outlier: 4.393A pdb=" N ASP C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 339 removed outlier: 5.963A pdb=" N ILE A 338 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 408 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 365 " --> pdb=" O CYS A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 339 removed outlier: 5.963A pdb=" N ILE A 338 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 408 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 347 removed outlier: 3.788A pdb=" N ALA A 346 " --> pdb=" O PHE A 391 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA5, first strand: chain 'B' and resid 432 through 436 removed outlier: 3.516A pdb=" N MET B 443 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS B 445 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS B 496 " --> pdb=" O CYS B 445 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP B 447 " --> pdb=" O TYR B 494 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 494 " --> pdb=" O TRP B 447 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 482 through 483 removed outlier: 3.768A pdb=" N THR B 459 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 514 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN B 461 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG B 512 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 463 " --> pdb=" O TRP B 510 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 520 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS B 515 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY B 518 " --> pdb=" O HIS B 515 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 482 through 483 removed outlier: 3.768A pdb=" N THR B 459 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 514 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN B 461 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG B 512 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 463 " --> pdb=" O TRP B 510 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR B 507 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 527 " --> pdb=" O TYR B 507 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET B 509 " --> pdb=" O THR B 525 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 525 " --> pdb=" O MET B 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 542 through 545 removed outlier: 3.816A pdb=" N LYS B 542 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 555 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 554 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 582 through 586 removed outlier: 3.933A pdb=" N VAL B 607 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 627 " --> pdb=" O VAL B 607 " (cutoff:3.500A) 137 hydrogen bonds defined for protein. 375 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: 0.93 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1122 1.34 - 1.46: 788 1.46 - 1.58: 1658 1.58 - 1.70: 1 1.70 - 1.81: 19 Bond restraints: 3588 Sorted by residual: bond pdb=" CB PRO B 472 " pdb=" CG PRO B 472 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.94e+00 bond pdb=" C2 NAG A 901 " pdb=" N2 NAG A 901 " ideal model delta sigma weight residual 1.439 1.463 -0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" C5 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" C5 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.10e+00 ... (remaining 3583 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.87: 80 105.87 - 112.93: 2021 112.93 - 119.98: 1144 119.98 - 127.04: 1586 127.04 - 134.10: 53 Bond angle restraints: 4884 Sorted by residual: angle pdb=" CA SER B 450 " pdb=" C SER B 450 " pdb=" N THR B 451 " ideal model delta sigma weight residual 116.84 125.69 -8.85 1.71e+00 3.42e-01 2.68e+01 angle pdb=" CA PRO B 472 " pdb=" N PRO B 472 " pdb=" CD PRO B 472 " ideal model delta sigma weight residual 112.00 104.86 7.14 1.40e+00 5.10e-01 2.60e+01 angle pdb=" CA SER B 450 " pdb=" C SER B 450 " pdb=" O SER B 450 " ideal model delta sigma weight residual 120.51 115.41 5.10 1.43e+00 4.89e-01 1.27e+01 angle pdb=" N LYS C 5 " pdb=" CA LYS C 5 " pdb=" C LYS C 5 " ideal model delta sigma weight residual 111.28 107.66 3.62 1.09e+00 8.42e-01 1.10e+01 angle pdb=" CA LEU C 104 " pdb=" CB LEU C 104 " pdb=" CG LEU C 104 " ideal model delta sigma weight residual 116.30 127.41 -11.11 3.50e+00 8.16e-02 1.01e+01 ... (remaining 4879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 1869 17.93 - 35.86: 279 35.86 - 53.79: 56 53.79 - 71.72: 9 71.72 - 89.64: 4 Dihedral angle restraints: 2217 sinusoidal: 919 harmonic: 1298 Sorted by residual: dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 496 " pdb=" CB CYS B 496 " ideal model delta sinusoidal sigma weight residual 93.00 55.09 37.91 1 1.00e+01 1.00e-02 2.03e+01 dihedral pdb=" CB GLU B 435 " pdb=" CG GLU B 435 " pdb=" CD GLU B 435 " pdb=" OE1 GLU B 435 " ideal model delta sinusoidal sigma weight residual 0.00 89.64 -89.64 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG C 35 " pdb=" CD ARG C 35 " pdb=" NE ARG C 35 " pdb=" CZ ARG C 35 " ideal model delta sinusoidal sigma weight residual -180.00 -135.34 -44.66 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 2214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 381 0.039 - 0.077: 135 0.077 - 0.116: 47 0.116 - 0.154: 7 0.154 - 0.193: 2 Chirality restraints: 572 Sorted by residual: chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 622 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" C2 NAG A 901 " pdb=" C1 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" N2 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CB VAL C 113 " pdb=" CA VAL C 113 " pdb=" CG1 VAL C 113 " pdb=" CG2 VAL C 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 569 not shown) Planarity restraints: 616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 471 " 0.048 5.00e-02 4.00e+02 6.92e-02 7.67e+00 pdb=" N PRO B 472 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 472 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 472 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 374 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.39e+00 pdb=" N PRO A 375 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 447 " 0.012 2.00e-02 2.50e+03 1.21e-02 3.66e+00 pdb=" CG TRP B 447 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 447 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 447 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 447 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 447 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 447 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 447 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 447 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 447 " 0.002 2.00e-02 2.50e+03 ... (remaining 613 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 139 2.70 - 3.25: 3307 3.25 - 3.80: 5152 3.80 - 4.35: 5698 4.35 - 4.90: 9630 Nonbonded interactions: 23926 Sorted by model distance: nonbonded pdb=" OE2 GLU B 563 " pdb=" OG1 THR C 19 " model vdw 2.155 2.440 nonbonded pdb=" O VAL C 64 " pdb=" OG SER C 67 " model vdw 2.216 2.440 nonbonded pdb=" O LEU B 455 " pdb=" OG SER B 458 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR B 470 " pdb=" OD2 ASP C 9 " model vdw 2.238 2.440 nonbonded pdb=" O ILE B 511 " pdb=" OG SER B 522 " model vdw 2.304 2.440 ... (remaining 23921 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 6.630 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.160 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 3588 Z= 0.230 Angle : 0.763 11.108 4884 Z= 0.392 Chirality : 0.045 0.193 572 Planarity : 0.005 0.069 614 Dihedral : 17.096 89.644 1358 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.49 % Allowed : 34.07 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: 0.08 (0.41), residues: 433 helix: 2.17 (0.52), residues: 106 sheet: 0.30 (0.54), residues: 103 loop : -1.15 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 447 HIS 0.002 0.001 HIS A 349 PHE 0.012 0.001 PHE B 502 TYR 0.014 0.001 TYR B 605 ARG 0.006 0.000 ARG B 571 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 PHE cc_start: 0.9397 (m-80) cc_final: 0.8920 (m-10) REVERT: B 504 LEU cc_start: 0.9139 (mp) cc_final: 0.8809 (tt) REVERT: C 87 LEU cc_start: 0.8920 (mt) cc_final: 0.8684 (mt) outliers start: 2 outliers final: 1 residues processed: 87 average time/residue: 0.1534 time to fit residues: 16.3285 Evaluate side-chains 82 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 569 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B 608 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3588 Z= 0.434 Angle : 0.812 8.568 4884 Z= 0.416 Chirality : 0.049 0.212 572 Planarity : 0.005 0.049 614 Dihedral : 7.063 53.182 518 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 7.41 % Allowed : 27.90 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.41), residues: 433 helix: 1.81 (0.50), residues: 110 sheet: 0.12 (0.54), residues: 95 loop : -1.61 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 447 HIS 0.004 0.001 HIS B 478 PHE 0.015 0.002 PHE B 502 TYR 0.020 0.002 TYR A 405 ARG 0.004 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 77 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 CYS cc_start: 0.6213 (OUTLIER) cc_final: 0.5721 (t) REVERT: A 378 GLN cc_start: 0.8931 (mt0) cc_final: 0.8370 (mt0) REVERT: A 417 HIS cc_start: 0.5794 (OUTLIER) cc_final: 0.5439 (t-90) REVERT: B 447 TRP cc_start: 0.8556 (p-90) cc_final: 0.7955 (p-90) REVERT: B 499 GLN cc_start: 0.9296 (tp-100) cc_final: 0.8735 (tp-100) REVERT: B 504 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8491 (tt) outliers start: 30 outliers final: 16 residues processed: 99 average time/residue: 0.1374 time to fit residues: 17.2937 Evaluate side-chains 92 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 0.0010 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 GLN C 75 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3588 Z= 0.210 Angle : 0.692 9.359 4884 Z= 0.337 Chirality : 0.045 0.234 572 Planarity : 0.004 0.041 614 Dihedral : 6.298 52.670 515 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 6.42 % Allowed : 29.63 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.27 (0.41), residues: 433 helix: 2.19 (0.52), residues: 110 sheet: -0.02 (0.51), residues: 102 loop : -1.57 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 447 HIS 0.002 0.001 HIS A 349 PHE 0.020 0.002 PHE B 568 TYR 0.015 0.001 TYR B 605 ARG 0.002 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 79 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 CYS cc_start: 0.5553 (OUTLIER) cc_final: 0.5289 (t) REVERT: A 417 HIS cc_start: 0.6026 (OUTLIER) cc_final: 0.5749 (t-90) REVERT: B 447 TRP cc_start: 0.8595 (p-90) cc_final: 0.7715 (p-90) REVERT: B 504 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8605 (tt) REVERT: B 509 MET cc_start: 0.8310 (ppp) cc_final: 0.7265 (ppp) REVERT: B 556 TRP cc_start: 0.9073 (p90) cc_final: 0.8769 (p90) outliers start: 26 outliers final: 12 residues processed: 100 average time/residue: 0.1427 time to fit residues: 17.7729 Evaluate side-chains 88 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 126 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3588 Z= 0.254 Angle : 0.694 9.176 4884 Z= 0.341 Chirality : 0.045 0.233 572 Planarity : 0.004 0.044 614 Dihedral : 6.168 52.323 515 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 5.93 % Allowed : 30.37 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.41 (0.41), residues: 433 helix: 2.04 (0.51), residues: 110 sheet: -0.23 (0.52), residues: 100 loop : -1.55 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 366 HIS 0.002 0.001 HIS B 465 PHE 0.010 0.002 PHE A 403 TYR 0.013 0.002 TYR A 405 ARG 0.003 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 CYS cc_start: 0.5724 (OUTLIER) cc_final: 0.5192 (t) REVERT: A 406 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6984 (t0) REVERT: A 417 HIS cc_start: 0.6070 (OUTLIER) cc_final: 0.5775 (t-90) REVERT: B 447 TRP cc_start: 0.8622 (p-90) cc_final: 0.7706 (p-90) REVERT: B 504 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8618 (tt) REVERT: B 509 MET cc_start: 0.8295 (ppp) cc_final: 0.7260 (ppp) REVERT: B 556 TRP cc_start: 0.9057 (p90) cc_final: 0.8577 (p90) outliers start: 24 outliers final: 17 residues processed: 92 average time/residue: 0.1281 time to fit residues: 15.0778 Evaluate side-chains 92 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 88 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3588 Z= 0.313 Angle : 0.709 8.955 4884 Z= 0.357 Chirality : 0.046 0.230 572 Planarity : 0.004 0.045 614 Dihedral : 6.137 52.932 515 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 6.91 % Allowed : 29.38 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.52 (0.41), residues: 433 helix: 2.08 (0.52), residues: 110 sheet: -0.41 (0.52), residues: 100 loop : -1.63 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 620 HIS 0.003 0.001 HIS B 465 PHE 0.012 0.002 PHE C 92 TYR 0.016 0.002 TYR A 405 ARG 0.003 0.001 ARG B 571 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 74 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6955 (t0) REVERT: A 417 HIS cc_start: 0.6200 (OUTLIER) cc_final: 0.5996 (t-90) REVERT: B 447 TRP cc_start: 0.8701 (p-90) cc_final: 0.7688 (p-90) REVERT: B 504 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8572 (tt) REVERT: B 556 TRP cc_start: 0.9115 (p90) cc_final: 0.8564 (p90) REVERT: B 620 TRP cc_start: 0.8399 (m100) cc_final: 0.6547 (m100) outliers start: 28 outliers final: 23 residues processed: 95 average time/residue: 0.1417 time to fit residues: 16.9578 Evaluate side-chains 97 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 71 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3588 Z= 0.220 Angle : 0.696 9.818 4884 Z= 0.334 Chirality : 0.045 0.237 572 Planarity : 0.004 0.043 614 Dihedral : 5.862 52.921 515 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 6.91 % Allowed : 30.62 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.47 (0.41), residues: 433 helix: 2.06 (0.52), residues: 110 sheet: -0.39 (0.52), residues: 100 loop : -1.56 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 620 HIS 0.002 0.001 HIS A 349 PHE 0.012 0.002 PHE A 403 TYR 0.013 0.001 TYR A 409 ARG 0.004 0.000 ARG B 610 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 74 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 CYS cc_start: 0.5557 (OUTLIER) cc_final: 0.5134 (t) REVERT: A 406 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6872 (t0) REVERT: A 409 TYR cc_start: 0.5851 (m-80) cc_final: 0.5601 (m-80) REVERT: B 447 TRP cc_start: 0.8710 (p-90) cc_final: 0.7662 (p-90) REVERT: B 504 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8534 (tt) REVERT: B 556 TRP cc_start: 0.9088 (p90) cc_final: 0.8497 (p90) REVERT: B 620 TRP cc_start: 0.8418 (m100) cc_final: 0.6606 (m100) outliers start: 28 outliers final: 20 residues processed: 96 average time/residue: 0.1255 time to fit residues: 15.2743 Evaluate side-chains 94 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3588 Z= 0.229 Angle : 0.691 9.951 4884 Z= 0.333 Chirality : 0.045 0.234 572 Planarity : 0.004 0.042 614 Dihedral : 5.770 52.820 515 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 7.16 % Allowed : 29.38 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.40 (0.41), residues: 433 helix: 2.14 (0.52), residues: 110 sheet: -0.36 (0.52), residues: 100 loop : -1.51 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 620 HIS 0.002 0.001 HIS A 349 PHE 0.010 0.002 PHE A 403 TYR 0.011 0.001 TYR A 409 ARG 0.003 0.000 ARG B 571 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 73 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 CYS cc_start: 0.5604 (OUTLIER) cc_final: 0.5185 (t) REVERT: A 406 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6841 (t0) REVERT: B 447 TRP cc_start: 0.8723 (p-90) cc_final: 0.7660 (p-90) REVERT: B 504 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8535 (tt) REVERT: B 556 TRP cc_start: 0.9117 (p90) cc_final: 0.8494 (p90) REVERT: B 620 TRP cc_start: 0.8453 (m100) cc_final: 0.6551 (m100) outliers start: 29 outliers final: 23 residues processed: 96 average time/residue: 0.1306 time to fit residues: 15.8769 Evaluate side-chains 96 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 70 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.0070 chunk 3 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3588 Z= 0.218 Angle : 0.713 10.428 4884 Z= 0.336 Chirality : 0.045 0.235 572 Planarity : 0.004 0.043 614 Dihedral : 5.724 52.893 515 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 6.42 % Allowed : 30.12 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.41 (0.41), residues: 433 helix: 2.08 (0.51), residues: 110 sheet: -0.37 (0.52), residues: 100 loop : -1.49 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 620 HIS 0.002 0.000 HIS A 349 PHE 0.008 0.001 PHE C 92 TYR 0.041 0.002 TYR A 409 ARG 0.003 0.000 ARG B 571 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 72 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 CYS cc_start: 0.5591 (OUTLIER) cc_final: 0.5228 (t) REVERT: A 406 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6738 (t0) REVERT: B 447 TRP cc_start: 0.8698 (p-90) cc_final: 0.7650 (p-90) REVERT: B 504 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8503 (tt) REVERT: B 556 TRP cc_start: 0.9105 (p90) cc_final: 0.8469 (p90) REVERT: B 620 TRP cc_start: 0.8476 (m100) cc_final: 0.6625 (m100) outliers start: 26 outliers final: 21 residues processed: 92 average time/residue: 0.1253 time to fit residues: 14.7448 Evaluate side-chains 94 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.0000 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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: 0.7326 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3588 Z= 0.187 Angle : 0.673 10.137 4884 Z= 0.320 Chirality : 0.044 0.238 572 Planarity : 0.004 0.042 614 Dihedral : 5.546 53.255 515 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 5.19 % Allowed : 31.11 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.24 (0.41), residues: 433 helix: 2.26 (0.52), residues: 110 sheet: -0.14 (0.52), residues: 97 loop : -1.47 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 447 HIS 0.002 0.000 HIS A 349 PHE 0.007 0.001 PHE C 92 TYR 0.033 0.002 TYR A 409 ARG 0.003 0.000 ARG B 610 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 TRP cc_start: 0.8746 (m100) cc_final: 0.8522 (m100) REVERT: A 406 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6446 (t0) REVERT: B 447 TRP cc_start: 0.8690 (p-90) cc_final: 0.7586 (p-90) REVERT: B 504 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8459 (tt) REVERT: B 556 TRP cc_start: 0.9073 (p90) cc_final: 0.8400 (p90) REVERT: C 87 LEU cc_start: 0.8944 (mt) cc_final: 0.8707 (mt) outliers start: 21 outliers final: 15 residues processed: 93 average time/residue: 0.1382 time to fit residues: 16.2646 Evaluate side-chains 90 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 20 optimal weight: 0.0170 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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: 0.7307 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3588 Z= 0.174 Angle : 0.696 10.691 4884 Z= 0.327 Chirality : 0.044 0.238 572 Planarity : 0.004 0.046 614 Dihedral : 5.493 53.680 515 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.20 % Allowed : 32.35 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.28 (0.41), residues: 433 helix: 2.08 (0.52), residues: 110 sheet: -0.20 (0.52), residues: 100 loop : -1.40 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 620 HIS 0.002 0.000 HIS A 349 PHE 0.017 0.001 PHE B 561 TYR 0.028 0.002 TYR A 409 ARG 0.007 0.000 ARG B 610 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.6376 (t0) REVERT: B 447 TRP cc_start: 0.8691 (p-90) cc_final: 0.7580 (p-90) REVERT: B 504 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8210 (tt) REVERT: B 556 TRP cc_start: 0.8975 (p90) cc_final: 0.8351 (p90) REVERT: B 563 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8123 (mt-10) REVERT: C 87 LEU cc_start: 0.8928 (mt) cc_final: 0.8711 (mt) outliers start: 17 outliers final: 14 residues processed: 90 average time/residue: 0.1313 time to fit residues: 15.0897 Evaluate side-chains 89 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.0020 chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.108336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.074385 restraints weight = 10306.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.076152 restraints weight = 5492.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.077142 restraints weight = 4119.158| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3588 Z= 0.178 Angle : 0.710 10.734 4884 Z= 0.333 Chirality : 0.045 0.239 572 Planarity : 0.004 0.043 614 Dihedral : 5.453 53.319 515 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.44 % Allowed : 33.58 % Favored : 61.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: -0.27 (0.41), residues: 433 helix: 2.11 (0.52), residues: 110 sheet: -0.02 (0.52), residues: 97 loop : -1.48 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 366 HIS 0.002 0.000 HIS A 349 PHE 0.015 0.002 PHE B 561 TYR 0.025 0.002 TYR A 409 ARG 0.004 0.000 ARG B 610 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1242.40 seconds wall clock time: 23 minutes 20.27 seconds (1400.27 seconds total)