Starting phenix.real_space_refine on Mon Mar 11 02:18:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/03_2024/7rto_24685.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/03_2024/7rto_24685.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/7rto_24685/03_2024/7rto_24685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/03_2024/7rto_24685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/03_2024/7rto_24685.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/03_2024/7rto_24685.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= 0.002 sd= 0.009 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 14 5.16 5 C 4160 2.51 5 N 1205 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 104": "OD1" <-> "OD2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6607 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2595 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 10, 'TRANS': 337} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 116 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Time building chain proxies: 4.02, per 1000 atoms: 0.61 Number of scatterers: 6607 At special positions: 0 Unit cell: (104.72, 110.16, 114.24, 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 14 16.00 O 1228 8.00 N 1205 7.00 C 4160 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: 2.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 61.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.716A pdb=" N SER A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 135 removed outlier: 3.558A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 340 Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.820A pdb=" N VAL A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 445 through 455 removed outlier: 3.575A pdb=" N ARG A 449 " --> pdb=" O MET A 445 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 483 through 491 removed outlier: 3.724A pdb=" N GLN A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 509 Processing helix chain 'B' and resid 65 through 79 Processing helix chain 'B' and resid 89 through 115 removed outlier: 4.241A pdb=" N TYR B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 135 removed outlier: 7.576A pdb=" N LYS B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLU B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 177 Processing helix chain 'B' and resid 184 through 204 Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.902A pdb=" N GLU B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 263 Processing helix chain 'B' and resid 296 through 330 Proline residue: B 326 - end of helix Processing helix chain 'B' and resid 424 through 438 Processing helix chain 'B' and resid 445 through 454 Processing helix chain 'B' and resid 469 through 482 Processing helix chain 'B' and resid 483 through 491 removed outlier: 3.572A pdb=" N GLN B 487 " --> pdb=" O ASP B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'B' and resid 510 through 513 Processing helix chain 'C' and resid 65 through 79 Processing helix chain 'C' and resid 89 through 135 removed outlier: 4.531A pdb=" N ASN C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 340 Proline residue: C 326 - end of helix removed outlier: 4.211A pdb=" N GLY C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 343 No H-bonds generated for 'chain 'C' and resid 341 through 343' Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 424 through 438 removed outlier: 3.524A pdb=" N SER C 438 " --> pdb=" O ASN C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 454 Processing helix chain 'C' and resid 469 through 483 Processing helix chain 'C' and resid 484 through 491 removed outlier: 3.786A pdb=" N HIS C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 509 Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 406 removed outlier: 3.721A pdb=" N GLY A 462 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER A 368 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR A 460 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 414 Processing sheet with id=AA3, first strand: chain 'B' and resid 401 through 408 removed outlier: 3.884A pdb=" N GLY B 462 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER B 368 " --> pdb=" O TYR B 460 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N TYR B 460 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AA5, first strand: chain 'C' and resid 401 through 406 removed outlier: 4.085A pdb=" N GLY C 462 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER C 368 " --> pdb=" O TYR C 460 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYR C 460 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 410 through 414 468 hydrogen bonds defined for protein. 1362 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2122 1.34 - 1.45: 955 1.45 - 1.57: 3635 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 6734 Sorted by residual: bond pdb=" N GLN A 360 " pdb=" CA GLN A 360 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.33e-02 5.65e+03 6.65e+00 bond pdb=" N ASP A 406 " pdb=" CA ASP A 406 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.31e-02 5.83e+03 6.35e+00 bond pdb=" N LEU C 113 " pdb=" CA LEU C 113 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.52e+00 bond pdb=" CG1 ILE C 490 " pdb=" CD1 ILE C 490 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.50e+00 bond pdb=" CB GLN C 361 " pdb=" CG GLN C 361 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.94e+00 ... (remaining 6729 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.84: 168 106.84 - 113.62: 3675 113.62 - 120.41: 2589 120.41 - 127.20: 2626 127.20 - 133.98: 72 Bond angle restraints: 9130 Sorted by residual: angle pdb=" O GLN A 360 " pdb=" C GLN A 360 " pdb=" N GLN A 361 " ideal model delta sigma weight residual 122.18 125.88 -3.70 9.90e-01 1.02e+00 1.39e+01 angle pdb=" CB LYS A 511 " pdb=" CG LYS A 511 " pdb=" CD LYS A 511 " ideal model delta sigma weight residual 111.30 119.34 -8.04 2.30e+00 1.89e-01 1.22e+01 angle pdb=" CG1 ILE C 356 " pdb=" CB ILE C 356 " pdb=" CG2 ILE C 356 " ideal model delta sigma weight residual 110.70 101.37 9.33 3.00e+00 1.11e-01 9.68e+00 angle pdb=" CA GLN C 478 " pdb=" CB GLN C 478 " pdb=" CG GLN C 478 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.16e+00 angle pdb=" C ALA C 359 " pdb=" N GLN C 360 " pdb=" CA GLN C 360 " ideal model delta sigma weight residual 122.23 126.83 -4.60 1.57e+00 4.06e-01 8.59e+00 ... (remaining 9125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3603 17.85 - 35.69: 322 35.69 - 53.53: 58 53.53 - 71.38: 9 71.38 - 89.22: 6 Dihedral angle restraints: 3998 sinusoidal: 1429 harmonic: 2569 Sorted by residual: dihedral pdb=" CA TYR C 65 " pdb=" C TYR C 65 " pdb=" N GLY C 66 " pdb=" CA GLY C 66 " ideal model delta harmonic sigma weight residual -180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA HIS A 385 " pdb=" C HIS A 385 " pdb=" N HIS A 386 " pdb=" CA HIS A 386 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA TYR B 404 " pdb=" C TYR B 404 " pdb=" N GLU B 405 " pdb=" CA GLU B 405 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 3995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 955 0.090 - 0.179: 61 0.179 - 0.269: 8 0.269 - 0.359: 0 0.359 - 0.448: 1 Chirality restraints: 1025 Sorted by residual: chirality pdb=" CB ILE A 356 " pdb=" CA ILE A 356 " pdb=" CG1 ILE A 356 " pdb=" CG2 ILE A 356 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CB ILE C 356 " pdb=" CA ILE C 356 " pdb=" CG1 ILE C 356 " pdb=" CG2 ILE C 356 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ILE C 364 " pdb=" N ILE C 364 " pdb=" C ILE C 364 " pdb=" CB ILE C 364 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1022 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 448 " 0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C ARG A 448 " -0.079 2.00e-02 2.50e+03 pdb=" O ARG A 448 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG A 449 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 466 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C TYR C 466 " 0.046 2.00e-02 2.50e+03 pdb=" O TYR C 466 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP C 467 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 477 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C ALA C 477 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA C 477 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN C 478 " -0.014 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 537 2.74 - 3.28: 6560 3.28 - 3.82: 10786 3.82 - 4.36: 11393 4.36 - 4.90: 20404 Nonbonded interactions: 49680 Sorted by model distance: nonbonded pdb=" O GLY A 493 " pdb=" NE2 GLN A 498 " model vdw 2.200 2.520 nonbonded pdb=" O LEU A 450 " pdb=" OG SER A 453 " model vdw 2.328 2.440 nonbonded pdb=" O HIS A 384 " pdb=" ND1 HIS A 385 " model vdw 2.336 2.520 nonbonded pdb=" O ALA A 369 " pdb=" OG SER A 373 " model vdw 2.356 2.440 nonbonded pdb=" O SER C 89 " pdb=" OG SER C 89 " model vdw 2.385 2.440 ... (remaining 49675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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: 1.730 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: 6.160 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.540 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 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 0.062 6734 Z= 0.243 Angle : 0.821 9.484 9130 Z= 0.449 Chirality : 0.052 0.448 1025 Planarity : 0.005 0.045 1206 Dihedral : 14.320 89.223 2334 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % 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: 1.09 (0.30), residues: 870 helix: 2.41 (0.23), residues: 490 sheet: -0.19 (0.49), residues: 124 loop : -2.30 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 371 HIS 0.010 0.001 HIS C 385 PHE 0.035 0.003 PHE C 470 TYR 0.027 0.002 TYR A 466 ARG 0.009 0.001 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.793 Fit side-chains REVERT: A 360 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6531 (tm-30) REVERT: A 490 ILE cc_start: 0.8918 (mt) cc_final: 0.8640 (mt) REVERT: B 108 ASN cc_start: 0.7412 (m110) cc_final: 0.7173 (m110) REVERT: B 132 ASN cc_start: 0.5924 (t0) cc_final: 0.5670 (t0) REVERT: C 448 ARG cc_start: 0.6949 (ttm-80) cc_final: 0.6679 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.1986 time to fit residues: 35.8666 Evaluate side-chains 94 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 7.9990 chunk 66 optimal weight: 0.2980 chunk 37 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 30.0000 chunk 35 optimal weight: 40.0000 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 overall best weight: 6.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 HIS ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6734 Z= 0.246 Angle : 0.607 6.973 9130 Z= 0.326 Chirality : 0.043 0.185 1025 Planarity : 0.004 0.026 1206 Dihedral : 4.762 40.454 954 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.80 % Allowed : 11.31 % Favored : 86.89 % 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: 1.37 (0.30), residues: 870 helix: 2.40 (0.23), residues: 506 sheet: 0.18 (0.48), residues: 128 loop : -2.17 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 411 HIS 0.008 0.001 HIS C 385 PHE 0.019 0.002 PHE B 378 TYR 0.028 0.002 TYR B 482 ARG 0.007 0.001 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.682 Fit side-chains REVERT: A 445 MET cc_start: 0.7452 (tmm) cc_final: 0.7222 (tmm) REVERT: B 108 ASN cc_start: 0.7616 (m110) cc_final: 0.7409 (m110) REVERT: B 125 LYS cc_start: 0.3780 (mtpp) cc_final: 0.3260 (mtpp) REVERT: B 132 ASN cc_start: 0.6364 (t0) cc_final: 0.5976 (t0) REVERT: B 467 ASP cc_start: 0.6251 (m-30) cc_final: 0.5536 (p0) REVERT: C 114 LYS cc_start: 0.2819 (tttp) cc_final: 0.2385 (tttm) outliers start: 11 outliers final: 10 residues processed: 108 average time/residue: 0.1651 time to fit residues: 24.7102 Evaluate side-chains 101 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 498 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 54 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 79 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 HIS ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6734 Z= 0.220 Angle : 0.571 6.856 9130 Z= 0.307 Chirality : 0.042 0.166 1025 Planarity : 0.003 0.024 1206 Dihedral : 4.356 18.551 951 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.30 % Allowed : 13.93 % Favored : 83.77 % 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: 1.38 (0.30), residues: 870 helix: 2.53 (0.23), residues: 503 sheet: 0.13 (0.48), residues: 128 loop : -2.36 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 411 HIS 0.007 0.001 HIS B 385 PHE 0.018 0.002 PHE B 378 TYR 0.021 0.002 TYR B 482 ARG 0.005 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.841 Fit side-chains REVERT: A 360 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: B 109 GLU cc_start: 0.5554 (tp30) cc_final: 0.5308 (tp30) REVERT: B 132 ASN cc_start: 0.6357 (t0) cc_final: 0.5978 (t0) REVERT: B 467 ASP cc_start: 0.6282 (m-30) cc_final: 0.5654 (p0) REVERT: C 114 LYS cc_start: 0.2742 (tttp) cc_final: 0.2226 (tttm) REVERT: C 118 LYS cc_start: 0.5302 (pttp) cc_final: 0.4222 (pttp) outliers start: 14 outliers final: 11 residues processed: 106 average time/residue: 0.1771 time to fit residues: 25.6923 Evaluate side-chains 101 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 424 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 40.0000 chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6734 Z= 0.263 Angle : 0.587 6.193 9130 Z= 0.318 Chirality : 0.042 0.165 1025 Planarity : 0.003 0.030 1206 Dihedral : 4.488 20.259 951 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.11 % Allowed : 16.07 % Favored : 80.82 % 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: 1.24 (0.29), residues: 870 helix: 2.37 (0.23), residues: 508 sheet: -0.02 (0.47), residues: 128 loop : -2.34 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 411 HIS 0.008 0.001 HIS B 385 PHE 0.019 0.002 PHE B 378 TYR 0.026 0.002 TYR B 482 ARG 0.004 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.742 Fit side-chains REVERT: A 356 ILE cc_start: 0.8632 (mp) cc_final: 0.8318 (mp) REVERT: B 109 GLU cc_start: 0.5588 (tp30) cc_final: 0.5385 (tp30) REVERT: B 132 ASN cc_start: 0.6215 (t0) cc_final: 0.5886 (t0) REVERT: C 114 LYS cc_start: 0.2885 (tttp) cc_final: 0.2415 (tttm) REVERT: C 118 LYS cc_start: 0.4832 (pttp) cc_final: 0.4022 (pttp) REVERT: C 364 ILE cc_start: 0.9091 (mm) cc_final: 0.8789 (mm) outliers start: 19 outliers final: 16 residues processed: 111 average time/residue: 0.1445 time to fit residues: 22.9294 Evaluate side-chains 106 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 496 HIS Chi-restraints excluded: chain C residue 498 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6734 Z= 0.213 Angle : 0.566 6.600 9130 Z= 0.304 Chirality : 0.041 0.169 1025 Planarity : 0.003 0.024 1206 Dihedral : 4.348 18.961 951 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.95 % Allowed : 18.36 % Favored : 78.69 % 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: 1.32 (0.30), residues: 870 helix: 2.43 (0.23), residues: 513 sheet: -0.09 (0.46), residues: 128 loop : -2.34 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 411 HIS 0.007 0.001 HIS B 385 PHE 0.018 0.002 PHE B 378 TYR 0.021 0.002 TYR B 482 ARG 0.008 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: B 132 ASN cc_start: 0.6104 (t0) cc_final: 0.5400 (t0) REVERT: C 118 LYS cc_start: 0.4834 (pttp) cc_final: 0.4108 (mmmt) REVERT: C 364 ILE cc_start: 0.9073 (mm) cc_final: 0.8783 (mm) outliers start: 18 outliers final: 17 residues processed: 107 average time/residue: 0.1497 time to fit residues: 22.6955 Evaluate side-chains 105 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 HIS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 431 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 50.0000 chunk 39 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 50.0000 chunk 82 optimal weight: 9.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6734 Z= 0.160 Angle : 0.547 7.614 9130 Z= 0.289 Chirality : 0.040 0.147 1025 Planarity : 0.003 0.022 1206 Dihedral : 4.096 17.397 951 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.28 % Allowed : 19.51 % Favored : 77.21 % 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: 1.55 (0.30), residues: 870 helix: 2.64 (0.23), residues: 511 sheet: -0.03 (0.47), residues: 128 loop : -2.24 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 411 HIS 0.007 0.001 HIS B 385 PHE 0.017 0.002 PHE B 391 TYR 0.016 0.001 TYR B 482 ARG 0.003 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: B 132 ASN cc_start: 0.6508 (t0) cc_final: 0.5749 (t0) REVERT: B 407 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7505 (pp) REVERT: B 467 ASP cc_start: 0.6360 (m-30) cc_final: 0.5910 (p0) REVERT: C 118 LYS cc_start: 0.5266 (pttp) cc_final: 0.4519 (mmmt) REVERT: C 364 ILE cc_start: 0.9005 (mm) cc_final: 0.8670 (mm) outliers start: 20 outliers final: 18 residues processed: 119 average time/residue: 0.1579 time to fit residues: 26.5971 Evaluate side-chains 115 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 HIS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 496 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 71 optimal weight: 0.0070 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6734 Z= 0.165 Angle : 0.555 7.769 9130 Z= 0.291 Chirality : 0.040 0.155 1025 Planarity : 0.003 0.035 1206 Dihedral : 4.045 16.723 951 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.95 % Allowed : 19.67 % Favored : 77.38 % 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: 1.53 (0.30), residues: 870 helix: 2.63 (0.22), residues: 511 sheet: -0.23 (0.46), residues: 134 loop : -2.19 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 411 HIS 0.007 0.001 HIS B 385 PHE 0.017 0.002 PHE B 391 TYR 0.017 0.001 TYR B 482 ARG 0.010 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.819 Fit side-chains REVERT: A 478 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8515 (mm-40) REVERT: B 132 ASN cc_start: 0.6457 (t0) cc_final: 0.5717 (t0) REVERT: B 407 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7406 (pp) REVERT: C 118 LYS cc_start: 0.5278 (pttp) cc_final: 0.4524 (mmmt) REVERT: C 364 ILE cc_start: 0.9041 (mm) cc_final: 0.8724 (mm) outliers start: 18 outliers final: 15 residues processed: 114 average time/residue: 0.1448 time to fit residues: 23.6117 Evaluate side-chains 112 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 HIS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 496 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6734 Z= 0.274 Angle : 0.623 8.549 9130 Z= 0.330 Chirality : 0.042 0.180 1025 Planarity : 0.003 0.024 1206 Dihedral : 4.385 19.274 951 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.44 % Allowed : 20.33 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.30), residues: 870 helix: 2.45 (0.22), residues: 511 sheet: -0.42 (0.45), residues: 144 loop : -2.25 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 411 HIS 0.008 0.001 HIS B 385 PHE 0.023 0.002 PHE C 497 TYR 0.025 0.002 TYR B 482 ARG 0.003 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.799 Fit side-chains REVERT: A 478 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8509 (mm-40) REVERT: B 132 ASN cc_start: 0.6318 (t0) cc_final: 0.5883 (t0) REVERT: B 169 MET cc_start: 0.7119 (tpt) cc_final: 0.6607 (mtt) REVERT: B 407 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7392 (pp) REVERT: C 118 LYS cc_start: 0.4886 (pttp) cc_final: 0.4141 (pttp) REVERT: C 364 ILE cc_start: 0.9007 (mm) cc_final: 0.8703 (mm) outliers start: 21 outliers final: 18 residues processed: 100 average time/residue: 0.1530 time to fit residues: 21.8352 Evaluate side-chains 100 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 HIS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 496 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 50.0000 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 71 optimal weight: 0.4980 chunk 74 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 0.0050 chunk 83 optimal weight: 10.0000 overall best weight: 3.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6734 Z= 0.181 Angle : 0.577 7.923 9130 Z= 0.305 Chirality : 0.041 0.170 1025 Planarity : 0.003 0.031 1206 Dihedral : 4.203 17.517 951 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.11 % Allowed : 20.49 % Favored : 76.39 % 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: 1.45 (0.30), residues: 870 helix: 2.60 (0.22), residues: 511 sheet: -0.39 (0.46), residues: 144 loop : -2.27 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 371 HIS 0.007 0.001 HIS B 385 PHE 0.023 0.002 PHE C 497 TYR 0.018 0.001 TYR A 65 ARG 0.011 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.701 Fit side-chains REVERT: A 478 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8491 (mm-40) REVERT: B 132 ASN cc_start: 0.6237 (t0) cc_final: 0.5496 (t0) REVERT: B 169 MET cc_start: 0.6830 (tpt) cc_final: 0.6415 (mtt) REVERT: C 118 LYS cc_start: 0.4932 (pttp) cc_final: 0.4247 (mmmt) REVERT: C 364 ILE cc_start: 0.8993 (mm) cc_final: 0.8636 (mm) outliers start: 19 outliers final: 17 residues processed: 103 average time/residue: 0.1495 time to fit residues: 21.8107 Evaluate side-chains 112 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 HIS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 496 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 30.0000 chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6734 Z= 0.161 Angle : 0.569 9.901 9130 Z= 0.299 Chirality : 0.040 0.179 1025 Planarity : 0.003 0.020 1206 Dihedral : 4.052 17.243 951 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.79 % Allowed : 20.98 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.30), residues: 870 helix: 2.70 (0.22), residues: 512 sheet: -0.44 (0.45), residues: 154 loop : -2.14 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 411 HIS 0.007 0.001 HIS B 385 PHE 0.023 0.002 PHE C 497 TYR 0.019 0.001 TYR A 65 ARG 0.002 0.000 ARG A 474 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.798 Fit side-chains REVERT: A 478 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8501 (mm-40) REVERT: B 132 ASN cc_start: 0.6184 (t0) cc_final: 0.5552 (t0) REVERT: B 169 MET cc_start: 0.6744 (tpt) cc_final: 0.6410 (mtt) REVERT: C 118 LYS cc_start: 0.5054 (pttp) cc_final: 0.4278 (mmmt) REVERT: C 364 ILE cc_start: 0.8983 (mm) cc_final: 0.8627 (mm) outliers start: 17 outliers final: 12 residues processed: 107 average time/residue: 0.1558 time to fit residues: 23.4470 Evaluate side-chains 100 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain C residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 0.0040 chunk 69 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.0370 chunk 8 optimal weight: 40.0000 chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 overall best weight: 3.2076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.155595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132942 restraints weight = 11950.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130736 restraints weight = 9962.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131051 restraints weight = 10978.477| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6734 Z= 0.175 Angle : 0.577 10.098 9130 Z= 0.302 Chirality : 0.040 0.182 1025 Planarity : 0.003 0.020 1206 Dihedral : 4.037 16.633 951 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.95 % Allowed : 21.31 % Favored : 75.74 % 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: 1.64 (0.30), residues: 870 helix: 2.75 (0.22), residues: 510 sheet: -0.29 (0.46), residues: 148 loop : -2.22 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 411 HIS 0.007 0.001 HIS B 385 PHE 0.022 0.002 PHE C 497 TYR 0.019 0.001 TYR A 65 ARG 0.002 0.000 ARG A 474 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1291.26 seconds wall clock time: 24 minutes 15.12 seconds (1455.12 seconds total)