Starting phenix.real_space_refine on Tue Sep 24 02:12:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/09_2024/7rto_24685.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/09_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_24685/09_2024/7rto_24685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/09_2024/7rto_24685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/09_2024/7rto_24685.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rto_24685/09_2024/7rto_24685.cif" } 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. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.56, per 1000 atoms: 0.84 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 992.7 milliseconds 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: 0.64 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: 2.41 Time building geometry restraints manager: 1.94 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: 0.00 - 1.90: 8754 1.90 - 3.79: 315 3.79 - 5.69: 47 5.69 - 7.59: 6 7.59 - 9.48: 8 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 3.120 nonbonded pdb=" O LEU A 450 " pdb=" OG SER A 453 " model vdw 2.328 3.040 nonbonded pdb=" O HIS A 384 " pdb=" ND1 HIS A 385 " model vdw 2.336 3.120 nonbonded pdb=" O ALA A 369 " pdb=" OG SER A 373 " model vdw 2.356 3.040 nonbonded pdb=" O SER C 89 " pdb=" OG SER C 89 " model vdw 2.385 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.370 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.090 ------------------------------------------------------------------------------- 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 : 0.781 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: 0.1940 time to fit residues: 34.9537 Evaluate side-chains 94 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 40.0000 chunk 35 optimal weight: 30.0000 chunk 68 optimal weight: 50.0000 chunk 26 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 HIS A 478 GLN B 177 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6734 Z= 0.283 Angle : 0.638 7.191 9130 Z= 0.346 Chirality : 0.044 0.183 1025 Planarity : 0.004 0.027 1206 Dihedral : 4.878 40.086 954 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.97 % Allowed : 10.98 % Favored : 87.05 % 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: 1.21 (0.30), residues: 870 helix: 2.25 (0.23), residues: 508 sheet: -0.07 (0.47), residues: 137 loop : -2.15 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 411 HIS 0.009 0.001 HIS B 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 117 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.748 Fit side-chains REVERT: A 488 MET cc_start: 0.7811 (tpp) cc_final: 0.7587 (tpp) REVERT: B 108 ASN cc_start: 0.7687 (m110) cc_final: 0.7388 (m-40) REVERT: B 125 LYS cc_start: 0.3826 (mtpp) cc_final: 0.3300 (mtpp) REVERT: B 132 ASN cc_start: 0.6408 (t0) cc_final: 0.6018 (t0) REVERT: B 467 ASP cc_start: 0.6274 (m-30) cc_final: 0.5591 (p0) REVERT: C 114 LYS cc_start: 0.2892 (tttp) cc_final: 0.2446 (tttm) REVERT: C 427 GLU cc_start: 0.7495 (pt0) cc_final: 0.7233 (pt0) outliers start: 12 outliers final: 10 residues processed: 113 average time/residue: 0.1628 time to fit residues: 25.3029 Evaluate side-chains 100 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 66 optimal weight: 9.9990 chunk 54 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 27 optimal weight: 30.0000 chunk 64 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 HIS A 498 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2212 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= 0.219 Angle : 0.578 6.225 9130 Z= 0.313 Chirality : 0.042 0.165 1025 Planarity : 0.003 0.024 1206 Dihedral : 4.408 18.822 951 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.13 % Allowed : 14.43 % Favored : 83.44 % 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: 1.27 (0.30), residues: 870 helix: 2.42 (0.23), residues: 503 sheet: 0.09 (0.49), residues: 128 loop : -2.34 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 411 HIS 0.009 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 118 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.804 Fit side-chains REVERT: A 360 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: A 445 MET cc_start: 0.7770 (tmm) cc_final: 0.7480 (tmm) REVERT: B 108 ASN cc_start: 0.7724 (m110) cc_final: 0.7473 (m110) REVERT: B 109 GLU cc_start: 0.5532 (tp30) cc_final: 0.5282 (tp30) REVERT: B 132 ASN cc_start: 0.6209 (t0) cc_final: 0.5921 (t0) REVERT: B 467 ASP cc_start: 0.6301 (m-30) cc_final: 0.5657 (p0) REVERT: C 114 LYS cc_start: 0.2939 (tttp) cc_final: 0.2431 (tttm) REVERT: C 118 LYS cc_start: 0.5179 (pttp) cc_final: 0.4267 (pttp) REVERT: C 364 ILE cc_start: 0.9065 (mm) cc_final: 0.8797 (mm) REVERT: C 427 GLU cc_start: 0.7365 (pt0) cc_final: 0.7144 (pt0) outliers start: 13 outliers final: 11 residues processed: 112 average time/residue: 0.1633 time to fit residues: 25.3582 Evaluate side-chains 110 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 360 GLN 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 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: 1.9990 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 38 optimal weight: 40.0000 chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 0.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 HIS ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2402 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= 0.143 Angle : 0.531 7.076 9130 Z= 0.285 Chirality : 0.040 0.153 1025 Planarity : 0.003 0.024 1206 Dihedral : 4.033 16.456 951 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.97 % Allowed : 17.05 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.30), residues: 870 helix: 2.59 (0.23), residues: 510 sheet: 0.21 (0.50), residues: 128 loop : -2.34 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 411 HIS 0.009 0.001 HIS B 385 PHE 0.017 0.002 PHE B 391 TYR 0.015 0.001 TYR A 65 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 121 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.776 Fit side-chains REVERT: A 356 ILE cc_start: 0.8610 (mp) cc_final: 0.8329 (mp) REVERT: B 132 ASN cc_start: 0.6572 (t0) cc_final: 0.6130 (t0) REVERT: B 407 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7582 (pp) REVERT: B 467 ASP cc_start: 0.6247 (m-30) cc_final: 0.5649 (p0) REVERT: C 114 LYS cc_start: 0.2766 (tttp) cc_final: 0.2471 (tttm) REVERT: C 364 ILE cc_start: 0.9045 (mm) cc_final: 0.8763 (mm) outliers start: 12 outliers final: 10 residues processed: 116 average time/residue: 0.1776 time to fit residues: 28.1323 Evaluate side-chains 106 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 185 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 496 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 30.0000 chunk 76 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6734 Z= 0.280 Angle : 0.607 6.928 9130 Z= 0.328 Chirality : 0.042 0.176 1025 Planarity : 0.003 0.025 1206 Dihedral : 4.465 19.903 951 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.44 % Allowed : 17.70 % Favored : 78.85 % 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: 1.33 (0.30), residues: 870 helix: 2.38 (0.23), residues: 512 sheet: -0.03 (0.47), residues: 135 loop : -2.25 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 411 HIS 0.010 0.001 HIS B 385 PHE 0.019 0.002 PHE B 378 TYR 0.022 0.002 TYR B 482 ARG 0.004 0.000 ARG A 474 *********************** 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 111 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.705 Fit side-chains REVERT: B 132 ASN cc_start: 0.6326 (t0) cc_final: 0.5680 (t0) REVERT: C 114 LYS cc_start: 0.2992 (tttp) cc_final: 0.2711 (tttm) REVERT: C 118 LYS cc_start: 0.4939 (pttp) cc_final: 0.4165 (mmmt) REVERT: C 364 ILE cc_start: 0.9029 (mm) cc_final: 0.8722 (mm) outliers start: 21 outliers final: 19 residues processed: 104 average time/residue: 0.1504 time to fit residues: 22.1490 Evaluate side-chains 103 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL 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 382 ILE 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 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 C residue 376 VAL Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 496 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 70 optimal weight: 50.0000 chunk 39 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2863 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= 0.183 Angle : 0.558 6.835 9130 Z= 0.298 Chirality : 0.041 0.166 1025 Planarity : 0.003 0.024 1206 Dihedral : 4.229 17.954 951 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.11 % Allowed : 19.51 % 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: 1.48 (0.30), residues: 870 helix: 2.51 (0.23), residues: 513 sheet: -0.01 (0.47), residues: 135 loop : -2.23 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 411 HIS 0.009 0.001 HIS B 385 PHE 0.017 0.002 PHE B 378 TYR 0.017 0.001 TYR A 65 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 117 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.762 Fit side-chains REVERT: A 478 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8541 (mm-40) REVERT: B 84 ILE cc_start: 0.9409 (mm) cc_final: 0.9109 (tt) REVERT: B 132 ASN cc_start: 0.6410 (t0) cc_final: 0.5690 (t0) REVERT: B 467 ASP cc_start: 0.6419 (m-30) cc_final: 0.5915 (p0) REVERT: C 118 LYS cc_start: 0.5202 (pttp) cc_final: 0.4441 (mmmt) REVERT: C 364 ILE cc_start: 0.8995 (mm) cc_final: 0.8645 (mm) outliers start: 19 outliers final: 17 residues processed: 110 average time/residue: 0.1455 time to fit residues: 22.8211 Evaluate side-chains 106 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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 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 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 456 VAL 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: 0.0470 chunk 48 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6734 Z= 0.177 Angle : 0.552 7.847 9130 Z= 0.296 Chirality : 0.041 0.178 1025 Planarity : 0.003 0.023 1206 Dihedral : 4.141 17.393 951 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.44 % Allowed : 20.49 % Favored : 76.07 % 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: 1.52 (0.30), residues: 870 helix: 2.59 (0.23), residues: 510 sheet: -0.09 (0.47), residues: 137 loop : -2.19 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 411 HIS 0.009 0.001 HIS B 385 PHE 0.017 0.002 PHE B 378 TYR 0.018 0.001 TYR A 65 ARG 0.003 0.000 ARG A 474 *********************** 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 116 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.759 Fit side-chains REVERT: A 478 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8550 (mm-40) REVERT: B 132 ASN cc_start: 0.6342 (t0) cc_final: 0.5653 (t0) REVERT: C 118 LYS cc_start: 0.5267 (pttp) cc_final: 0.4539 (mmmt) REVERT: C 364 ILE cc_start: 0.8984 (mm) cc_final: 0.8642 (mm) REVERT: C 405 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5809 (mt-10) outliers start: 21 outliers final: 18 residues processed: 109 average time/residue: 0.1436 time to fit residues: 22.3956 Evaluate side-chains 113 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 456 VAL 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: 20.0000 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 77 optimal weight: 30.0000 chunk 81 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3117 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= 0.249 Angle : 0.597 8.521 9130 Z= 0.321 Chirality : 0.042 0.181 1025 Planarity : 0.003 0.024 1206 Dihedral : 4.409 19.113 951 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.61 % Allowed : 20.82 % Favored : 75.57 % 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: 2.41 (0.22), residues: 510 sheet: -0.31 (0.46), residues: 144 loop : -2.20 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 411 HIS 0.010 0.001 HIS B 385 PHE 0.018 0.002 PHE B 378 TYR 0.017 0.002 TYR A 65 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 111 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.762 Fit side-chains REVERT: A 478 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: B 132 ASN cc_start: 0.6300 (t0) cc_final: 0.5577 (t0) REVERT: C 118 LYS cc_start: 0.4872 (pttp) cc_final: 0.4168 (mmmt) REVERT: C 364 ILE cc_start: 0.8995 (mm) cc_final: 0.8684 (mm) outliers start: 22 outliers final: 19 residues processed: 104 average time/residue: 0.1478 time to fit residues: 22.1029 Evaluate side-chains 105 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 382 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 77 VAL 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 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 389 GLU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 456 VAL 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: 3.9990 chunk 81 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 34 optimal weight: 40.0000 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6734 Z= 0.225 Angle : 0.589 9.185 9130 Z= 0.314 Chirality : 0.042 0.176 1025 Planarity : 0.003 0.027 1206 Dihedral : 4.370 18.318 951 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.28 % Allowed : 21.31 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.30), residues: 870 helix: 2.44 (0.22), residues: 510 sheet: -0.30 (0.47), residues: 137 loop : -2.24 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 411 HIS 0.010 0.001 HIS B 385 PHE 0.018 0.002 PHE B 378 TYR 0.018 0.002 TYR A 65 ARG 0.003 0.000 ARG A 474 *********************** 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 110 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.768 Fit side-chains REVERT: A 478 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8557 (mm-40) REVERT: B 84 ILE cc_start: 0.9432 (mm) cc_final: 0.9095 (tt) REVERT: B 132 ASN cc_start: 0.6123 (t0) cc_final: 0.5451 (t0) REVERT: C 118 LYS cc_start: 0.4903 (pttp) cc_final: 0.4218 (mmmt) REVERT: C 364 ILE cc_start: 0.8985 (mm) cc_final: 0.8622 (mm) outliers start: 20 outliers final: 18 residues processed: 104 average time/residue: 0.1473 time to fit residues: 22.0310 Evaluate side-chains 106 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 385 HIS 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 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 389 GLU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 456 VAL 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: 4.9990 chunk 39 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 69 optimal weight: 50.0000 chunk 7 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3213 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= 0.217 Angle : 0.604 9.791 9130 Z= 0.319 Chirality : 0.042 0.176 1025 Planarity : 0.003 0.025 1206 Dihedral : 4.356 18.223 951 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.28 % Allowed : 21.48 % Favored : 75.25 % 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: 1.28 (0.30), residues: 870 helix: 2.41 (0.22), residues: 511 sheet: -0.37 (0.46), residues: 144 loop : -2.26 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 411 HIS 0.010 0.001 HIS B 385 PHE 0.017 0.002 PHE B 378 TYR 0.019 0.002 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 106 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.757 Fit side-chains REVERT: A 478 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8548 (mm-40) REVERT: B 132 ASN cc_start: 0.6129 (t0) cc_final: 0.5440 (t0) REVERT: C 118 LYS cc_start: 0.4737 (pttp) cc_final: 0.4042 (mmmt) REVERT: C 364 ILE cc_start: 0.8977 (mm) cc_final: 0.8619 (mm) outliers start: 20 outliers final: 19 residues processed: 100 average time/residue: 0.1445 time to fit residues: 20.6303 Evaluate side-chains 109 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 382 ILE Chi-restraints excluded: chain A residue 385 HIS 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 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 389 GLU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 456 VAL 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 21 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 69 optimal weight: 50.0000 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.157818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137715 restraints weight = 11890.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137023 restraints weight = 14468.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137617 restraints weight = 11430.365| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6734 Z= 0.141 Angle : 0.558 9.976 9130 Z= 0.293 Chirality : 0.040 0.171 1025 Planarity : 0.003 0.020 1206 Dihedral : 3.979 17.938 951 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.97 % Allowed : 22.79 % Favored : 75.25 % 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: 1.61 (0.30), residues: 870 helix: 2.70 (0.23), residues: 509 sheet: -0.13 (0.48), residues: 142 loop : -2.26 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 371 HIS 0.009 0.001 HIS B 385 PHE 0.018 0.002 PHE B 391 TYR 0.020 0.001 TYR A 65 ARG 0.002 0.000 ARG A 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1310.76 seconds wall clock time: 24 minutes 29.34 seconds (1469.34 seconds total)