Starting phenix.real_space_refine on Tue Feb 13 17:49:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efd_28080/02_2024/8efd_28080.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efd_28080/02_2024/8efd_28080.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/8efd_28080/02_2024/8efd_28080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efd_28080/02_2024/8efd_28080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efd_28080/02_2024/8efd_28080.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efd_28080/02_2024/8efd_28080.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 40 5.16 5 C 4524 2.51 5 N 1210 2.21 5 O 1333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 371": "OE1" <-> "OE2" Residue "A PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7107 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5967 Classifications: {'peptide': 740} Link IDs: {'PTRANS': 28, 'TRANS': 711} Chain breaks: 3 Chain: "B" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1140 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 142} Time building chain proxies: 4.36, per 1000 atoms: 0.61 Number of scatterers: 7107 At special positions: 0 Unit cell: (86.24, 127.204, 117.502, 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 40 16.00 O 1333 8.00 N 1210 7.00 C 4524 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: 2.51 Conformation dependent library (CDL) restraints added in 1.2 seconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 9 sheets defined 57.2% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 removed outlier: 6.202A pdb=" N ALA A 11 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 17 removed outlier: 3.524A pdb=" N LEU A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.759A pdb=" N THR A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.675A pdb=" N LEU A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 removed outlier: 4.436A pdb=" N TYR A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 217 through 231 Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 283 through 290 removed outlier: 4.434A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 343 through 359 removed outlier: 3.577A pdb=" N ASN A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 416 through 448 Processing helix chain 'A' and resid 472 through 504 Processing helix chain 'A' and resid 513 through 526 removed outlier: 3.709A pdb=" N LEU A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 519 " --> pdb=" O MET A 515 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 540 removed outlier: 3.551A pdb=" N CYS A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 557 Processing helix chain 'A' and resid 592 through 598 removed outlier: 3.971A pdb=" N LYS A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 647 through 664 removed outlier: 3.913A pdb=" N SER A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 697 through 707 Processing helix chain 'A' and resid 715 through 723 removed outlier: 3.506A pdb=" N ARG A 723 " --> pdb=" O ARG A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 766 through 796 removed outlier: 3.915A pdb=" N LEU A 770 " --> pdb=" O LYS A 766 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.962A pdb=" N VAL B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 103 through 116 Proline residue: B 109 - end of helix removed outlier: 3.655A pdb=" N ASN B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 removed outlier: 3.547A pdb=" N VAL B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 153 Processing helix chain 'B' and resid 158 through 166 Processing helix chain 'B' and resid 178 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 4.053A pdb=" N PHE A 121 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 266 removed outlier: 6.691A pdb=" N LYS A 246 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A 460 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 248 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY A 458 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE A 250 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE A 456 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A 172 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'A' and resid 403 through 406 Processing sheet with id=AA7, first strand: chain 'A' and resid 577 through 581 removed outlier: 3.726A pdb=" N PHE A 577 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 711 through 714 Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 142 removed outlier: 3.630A pdb=" N VAL B 141 " --> pdb=" O ILE B 176 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1032 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: 2.25 Time building geometry restraints manager: 2.76 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: 2344 1.34 - 1.46: 1365 1.46 - 1.58: 3466 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 7245 Sorted by residual: bond pdb=" CG GLU A 775 " pdb=" CD GLU A 775 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.11e+00 bond pdb=" C GLU A 374 " pdb=" O GLU A 374 " ideal model delta sigma weight residual 1.245 1.229 0.016 1.53e-02 4.27e+03 1.08e+00 bond pdb=" CG1 ILE A 289 " pdb=" CD1 ILE A 289 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 9.80e-01 bond pdb=" N LYS A 570 " pdb=" CA LYS A 570 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.48e-01 bond pdb=" C GLU A 374 " pdb=" N PRO A 375 " ideal model delta sigma weight residual 1.330 1.339 -0.009 1.22e-02 6.72e+03 5.83e-01 ... (remaining 7240 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.43: 121 105.43 - 112.57: 3624 112.57 - 119.70: 2474 119.70 - 126.84: 3468 126.84 - 133.97: 67 Bond angle restraints: 9754 Sorted by residual: angle pdb=" N GLU A 775 " pdb=" CA GLU A 775 " pdb=" CB GLU A 775 " ideal model delta sigma weight residual 110.28 115.42 -5.14 1.55e+00 4.16e-01 1.10e+01 angle pdb=" C GLU A 774 " pdb=" N GLU A 775 " pdb=" CA GLU A 775 " ideal model delta sigma weight residual 120.31 115.74 4.57 1.52e+00 4.33e-01 9.04e+00 angle pdb=" CA GLU A 775 " pdb=" CB GLU A 775 " pdb=" CG GLU A 775 " ideal model delta sigma weight residual 114.10 118.94 -4.84 2.00e+00 2.50e-01 5.85e+00 angle pdb=" CA PRO A 375 " pdb=" C PRO A 375 " pdb=" O PRO A 375 " ideal model delta sigma weight residual 122.08 119.30 2.78 1.28e+00 6.10e-01 4.73e+00 angle pdb=" N PHE A 364 " pdb=" CA PHE A 364 " pdb=" C PHE A 364 " ideal model delta sigma weight residual 110.91 113.33 -2.42 1.17e+00 7.31e-01 4.26e+00 ... (remaining 9749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3959 17.91 - 35.81: 365 35.81 - 53.72: 61 53.72 - 71.63: 6 71.63 - 89.53: 9 Dihedral angle restraints: 4400 sinusoidal: 1829 harmonic: 2571 Sorted by residual: dihedral pdb=" CB GLU A 328 " pdb=" CG GLU A 328 " pdb=" CD GLU A 328 " pdb=" OE1 GLU A 328 " ideal model delta sinusoidal sigma weight residual 0.00 -89.53 89.53 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 98 " pdb=" CG GLU A 98 " pdb=" CD GLU A 98 " pdb=" OE1 GLU A 98 " ideal model delta sinusoidal sigma weight residual 0.00 -88.09 88.09 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA ARG A 706 " pdb=" CB ARG A 706 " pdb=" CG ARG A 706 " pdb=" CD ARG A 706 " ideal model delta sinusoidal sigma weight residual -60.00 -110.94 50.94 3 1.50e+01 4.44e-03 8.96e+00 ... (remaining 4397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 682 0.027 - 0.055: 248 0.055 - 0.082: 75 0.082 - 0.109: 38 0.109 - 0.136: 17 Chirality restraints: 1060 Sorted by residual: chirality pdb=" CA VAL A 459 " pdb=" N VAL A 459 " pdb=" C VAL A 459 " pdb=" CB VAL A 459 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE A 674 " pdb=" N ILE A 674 " pdb=" C ILE A 674 " pdb=" CB ILE A 674 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA PRO A 710 " pdb=" N PRO A 710 " pdb=" C PRO A 710 " pdb=" CB PRO A 710 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1057 not shown) Planarity restraints: 1269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 224 " -0.016 5.00e-02 4.00e+02 2.46e-02 9.65e-01 pdb=" N PRO A 225 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 225 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 225 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 609 " 0.006 2.00e-02 2.50e+03 6.55e-03 8.57e-01 pdb=" CG TYR A 609 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 609 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 609 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 609 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 609 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 609 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 609 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 709 " 0.015 5.00e-02 4.00e+02 2.22e-02 7.85e-01 pdb=" N PRO A 710 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 710 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 710 " 0.012 5.00e-02 4.00e+02 ... (remaining 1266 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 117 2.62 - 3.19: 6966 3.19 - 3.76: 11311 3.76 - 4.33: 14687 4.33 - 4.90: 24028 Nonbonded interactions: 57109 Sorted by model distance: nonbonded pdb=" OG1 THR A 235 " pdb=" O ASN A 238 " model vdw 2.048 2.440 nonbonded pdb=" O THR A 449 " pdb=" NH2 ARG A 453 " model vdw 2.086 2.520 nonbonded pdb=" O ALA A 141 " pdb=" NZ LYS A 145 " model vdw 2.092 2.520 nonbonded pdb=" OG1 THR A 94 " pdb=" O ALA A 767 " model vdw 2.098 2.440 nonbonded pdb=" O LEU A 166 " pdb=" NH1 ARG A 169 " model vdw 2.119 2.520 ... (remaining 57104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 16.600 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 22.430 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.002 0.039 7245 Z= 0.144 Angle : 0.492 5.144 9754 Z= 0.272 Chirality : 0.037 0.136 1060 Planarity : 0.002 0.025 1269 Dihedral : 14.097 89.535 2742 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.13 % Allowed : 0.39 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 876 helix: 1.91 (0.25), residues: 446 sheet: -1.37 (0.62), residues: 82 loop : -0.78 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 130 HIS 0.006 0.001 HIS B 148 PHE 0.013 0.001 PHE A 510 TYR 0.016 0.001 TYR A 609 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.816 Fit side-chains REVERT: A 165 MET cc_start: 0.8946 (tmm) cc_final: 0.8712 (tmm) REVERT: A 388 MET cc_start: 0.8990 (mpp) cc_final: 0.8761 (mpp) REVERT: A 439 MET cc_start: 0.9109 (mpp) cc_final: 0.8881 (mpp) REVERT: A 546 MET cc_start: 0.8837 (tpt) cc_final: 0.8613 (tpp) REVERT: A 776 MET cc_start: 0.9460 (mmp) cc_final: 0.9223 (mmm) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.1593 time to fit residues: 13.9458 Evaluate side-chains 45 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.0770 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 691 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7245 Z= 0.174 Angle : 0.527 5.670 9754 Z= 0.276 Chirality : 0.039 0.140 1060 Planarity : 0.003 0.038 1269 Dihedral : 3.774 16.381 954 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.04 % Allowed : 6.76 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 876 helix: 1.88 (0.25), residues: 452 sheet: -1.30 (0.60), residues: 82 loop : -0.86 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 593 HIS 0.002 0.001 HIS A 401 PHE 0.027 0.001 PHE B 181 TYR 0.017 0.001 TYR A 609 ARG 0.003 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.758 Fit side-chains REVERT: A 6 MET cc_start: 0.7884 (tmm) cc_final: 0.7624 (tmm) REVERT: A 388 MET cc_start: 0.8973 (mpp) cc_final: 0.8455 (mpp) REVERT: A 546 MET cc_start: 0.8816 (tpt) cc_final: 0.8552 (tpp) REVERT: A 609 TYR cc_start: 0.8873 (m-80) cc_final: 0.8595 (m-80) REVERT: B 97 MET cc_start: 0.4723 (ptt) cc_final: 0.3537 (tpt) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 0.1620 time to fit residues: 12.6586 Evaluate side-chains 48 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.0980 chunk 86 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 711 ASN B 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7245 Z= 0.207 Angle : 0.521 6.597 9754 Z= 0.273 Chirality : 0.040 0.146 1060 Planarity : 0.003 0.036 1269 Dihedral : 3.968 15.661 954 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.82 % Allowed : 10.66 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.29), residues: 876 helix: 1.59 (0.25), residues: 456 sheet: -1.38 (0.60), residues: 82 loop : -0.92 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 508 HIS 0.003 0.001 HIS A 581 PHE 0.012 0.001 PHE A 669 TYR 0.012 0.001 TYR A 609 ARG 0.002 0.000 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: A 609 TYR cc_start: 0.8830 (m-80) cc_final: 0.8540 (m-80) REVERT: B 97 MET cc_start: 0.4738 (ptt) cc_final: 0.3741 (tpt) outliers start: 14 outliers final: 8 residues processed: 55 average time/residue: 0.1756 time to fit residues: 14.1244 Evaluate side-chains 53 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS 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: 1.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.0370 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 0.0170 chunk 80 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7245 Z= 0.153 Angle : 0.506 6.260 9754 Z= 0.258 Chirality : 0.038 0.156 1060 Planarity : 0.003 0.031 1269 Dihedral : 3.864 20.133 954 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.43 % Allowed : 12.87 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.29), residues: 876 helix: 1.71 (0.25), residues: 462 sheet: -1.25 (0.61), residues: 82 loop : -0.87 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 508 HIS 0.002 0.001 HIS A 491 PHE 0.021 0.001 PHE B 181 TYR 0.010 0.001 TYR B 123 ARG 0.003 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 546 MET cc_start: 0.8870 (tpt) cc_final: 0.8600 (tpp) REVERT: A 609 TYR cc_start: 0.8829 (m-80) cc_final: 0.8542 (m-80) REVERT: B 97 MET cc_start: 0.5027 (ptt) cc_final: 0.4252 (tpt) outliers start: 11 outliers final: 5 residues processed: 49 average time/residue: 0.1480 time to fit residues: 11.3294 Evaluate side-chains 49 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7245 Z= 0.153 Angle : 0.499 7.933 9754 Z= 0.256 Chirality : 0.038 0.144 1060 Planarity : 0.003 0.031 1269 Dihedral : 3.846 19.059 954 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.43 % Allowed : 13.65 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.29), residues: 876 helix: 1.68 (0.25), residues: 461 sheet: -1.22 (0.62), residues: 82 loop : -0.88 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 508 HIS 0.002 0.001 HIS A 581 PHE 0.010 0.001 PHE A 230 TYR 0.009 0.001 TYR B 123 ARG 0.002 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 6 MET cc_start: 0.8240 (tmm) cc_final: 0.8011 (tmm) REVERT: A 113 MET cc_start: 0.6473 (ttm) cc_final: 0.6111 (ttm) REVERT: A 195 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: A 546 MET cc_start: 0.8882 (tpt) cc_final: 0.8607 (tpp) REVERT: A 609 TYR cc_start: 0.8857 (m-80) cc_final: 0.8579 (m-80) REVERT: B 97 MET cc_start: 0.5247 (ptt) cc_final: 0.4491 (tpt) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 0.1527 time to fit residues: 12.1242 Evaluate side-chains 52 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 163 GLN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7245 Z= 0.266 Angle : 0.601 10.103 9754 Z= 0.307 Chirality : 0.040 0.166 1060 Planarity : 0.004 0.042 1269 Dihedral : 4.304 18.403 954 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.47 % Allowed : 14.95 % Favored : 82.57 % 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: 0.41 (0.29), residues: 876 helix: 1.50 (0.25), residues: 456 sheet: -1.41 (0.61), residues: 82 loop : -0.96 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.003 0.001 HIS A 651 PHE 0.021 0.002 PHE B 181 TYR 0.016 0.002 TYR A 142 ARG 0.003 0.001 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.8117 (tmm) cc_final: 0.7788 (tmm) REVERT: A 113 MET cc_start: 0.6626 (ttm) cc_final: 0.6139 (ttm) REVERT: A 195 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: A 609 TYR cc_start: 0.8877 (m-80) cc_final: 0.8629 (m-80) REVERT: B 97 MET cc_start: 0.5046 (ptt) cc_final: 0.4360 (tpt) outliers start: 19 outliers final: 10 residues processed: 58 average time/residue: 0.1578 time to fit residues: 14.1838 Evaluate side-chains 57 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7245 Z= 0.199 Angle : 0.574 8.928 9754 Z= 0.285 Chirality : 0.039 0.146 1060 Planarity : 0.003 0.037 1269 Dihedral : 4.168 17.260 954 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.82 % Allowed : 16.12 % Favored : 82.05 % 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: 0.38 (0.29), residues: 876 helix: 1.48 (0.25), residues: 462 sheet: -1.36 (0.62), residues: 82 loop : -1.06 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 508 HIS 0.003 0.001 HIS A 401 PHE 0.012 0.001 PHE A 230 TYR 0.017 0.001 TYR A 164 ARG 0.002 0.000 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.8011 (tmm) cc_final: 0.7673 (tmm) REVERT: A 113 MET cc_start: 0.6650 (ttm) cc_final: 0.6141 (ttm) REVERT: A 195 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: A 609 TYR cc_start: 0.8874 (m-80) cc_final: 0.8634 (m-80) REVERT: B 97 MET cc_start: 0.5082 (ptt) cc_final: 0.4479 (tpt) outliers start: 14 outliers final: 8 residues processed: 53 average time/residue: 0.1493 time to fit residues: 12.3466 Evaluate side-chains 54 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 0.0070 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7245 Z= 0.175 Angle : 0.555 9.231 9754 Z= 0.277 Chirality : 0.039 0.151 1060 Planarity : 0.003 0.033 1269 Dihedral : 4.119 16.526 954 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.34 % Allowed : 15.73 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.29), residues: 876 helix: 1.57 (0.25), residues: 456 sheet: -1.30 (0.63), residues: 82 loop : -0.99 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 508 HIS 0.002 0.001 HIS A 401 PHE 0.019 0.001 PHE B 181 TYR 0.009 0.001 TYR B 123 ARG 0.002 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 46 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.6603 (ttm) cc_final: 0.6093 (ttm) REVERT: A 195 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: A 358 HIS cc_start: 0.6838 (OUTLIER) cc_final: 0.6592 (t-90) REVERT: A 435 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8494 (tpt) REVERT: A 609 TYR cc_start: 0.8868 (m-80) cc_final: 0.8634 (m-80) REVERT: B 97 MET cc_start: 0.5095 (ptt) cc_final: 0.4591 (tpt) outliers start: 18 outliers final: 10 residues processed: 57 average time/residue: 0.1502 time to fit residues: 13.0763 Evaluate side-chains 58 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.2980 chunk 81 optimal weight: 0.0870 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN B 45 GLN B 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7245 Z= 0.162 Angle : 0.579 10.962 9754 Z= 0.282 Chirality : 0.039 0.148 1060 Planarity : 0.003 0.033 1269 Dihedral : 4.045 16.491 954 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.21 % Allowed : 16.38 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.29), residues: 876 helix: 1.68 (0.25), residues: 453 sheet: -1.24 (0.64), residues: 82 loop : -0.89 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 508 HIS 0.002 0.001 HIS A 153 PHE 0.010 0.001 PHE B 53 TYR 0.009 0.001 TYR B 123 ARG 0.002 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7836 (t0) REVERT: A 113 MET cc_start: 0.6561 (ttm) cc_final: 0.6061 (ttm) REVERT: A 195 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: A 358 HIS cc_start: 0.6789 (OUTLIER) cc_final: 0.6569 (t-90) REVERT: A 435 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8425 (tpt) REVERT: A 609 TYR cc_start: 0.8868 (m-80) cc_final: 0.8640 (m-80) REVERT: B 97 MET cc_start: 0.5096 (ptt) cc_final: 0.4666 (tpt) outliers start: 17 outliers final: 8 residues processed: 58 average time/residue: 0.1620 time to fit residues: 14.2058 Evaluate side-chains 57 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 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: 2.9990 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7245 Z= 0.177 Angle : 0.595 9.261 9754 Z= 0.292 Chirality : 0.040 0.318 1060 Planarity : 0.003 0.038 1269 Dihedral : 4.097 16.323 954 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.82 % Allowed : 17.17 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.30), residues: 876 helix: 1.65 (0.25), residues: 453 sheet: -1.23 (0.64), residues: 82 loop : -0.89 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 508 HIS 0.002 0.001 HIS A 401 PHE 0.021 0.001 PHE B 181 TYR 0.011 0.001 TYR B 123 ARG 0.002 0.000 ARG B 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8785 (mmm) cc_final: 0.8536 (mmm) REVERT: A 113 MET cc_start: 0.6613 (ttm) cc_final: 0.6095 (ttm) REVERT: A 195 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: A 358 HIS cc_start: 0.6808 (OUTLIER) cc_final: 0.6580 (t-90) REVERT: A 435 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8471 (tpt) REVERT: A 546 MET cc_start: 0.8865 (tpt) cc_final: 0.8559 (tpp) REVERT: A 609 TYR cc_start: 0.8865 (m-80) cc_final: 0.8644 (m-80) REVERT: B 97 MET cc_start: 0.5104 (ptt) cc_final: 0.4685 (tpt) outliers start: 14 outliers final: 9 residues processed: 53 average time/residue: 0.1531 time to fit residues: 12.2679 Evaluate side-chains 56 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 0.0050 overall best weight: 0.1172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.050167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.040171 restraints weight = 60242.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.041121 restraints weight = 33153.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.041764 restraints weight = 21550.926| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7245 Z= 0.134 Angle : 0.583 10.326 9754 Z= 0.283 Chirality : 0.040 0.252 1060 Planarity : 0.003 0.028 1269 Dihedral : 3.872 16.369 954 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.43 % Allowed : 17.30 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.30), residues: 876 helix: 1.64 (0.26), residues: 451 sheet: -1.23 (0.63), residues: 84 loop : -0.82 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 508 HIS 0.001 0.000 HIS B 184 PHE 0.015 0.001 PHE B 181 TYR 0.008 0.001 TYR A 310 ARG 0.002 0.000 ARG A 783 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.08 seconds wall clock time: 31 minutes 54.98 seconds (1914.98 seconds total)