Starting phenix.real_space_refine on Wed Mar 12 00:43:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3s_32829/03_2025/8h3s_32829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3s_32829/03_2025/8h3s_32829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h3s_32829/03_2025/8h3s_32829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3s_32829/03_2025/8h3s_32829.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3s_32829/03_2025/8h3s_32829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3s_32829/03_2025/8h3s_32829.cif" } resolution = 4.9 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 45 5.16 5 C 4353 2.51 5 N 1178 2.21 5 O 1325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6901 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3510 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 29, 'TRANS': 419} Chain: "B" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1714 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 203} Chain breaks: 2 Chain: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1677 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Time building chain proxies: 4.55, per 1000 atoms: 0.66 Number of scatterers: 6901 At special positions: 0 Unit cell: (83.3, 85, 146.2, 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 45 16.00 O 1325 8.00 N 1178 7.00 C 4353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 422 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS A 772 " - pdb=" SG CYS B 896 " distance=2.03 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 826 " distance=2.03 Simple disulfide: pdb=" SG CYS B 910 " - pdb=" SG CYS B 977 " distance=2.03 Simple disulfide: pdb=" SG CYS B 941 " - pdb=" SG CYS B 956 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 206 " distance=2.03 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 185 " distance=2.03 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: 1.65 Conformation dependent library (CDL) restraints added in 1.1 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: 1622 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 15 sheets defined 7.4% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 1007 through 1009 No H-bonds generated for 'chain 'B' and resid 1007 through 1009' Processing helix chain 'B' and resid 1010 through 1019 removed outlier: 4.145A pdb=" N PHE B1017 " --> pdb=" O TRP B1013 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N HIS B1019 " --> pdb=" O GLN B1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 167 through 175 Processing helix chain 'C' and resid 235 through 245 Processing sheet with id=AA1, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.827A pdb=" N GLU A 367 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 405 through 410 removed outlier: 3.670A pdb=" N LEU A 437 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 454 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 439 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE A 452 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ILE A 441 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR A 450 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 467 removed outlier: 5.123A pdb=" N TRP A 426 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP A 494 " --> pdb=" O TRP A 426 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 553 through 557 removed outlier: 3.790A pdb=" N LEU A 615 " --> pdb=" O GLU A 581 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 581 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 580 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL A 595 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE A 582 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AA6, first strand: chain 'A' and resid 688 through 689 removed outlier: 3.898A pdb=" N GLY A 689 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 764 " --> pdb=" O LYS A 728 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 728 " --> pdb=" O ARG A 764 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 693 through 694 Processing sheet with id=AA8, first strand: chain 'A' and resid 740 through 741 Processing sheet with id=AA9, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AB1, first strand: chain 'B' and resid 799 through 804 removed outlier: 3.847A pdb=" N VAL B 800 " --> pdb=" O ALA B 812 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 812 " --> pdb=" O VAL B 800 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS B 810 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR B 804 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU B 808 " --> pdb=" O TYR B 804 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY B 811 " --> pdb=" O ALA B 823 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA B 823 " --> pdb=" O GLY B 811 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B 861 " --> pdb=" O HIS B 881 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 859 " --> pdb=" O TRP B 837 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP B 837 " --> pdb=" O ILE B 859 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 801 " --> pdb=" O ILE B 840 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 910 through 911 Processing sheet with id=AB3, first strand: chain 'B' and resid 954 through 956 Processing sheet with id=AB4, first strand: chain 'B' and resid 974 through 978 removed outlier: 3.766A pdb=" N GLY B 987 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N CYS B 977 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU B 985 " --> pdb=" O CYS B 977 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 46 through 49 removed outlier: 4.284A pdb=" N CYS C 48 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS C 112 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE C 93 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU C 110 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 159 through 164 removed outlier: 3.684A pdb=" N SER C 142 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL C 204 " --> pdb=" O GLN C 211 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL C 228 " --> pdb=" O SER C 215 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLY C 227 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C 186 " --> pdb=" O GLY C 227 " (cutoff:3.500A) 131 hydrogen bonds defined for protein. 336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2300 1.35 - 1.46: 1626 1.46 - 1.58: 3091 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 7073 Sorted by residual: bond pdb=" N VAL A 513 " pdb=" CA VAL A 513 " ideal model delta sigma weight residual 1.465 1.494 -0.029 1.02e-02 9.61e+03 8.18e+00 bond pdb=" N THR A 511 " pdb=" CA THR A 511 " ideal model delta sigma weight residual 1.461 1.488 -0.026 1.20e-02 6.94e+03 4.86e+00 bond pdb=" N LEU A 512 " pdb=" CA LEU A 512 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.26e-02 6.30e+03 4.66e+00 bond pdb=" CA THR A 511 " pdb=" C THR A 511 " ideal model delta sigma weight residual 1.519 1.532 -0.013 1.14e-02 7.69e+03 1.25e+00 bond pdb=" CA VAL A 513 " pdb=" CB VAL A 513 " ideal model delta sigma weight residual 1.526 1.541 -0.015 1.55e-02 4.16e+03 9.99e-01 ... (remaining 7068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 9412 1.30 - 2.59: 170 2.59 - 3.89: 41 3.89 - 5.18: 2 5.18 - 6.48: 1 Bond angle restraints: 9626 Sorted by residual: angle pdb=" N ASP A 460 " pdb=" CA ASP A 460 " pdb=" C ASP A 460 " ideal model delta sigma weight residual 114.39 110.79 3.60 1.45e+00 4.76e-01 6.15e+00 angle pdb=" C SER A 545 " pdb=" N TYR A 546 " pdb=" CA TYR A 546 " ideal model delta sigma weight residual 120.97 114.49 6.48 2.84e+00 1.24e-01 5.20e+00 angle pdb=" CA LEU A 512 " pdb=" C LEU A 512 " pdb=" O LEU A 512 " ideal model delta sigma weight residual 120.92 118.68 2.24 1.04e+00 9.25e-01 4.65e+00 angle pdb=" C VAL A 513 " pdb=" N PRO A 514 " pdb=" CA PRO A 514 " ideal model delta sigma weight residual 119.84 122.37 -2.53 1.25e+00 6.40e-01 4.11e+00 angle pdb=" N PHE A 542 " pdb=" CA PHE A 542 " pdb=" C PHE A 542 " ideal model delta sigma weight residual 113.16 115.82 -2.66 1.42e+00 4.96e-01 3.50e+00 ... (remaining 9621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 4014 17.30 - 34.59: 166 34.59 - 51.89: 24 51.89 - 69.18: 6 69.18 - 86.48: 4 Dihedral angle restraints: 4214 sinusoidal: 1679 harmonic: 2535 Sorted by residual: dihedral pdb=" CA GLU A 532 " pdb=" C GLU A 532 " pdb=" N PRO A 533 " pdb=" CA PRO A 533 " ideal model delta harmonic sigma weight residual -180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CB CYS A 716 " pdb=" SG CYS A 716 " pdb=" SG CYS A 767 " pdb=" CB CYS A 767 " ideal model delta sinusoidal sigma weight residual 93.00 127.85 -34.85 1 1.00e+01 1.00e-02 1.72e+01 dihedral pdb=" CA SER A 539 " pdb=" C SER A 539 " pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta harmonic sigma weight residual 180.00 162.42 17.58 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 4211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 593 0.025 - 0.050: 269 0.050 - 0.075: 73 0.075 - 0.101: 53 0.101 - 0.126: 50 Chirality restraints: 1038 Sorted by residual: chirality pdb=" CA VAL A 513 " pdb=" N VAL A 513 " pdb=" C VAL A 513 " pdb=" CB VAL A 513 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE A 490 " pdb=" N ILE A 490 " pdb=" C ILE A 490 " pdb=" CB ILE A 490 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL B 988 " pdb=" N VAL B 988 " pdb=" C VAL B 988 " pdb=" CB VAL B 988 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 1035 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 515 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 516 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 517 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 518 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 542 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 543 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " 0.016 5.00e-02 4.00e+02 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 541 2.74 - 3.28: 6922 3.28 - 3.82: 11384 3.82 - 4.36: 13020 4.36 - 4.90: 22240 Nonbonded interactions: 54107 Sorted by model distance: nonbonded pdb=" O GLU A 574 " pdb=" OG1 THR A 597 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP A 584 " pdb=" OG1 THR A 609 " model vdw 2.262 3.040 nonbonded pdb=" O SER A 375 " pdb=" OG1 THR A 378 " model vdw 2.276 3.040 nonbonded pdb=" OD2 ASP A 383 " pdb=" OG1 THR A 385 " model vdw 2.296 3.040 nonbonded pdb=" O ILE C 243 " pdb=" OG SER C 247 " model vdw 2.301 3.040 ... (remaining 54102 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.760 Find NCS groups from input model: 0.070 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 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 0.044 7073 Z= 0.118 Angle : 0.445 6.478 9626 Z= 0.246 Chirality : 0.041 0.126 1038 Planarity : 0.003 0.044 1276 Dihedral : 9.515 86.476 2556 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.76 % Allowed : 5.77 % Favored : 91.47 % 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: -4.26 (0.24), residues: 876 helix: -2.90 (0.45), residues: 58 sheet: -2.77 (0.33), residues: 196 loop : -3.05 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 366 HIS 0.001 0.000 HIS A 700 PHE 0.006 0.001 PHE A 475 TYR 0.005 0.000 TYR A 546 ARG 0.003 0.000 ARG B1000 *********************** 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 197 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: A 419 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8170 (pm20) REVERT: A 437 LEU cc_start: 0.8326 (pt) cc_final: 0.7838 (pp) REVERT: A 520 LEU cc_start: 0.8906 (mp) cc_final: 0.8388 (pp) REVERT: A 582 ILE cc_start: 0.8552 (mt) cc_final: 0.8197 (tt) REVERT: A 714 ASP cc_start: 0.8561 (m-30) cc_final: 0.8143 (m-30) REVERT: B 867 HIS cc_start: 0.9104 (m-70) cc_final: 0.8868 (t-90) REVERT: B 975 LEU cc_start: 0.9317 (tp) cc_final: 0.9050 (tp) REVERT: B 1017 PHE cc_start: 0.8326 (m-80) cc_final: 0.8009 (m-80) REVERT: C 30 CYS cc_start: 0.4856 (t) cc_final: 0.4323 (p) outliers start: 21 outliers final: 4 residues processed: 192 average time/residue: 0.2454 time to fit residues: 59.1290 Evaluate side-chains 94 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN A 548 ASN A 567 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 HIS A 713 ASN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 HIS B 938 ASN B 943 GLN ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.066013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.051116 restraints weight = 71403.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.051948 restraints weight = 61925.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.052620 restraints weight = 55293.438| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 7073 Z= 0.425 Angle : 0.871 8.256 9626 Z= 0.462 Chirality : 0.050 0.165 1038 Planarity : 0.006 0.054 1276 Dihedral : 5.552 30.137 943 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 31.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.44 % Favored : 87.44 % Rotamer: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -3.84 (0.25), residues: 876 helix: -2.29 (0.48), residues: 54 sheet: -2.66 (0.36), residues: 148 loop : -2.77 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A 554 HIS 0.009 0.002 HIS A 567 PHE 0.022 0.003 PHE A 568 TYR 0.023 0.004 TYR C 28 ARG 0.019 0.002 ARG A 403 *********************** 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 104 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 LEU cc_start: 0.9071 (pt) cc_final: 0.8795 (pt) REVERT: A 490 ILE cc_start: 0.9481 (mt) cc_final: 0.9106 (mt) REVERT: A 579 VAL cc_start: 0.8319 (m) cc_final: 0.8088 (m) REVERT: B 867 HIS cc_start: 0.8860 (m-70) cc_final: 0.8546 (t70) REVERT: B 874 ASP cc_start: 0.7574 (p0) cc_final: 0.7238 (p0) REVERT: B 1017 PHE cc_start: 0.8700 (m-80) cc_final: 0.8276 (m-80) REVERT: C 30 CYS cc_start: 0.4001 (t) cc_final: 0.3382 (p) REVERT: C 94 ILE cc_start: 0.7485 (tp) cc_final: 0.7243 (tp) REVERT: C 109 MET cc_start: 0.7416 (ttp) cc_final: 0.6942 (ttp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2344 time to fit residues: 31.4747 Evaluate side-chains 59 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 55 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 ASN B 844 HIS B 926 ASN B 944 GLN ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.067083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.051763 restraints weight = 69921.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.052644 restraints weight = 60861.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.053292 restraints weight = 54419.219| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7073 Z= 0.237 Angle : 0.634 6.851 9626 Z= 0.333 Chirality : 0.046 0.181 1038 Planarity : 0.005 0.053 1276 Dihedral : 4.946 28.512 943 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: -3.58 (0.25), residues: 876 helix: -1.51 (0.51), residues: 63 sheet: -2.53 (0.34), residues: 172 loop : -2.61 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 983 HIS 0.006 0.001 HIS C 76 PHE 0.024 0.002 PHE A 693 TYR 0.017 0.002 TYR B1004 ARG 0.007 0.001 ARG A 403 *********************** 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 81 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 LEU cc_start: 0.9076 (pt) cc_final: 0.8761 (pt) REVERT: A 490 ILE cc_start: 0.9402 (mt) cc_final: 0.8943 (mm) REVERT: A 615 LEU cc_start: 0.9350 (mm) cc_final: 0.9117 (mm) REVERT: B 867 HIS cc_start: 0.8926 (m-70) cc_final: 0.8670 (t70) REVERT: B 900 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8836 (tm-30) REVERT: B 910 CYS cc_start: 0.7498 (p) cc_final: 0.7274 (p) REVERT: B 1017 PHE cc_start: 0.8686 (m-80) cc_final: 0.8283 (m-80) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2303 time to fit residues: 24.5834 Evaluate side-chains 60 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 0.0030 chunk 43 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.065484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.050525 restraints weight = 74262.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.051357 restraints weight = 64612.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.052007 restraints weight = 57865.924| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7073 Z= 0.223 Angle : 0.625 5.986 9626 Z= 0.328 Chirality : 0.046 0.182 1038 Planarity : 0.005 0.053 1276 Dihedral : 5.027 30.610 943 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -3.43 (0.26), residues: 876 helix: -1.28 (0.58), residues: 56 sheet: -2.53 (0.35), residues: 178 loop : -2.47 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1013 HIS 0.004 0.001 HIS C 76 PHE 0.013 0.002 PHE A 479 TYR 0.013 0.002 TYR A 342 ARG 0.003 0.000 ARG A 403 *********************** 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 78 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 ILE cc_start: 0.9412 (mt) cc_final: 0.8963 (mm) REVERT: A 611 ARG cc_start: 0.9449 (tpt90) cc_final: 0.9247 (tpp-160) REVERT: B 1017 PHE cc_start: 0.8688 (m-80) cc_final: 0.8305 (m-80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2329 time to fit residues: 23.8801 Evaluate side-chains 61 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.065510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.050457 restraints weight = 71033.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.051287 restraints weight = 61650.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.051965 restraints weight = 55081.365| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7073 Z= 0.199 Angle : 0.602 6.548 9626 Z= 0.313 Chirality : 0.045 0.200 1038 Planarity : 0.005 0.051 1276 Dihedral : 4.902 29.167 943 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: -3.32 (0.26), residues: 876 helix: -1.23 (0.61), residues: 56 sheet: -2.48 (0.34), residues: 188 loop : -2.36 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 796 HIS 0.003 0.001 HIS A 700 PHE 0.012 0.001 PHE C 18 TYR 0.010 0.001 TYR B1004 ARG 0.005 0.001 ARG A 403 *********************** 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 81 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 ILE cc_start: 0.9400 (mt) cc_final: 0.8934 (mm) REVERT: A 506 LEU cc_start: 0.8607 (mt) cc_final: 0.8338 (pp) REVERT: A 507 TYR cc_start: 0.8935 (m-80) cc_final: 0.8604 (m-80) REVERT: A 579 VAL cc_start: 0.8593 (p) cc_final: 0.8278 (p) REVERT: B 867 HIS cc_start: 0.8328 (t70) cc_final: 0.7918 (t70) REVERT: B 910 CYS cc_start: 0.7160 (p) cc_final: 0.6879 (p) REVERT: B 976 MET cc_start: 0.7590 (ptt) cc_final: 0.6847 (pmm) REVERT: B 1017 PHE cc_start: 0.8648 (m-80) cc_final: 0.8180 (m-80) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2414 time to fit residues: 25.2057 Evaluate side-chains 63 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 63 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 929 GLN ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.059536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.045304 restraints weight = 77200.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.046076 restraints weight = 66898.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.046691 restraints weight = 59856.063| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.7643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7073 Z= 0.332 Angle : 0.736 7.019 9626 Z= 0.390 Chirality : 0.048 0.165 1038 Planarity : 0.006 0.054 1276 Dihedral : 5.962 31.679 943 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 32.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.73 % Favored : 85.27 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -3.60 (0.26), residues: 876 helix: -1.44 (0.58), residues: 56 sheet: -2.61 (0.33), residues: 190 loop : -2.59 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B1013 HIS 0.011 0.002 HIS C 96 PHE 0.020 0.002 PHE A 382 TYR 0.015 0.003 TYR B 948 ARG 0.009 0.001 ARG A 583 *********************** 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 71 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 LEU cc_start: 0.8720 (mt) cc_final: 0.8405 (pp) REVERT: A 507 TYR cc_start: 0.9023 (m-80) cc_final: 0.8605 (m-80) REVERT: A 531 TRP cc_start: 0.8826 (m100) cc_final: 0.7811 (p-90) REVERT: A 579 VAL cc_start: 0.8877 (p) cc_final: 0.8421 (m) REVERT: A 765 LEU cc_start: 0.9150 (tp) cc_final: 0.8944 (tp) REVERT: B 867 HIS cc_start: 0.8316 (t70) cc_final: 0.8015 (t70) REVERT: B 900 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9084 (tm-30) REVERT: B 976 MET cc_start: 0.8197 (ptt) cc_final: 0.6767 (pmm) REVERT: B 1017 PHE cc_start: 0.8721 (m-80) cc_final: 0.8354 (m-80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2907 time to fit residues: 27.0600 Evaluate side-chains 53 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 30 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 41 optimal weight: 30.0000 chunk 70 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 929 GLN ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.059948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.045644 restraints weight = 74929.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.046408 restraints weight = 65102.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.047002 restraints weight = 58349.114| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.7857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7073 Z= 0.256 Angle : 0.664 6.213 9626 Z= 0.350 Chirality : 0.046 0.151 1038 Planarity : 0.005 0.052 1276 Dihedral : 5.781 31.015 943 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.67 % Favored : 87.33 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -3.43 (0.26), residues: 876 helix: -1.33 (0.61), residues: 56 sheet: -2.32 (0.34), residues: 189 loop : -2.53 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 819 HIS 0.007 0.001 HIS A 384 PHE 0.027 0.002 PHE B1010 TYR 0.020 0.002 TYR B 804 ARG 0.005 0.001 ARG A 403 *********************** 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 74 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 LEU cc_start: 0.8756 (mt) cc_final: 0.8456 (pp) REVERT: A 507 TYR cc_start: 0.9034 (m-80) cc_final: 0.8622 (m-80) REVERT: A 531 TRP cc_start: 0.8808 (m100) cc_final: 0.7778 (p-90) REVERT: A 579 VAL cc_start: 0.8828 (p) cc_final: 0.8357 (m) REVERT: A 636 HIS cc_start: 0.8900 (m-70) cc_final: 0.8526 (p-80) REVERT: B 867 HIS cc_start: 0.8342 (t70) cc_final: 0.8043 (t70) REVERT: B 976 MET cc_start: 0.8222 (ptt) cc_final: 0.7285 (pmm) REVERT: B 1017 PHE cc_start: 0.8691 (m-80) cc_final: 0.8268 (m-80) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2651 time to fit residues: 25.5631 Evaluate side-chains 58 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 25 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 84 optimal weight: 0.0170 chunk 66 optimal weight: 5.9990 overall best weight: 3.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 929 GLN ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.059543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.045353 restraints weight = 76259.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.046133 restraints weight = 66141.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.046729 restraints weight = 58998.375| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.8236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7073 Z= 0.257 Angle : 0.685 9.662 9626 Z= 0.359 Chirality : 0.047 0.163 1038 Planarity : 0.005 0.053 1276 Dihedral : 5.990 31.455 943 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 26.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -3.52 (0.26), residues: 876 helix: -1.39 (0.62), residues: 56 sheet: -2.66 (0.32), residues: 197 loop : -2.47 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 819 HIS 0.008 0.002 HIS A 384 PHE 0.023 0.002 PHE B1010 TYR 0.021 0.002 TYR B 804 ARG 0.005 0.001 ARG A 403 *********************** 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 71 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 TRP cc_start: 0.8760 (m100) cc_final: 0.7701 (p-90) REVERT: A 579 VAL cc_start: 0.8864 (p) cc_final: 0.8412 (m) REVERT: A 636 HIS cc_start: 0.8903 (m-70) cc_final: 0.8532 (p-80) REVERT: A 765 LEU cc_start: 0.9126 (tp) cc_final: 0.8863 (tp) REVERT: B 900 GLU cc_start: 0.9366 (mm-30) cc_final: 0.9032 (tm-30) REVERT: B 976 MET cc_start: 0.8437 (ptt) cc_final: 0.7600 (pmm) REVERT: B 1017 PHE cc_start: 0.8715 (m-80) cc_final: 0.8244 (m-80) REVERT: C 98 GLN cc_start: 0.9540 (tt0) cc_final: 0.9332 (mp10) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2571 time to fit residues: 23.6285 Evaluate side-chains 53 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 0.0770 chunk 58 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 GLN ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.059283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.044954 restraints weight = 76842.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.045754 restraints weight = 66620.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.046337 restraints weight = 59317.112| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.8488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7073 Z= 0.260 Angle : 0.696 9.281 9626 Z= 0.363 Chirality : 0.048 0.207 1038 Planarity : 0.005 0.052 1276 Dihedral : 5.950 31.360 943 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 26.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -3.43 (0.26), residues: 876 helix: -1.33 (0.61), residues: 56 sheet: -2.51 (0.32), residues: 201 loop : -2.44 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 356 HIS 0.005 0.001 HIS A 384 PHE 0.016 0.002 PHE A 382 TYR 0.023 0.002 TYR B1004 ARG 0.007 0.001 ARG A 403 *********************** 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 68 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 ILE cc_start: 0.9424 (mt) cc_final: 0.9142 (mt) REVERT: A 531 TRP cc_start: 0.8792 (m100) cc_final: 0.7678 (p-90) REVERT: A 579 VAL cc_start: 0.8758 (p) cc_final: 0.8501 (m) REVERT: A 636 HIS cc_start: 0.8913 (m-70) cc_final: 0.8537 (p-80) REVERT: A 765 LEU cc_start: 0.9192 (tp) cc_final: 0.8933 (tp) REVERT: B 900 GLU cc_start: 0.9376 (mm-30) cc_final: 0.8957 (tm-30) REVERT: B 976 MET cc_start: 0.8483 (ptt) cc_final: 0.7699 (pmm) REVERT: B 1017 PHE cc_start: 0.8730 (m-80) cc_final: 0.8312 (m-80) REVERT: C 228 VAL cc_start: 0.5760 (t) cc_final: 0.5190 (t) REVERT: C 229 TYR cc_start: 0.8524 (m-80) cc_final: 0.8303 (m-80) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2571 time to fit residues: 22.8371 Evaluate side-chains 53 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.058852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.044579 restraints weight = 77580.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.045361 restraints weight = 67110.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.045977 restraints weight = 59826.197| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.8769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7073 Z= 0.262 Angle : 0.703 9.394 9626 Z= 0.366 Chirality : 0.048 0.201 1038 Planarity : 0.006 0.053 1276 Dihedral : 6.137 31.965 943 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 27.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -3.42 (0.26), residues: 876 helix: -1.29 (0.63), residues: 54 sheet: -2.31 (0.34), residues: 181 loop : -2.53 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 819 HIS 0.006 0.002 HIS A 428 PHE 0.023 0.002 PHE B1010 TYR 0.023 0.002 TYR B 804 ARG 0.011 0.001 ARG A 692 ********************** 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 70 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 ILE cc_start: 0.9383 (mt) cc_final: 0.8987 (mt) REVERT: A 579 VAL cc_start: 0.8784 (p) cc_final: 0.8528 (m) REVERT: A 636 HIS cc_start: 0.8917 (m-70) cc_final: 0.8542 (p-80) REVERT: A 765 LEU cc_start: 0.9191 (tp) cc_final: 0.8927 (tp) REVERT: B 900 GLU cc_start: 0.9296 (mm-30) cc_final: 0.9037 (tm-30) REVERT: B 976 MET cc_start: 0.8539 (ptt) cc_final: 0.7734 (pmm) REVERT: B 1017 PHE cc_start: 0.8730 (m-80) cc_final: 0.8249 (m-80) REVERT: C 228 VAL cc_start: 0.5766 (t) cc_final: 0.5185 (t) REVERT: C 229 TYR cc_start: 0.8448 (m-80) cc_final: 0.8206 (m-80) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2748 time to fit residues: 24.7015 Evaluate side-chains 51 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 929 GLN ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.061609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.047092 restraints weight = 75165.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.047949 restraints weight = 64591.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.048627 restraints weight = 57231.725| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.8596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7073 Z= 0.188 Angle : 0.650 8.142 9626 Z= 0.336 Chirality : 0.047 0.190 1038 Planarity : 0.005 0.053 1276 Dihedral : 5.728 29.932 943 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.27), residues: 876 helix: -1.06 (0.64), residues: 56 sheet: -2.50 (0.32), residues: 219 loop : -2.32 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 356 HIS 0.011 0.001 HIS A 428 PHE 0.021 0.002 PHE B1010 TYR 0.017 0.002 TYR B 804 ARG 0.004 0.001 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2431.27 seconds wall clock time: 43 minutes 5.46 seconds (2585.46 seconds total)