Starting phenix.real_space_refine on Fri Dec 27 23:03:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3s_32829/12_2024/8h3s_32829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3s_32829/12_2024/8h3s_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_32829/12_2024/8h3s_32829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3s_32829/12_2024/8h3s_32829.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3s_32829/12_2024/8h3s_32829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3s_32829/12_2024/8h3s_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.58, 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: 1.69 Conformation dependent library (CDL) restraints added in 989.1 milliseconds 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: 0.75 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: 2.08 Time building geometry restraints manager: 2.00 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: 0.900 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.830 Find NCS groups from input model: 0.080 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- 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 : 0.813 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: 0.2562 time to fit residues: 61.2523 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 : 0.812 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 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 8.257 9626 Z= 0.462 Chirality : 0.050 0.165 1038 Planarity : 0.006 0.054 1276 Dihedral : 5.552 30.138 943 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 : 0.726 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 437 LEU cc_start: 0.8805 (pt) cc_final: 0.8496 (pt) REVERT: A 490 ILE cc_start: 0.9517 (mt) cc_final: 0.9103 (mt) REVERT: A 579 VAL cc_start: 0.8378 (m) cc_final: 0.8145 (m) REVERT: B 867 HIS cc_start: 0.8694 (m-70) cc_final: 0.8473 (t70) REVERT: B 874 ASP cc_start: 0.7779 (p0) cc_final: 0.7568 (p0) REVERT: B 1017 PHE cc_start: 0.8202 (m-80) cc_final: 0.7813 (m-80) REVERT: B 1018 LEU cc_start: 0.7647 (mt) cc_final: 0.7350 (pp) REVERT: C 30 CYS cc_start: 0.4525 (t) cc_final: 0.3909 (p) REVERT: C 94 ILE cc_start: 0.7442 (tp) cc_final: 0.7158 (tp) REVERT: C 109 MET cc_start: 0.7490 (ttp) cc_final: 0.6960 (ttp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2476 time to fit residues: 33.1625 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 : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 78 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7073 Z= 0.229 Angle : 0.633 6.949 9626 Z= 0.335 Chirality : 0.046 0.167 1038 Planarity : 0.005 0.051 1276 Dihedral : 5.004 28.663 943 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: -3.60 (0.25), residues: 876 helix: -1.51 (0.51), residues: 63 sheet: -2.54 (0.34), residues: 172 loop : -2.63 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 983 HIS 0.005 0.001 HIS C 76 PHE 0.027 0.002 PHE A 693 TYR 0.018 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 82 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.876 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: 0.8823 (pt) cc_final: 0.8480 (pt) REVERT: A 490 ILE cc_start: 0.9470 (mt) cc_final: 0.8984 (mm) REVERT: A 612 MET cc_start: 0.8491 (mmp) cc_final: 0.8215 (mmm) REVERT: A 615 LEU cc_start: 0.9333 (mm) cc_final: 0.9106 (mm) REVERT: B 900 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8728 (tm-30) REVERT: B 910 CYS cc_start: 0.7055 (p) cc_final: 0.6759 (p) REVERT: B 1017 PHE cc_start: 0.8285 (m-80) cc_final: 0.8001 (m-80) REVERT: B 1018 LEU cc_start: 0.7682 (mt) cc_final: 0.7423 (mt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2296 time to fit residues: 24.6919 Evaluate side-chains 62 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 30.0000 chunk 59 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- 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** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7073 Z= 0.318 Angle : 0.721 6.486 9626 Z= 0.383 Chirality : 0.047 0.163 1038 Planarity : 0.006 0.054 1276 Dihedral : 5.666 32.836 943 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 28.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.67 % Favored : 87.33 % Rotamer: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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: -3.67 (0.25), residues: 876 helix: -1.48 (0.57), residues: 54 sheet: -2.67 (0.34), residues: 178 loop : -2.65 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B1013 HIS 0.010 0.002 HIS B 867 PHE 0.016 0.002 PHE A 479 TYR 0.012 0.002 TYR C 37 ARG 0.006 0.001 ARG A 583 *********************** 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 : 0.761 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: 0.8558 (mt) cc_final: 0.8344 (pp) REVERT: A 507 TYR cc_start: 0.8953 (m-80) cc_final: 0.8648 (m-80) REVERT: A 612 MET cc_start: 0.8768 (mmp) cc_final: 0.8327 (mmm) REVERT: B 867 HIS cc_start: 0.8313 (t70) cc_final: 0.8033 (t70) REVERT: B 900 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8844 (tm-30) REVERT: B 1017 PHE cc_start: 0.8217 (m-80) cc_final: 0.7985 (m-80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2687 time to fit residues: 27.0630 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 : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 71 optimal weight: 0.2980 chunk 58 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 overall best weight: 4.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.7772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7073 Z= 0.345 Angle : 0.765 8.244 9626 Z= 0.405 Chirality : 0.049 0.206 1038 Planarity : 0.006 0.053 1276 Dihedral : 6.202 32.472 943 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 33.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % 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: -3.76 (0.26), residues: 876 helix: -1.75 (0.58), residues: 54 sheet: -2.56 (0.32), residues: 206 loop : -2.72 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 796 HIS 0.008 0.002 HIS B 867 PHE 0.017 0.002 PHE C 18 TYR 0.024 0.003 TYR A 458 ARG 0.011 0.001 ARG A 583 *********************** 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 68 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.865 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: A 490 ILE cc_start: 0.9510 (mt) cc_final: 0.9295 (mm) REVERT: A 506 LEU cc_start: 0.8657 (mt) cc_final: 0.8374 (pp) REVERT: A 507 TYR cc_start: 0.8953 (m-80) cc_final: 0.8629 (m-80) REVERT: A 579 VAL cc_start: 0.8880 (p) cc_final: 0.8590 (m) REVERT: B 900 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8850 (tm-30) REVERT: B 976 MET cc_start: 0.7904 (ptt) cc_final: 0.6887 (pmm) REVERT: B 1017 PHE cc_start: 0.8168 (m-80) cc_final: 0.7892 (m-80) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2657 time to fit residues: 23.3809 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 : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 81 optimal weight: 9.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- 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 463 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.7796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7073 Z= 0.231 Angle : 0.652 6.514 9626 Z= 0.346 Chirality : 0.046 0.150 1038 Planarity : 0.005 0.052 1276 Dihedral : 5.931 30.892 943 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: -3.57 (0.26), residues: 876 helix: -1.56 (0.57), residues: 56 sheet: -2.43 (0.33), residues: 194 loop : -2.60 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 531 HIS 0.007 0.002 HIS A 384 PHE 0.031 0.002 PHE B1010 TYR 0.021 0.002 TYR B 804 ARG 0.005 0.001 ARG A 403 *********************** 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 : 0.745 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: 0.9399 (mt) cc_final: 0.8936 (mm) REVERT: A 506 LEU cc_start: 0.8629 (mt) cc_final: 0.8341 (pp) REVERT: A 507 TYR cc_start: 0.8939 (m-80) cc_final: 0.8617 (m-80) REVERT: A 579 VAL cc_start: 0.8747 (p) cc_final: 0.8411 (m) REVERT: B 900 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8824 (tm-30) REVERT: B 976 MET cc_start: 0.7972 (ptt) cc_final: 0.7019 (pmm) REVERT: B 1017 PHE cc_start: 0.8098 (m-80) cc_final: 0.7786 (m-80) REVERT: B 1018 LEU cc_start: 0.7805 (mt) cc_final: 0.7381 (pp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2617 time to fit residues: 23.9507 Evaluate side-chains 54 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 463 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.8226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7073 Z= 0.263 Angle : 0.683 7.078 9626 Z= 0.358 Chirality : 0.047 0.171 1038 Planarity : 0.005 0.052 1276 Dihedral : 6.038 31.622 943 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 27.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: -3.62 (0.26), residues: 876 helix: -1.32 (0.59), residues: 56 sheet: -2.64 (0.31), residues: 213 loop : -2.57 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B1013 HIS 0.006 0.002 HIS A 384 PHE 0.023 0.002 PHE B1010 TYR 0.031 0.002 TYR A 458 ARG 0.004 0.001 ARG A 679 *********************** 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 65 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.732 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: A 506 LEU cc_start: 0.8640 (mt) cc_final: 0.8337 (pp) REVERT: A 507 TYR cc_start: 0.8967 (m-80) cc_final: 0.8638 (m-80) REVERT: A 579 VAL cc_start: 0.8791 (p) cc_final: 0.8454 (m) REVERT: B 976 MET cc_start: 0.8054 (ptt) cc_final: 0.7128 (pmm) REVERT: B 1017 PHE cc_start: 0.8065 (m-80) cc_final: 0.7773 (m-80) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2625 time to fit residues: 21.9229 Evaluate side-chains 49 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.0970 chunk 7 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 76 optimal weight: 0.0060 chunk 80 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- 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 ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.8085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7073 Z= 0.182 Angle : 0.633 7.952 9626 Z= 0.330 Chirality : 0.047 0.154 1038 Planarity : 0.005 0.068 1276 Dihedral : 5.614 30.206 943 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -3.45 (0.26), residues: 876 helix: -1.46 (0.60), residues: 56 sheet: -2.43 (0.33), residues: 206 loop : -2.48 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 837 HIS 0.009 0.001 HIS C 96 PHE 0.010 0.002 PHE A 475 TYR 0.020 0.002 TYR C 235 ARG 0.004 0.001 ARG B 807 *********************** 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 73 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.931 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 531 TRP cc_start: 0.8712 (m100) cc_final: 0.7678 (p-90) REVERT: A 579 VAL cc_start: 0.8643 (p) cc_final: 0.8249 (m) REVERT: B 900 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8818 (tm-30) REVERT: B 976 MET cc_start: 0.8119 (ptt) cc_final: 0.7239 (pmm) REVERT: B 1017 PHE cc_start: 0.7967 (m-80) cc_final: 0.7565 (m-80) REVERT: B 1018 LEU cc_start: 0.7809 (mt) cc_final: 0.7416 (pp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2676 time to fit residues: 25.0055 Evaluate side-chains 57 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.0470 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.8194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7073 Z= 0.190 Angle : 0.623 7.356 9626 Z= 0.323 Chirality : 0.046 0.203 1038 Planarity : 0.005 0.060 1276 Dihedral : 5.473 31.110 943 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % 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 : 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: -3.39 (0.27), residues: 876 helix: -1.15 (0.63), residues: 56 sheet: -2.45 (0.33), residues: 206 loop : -2.44 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 238 HIS 0.007 0.001 HIS A 428 PHE 0.021 0.002 PHE B1010 TYR 0.018 0.002 TYR B 804 ARG 0.003 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 67 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 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: symmetry clash revert: symmetry clash REVERT: A 531 TRP cc_start: 0.8669 (m100) cc_final: 0.7661 (p-90) REVERT: A 579 VAL cc_start: 0.8652 (p) cc_final: 0.8309 (m) REVERT: B 900 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8805 (tm-30) REVERT: B 945 MET cc_start: 0.4216 (mpp) cc_final: 0.3249 (mpp) REVERT: B 976 MET cc_start: 0.8003 (ptt) cc_final: 0.6885 (pmm) REVERT: B 1017 PHE cc_start: 0.7900 (m-80) cc_final: 0.7509 (m-80) REVERT: B 1018 LEU cc_start: 0.7834 (mt) cc_final: 0.7344 (pp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2634 time to fit residues: 22.9455 Evaluate side-chains 55 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.8723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7073 Z= 0.244 Angle : 0.669 6.754 9626 Z= 0.348 Chirality : 0.047 0.190 1038 Planarity : 0.005 0.053 1276 Dihedral : 5.751 31.889 943 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 26.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.46 (0.26), residues: 876 helix: -1.08 (0.63), residues: 56 sheet: -2.54 (0.32), residues: 211 loop : -2.47 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 819 HIS 0.005 0.001 HIS A 428 PHE 0.017 0.002 PHE A 479 TYR 0.022 0.002 TYR B 804 ARG 0.006 0.001 ARG A 679 ********************** 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 65 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.822 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 531 TRP cc_start: 0.8758 (m100) cc_final: 0.7632 (p-90) REVERT: A 579 VAL cc_start: 0.8732 (p) cc_final: 0.8413 (m) REVERT: B 945 MET cc_start: 0.4594 (mpp) cc_final: 0.3615 (mpp) REVERT: B 976 MET cc_start: 0.8027 (ptt) cc_final: 0.7104 (pmm) REVERT: B 1017 PHE cc_start: 0.8044 (m-80) cc_final: 0.7695 (m-80) REVERT: B 1018 LEU cc_start: 0.7948 (mt) cc_final: 0.7527 (mt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2838 time to fit residues: 23.5822 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 : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.0870 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 70 optimal weight: 0.0010 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 overall best weight: 2.7568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 867 HIS ** 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 = 0.3734 r_free = 0.3734 target = 0.059005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.044774 restraints weight = 75610.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.045539 restraints weight = 65757.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.046143 restraints weight = 58815.011| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.9049 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= 0.229 Angle : 0.657 7.290 9626 Z= 0.342 Chirality : 0.047 0.190 1038 Planarity : 0.005 0.053 1276 Dihedral : 5.806 31.242 943 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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 (0.27), residues: 876 helix: -1.10 (0.64), residues: 56 sheet: -2.45 (0.33), residues: 193 loop : -2.50 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 356 HIS 0.006 0.001 HIS A 428 PHE 0.013 0.002 PHE A 479 TYR 0.021 0.002 TYR B 804 ARG 0.005 0.001 ARG A 679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1698.63 seconds wall clock time: 32 minutes 7.17 seconds (1927.17 seconds total)