Starting phenix.real_space_refine on Fri Jul 25 02:08:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3s_32829/07_2025/8h3s_32829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3s_32829/07_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_32829/07_2025/8h3s_32829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3s_32829/07_2025/8h3s_32829.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3s_32829/07_2025/8h3s_32829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3s_32829/07_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-5711/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: 4.12, per 1000 atoms: 0.60 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: 1.50 Conformation dependent library (CDL) restraints added in 893.0 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: 0.73 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: 1.82 Time building geometry restraints manager: 1.81 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.260 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.400 ------------------------------------------------------------------------------- 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 7085 Z= 0.103 Angle : 0.445 6.478 9650 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 Details of bonding type rmsd hydrogen bonds : bond 0.28779 ( 131) hydrogen bonds : angle 11.70257 ( 336) SS BOND : bond 0.00144 ( 12) SS BOND : angle 0.48588 ( 24) covalent geometry : bond 0.00178 ( 7073) covalent geometry : angle 0.44487 ( 9626) *********************** 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 : 0.743 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: 0.2409 time to fit residues: 57.9020 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 : 0.751 ------------------------------------------------------------------------------- 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 7085 Z= 0.305 Angle : 0.879 8.256 9650 Z= 0.465 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 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 131) hydrogen bonds : angle 8.85863 ( 336) SS BOND : bond 0.00918 ( 12) SS BOND : angle 2.46138 ( 24) covalent geometry : bond 0.00641 ( 7073) covalent geometry : angle 0.87109 ( 9626) *********************** 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 : 0.822 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 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: 0.2349 time to fit residues: 31.5406 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 : 0.825 ------------------------------------------------------------------------------- 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: 4.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 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 ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.068003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.052598 restraints weight = 69005.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.053480 restraints weight = 59973.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.054167 restraints weight = 53606.232| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7085 Z= 0.137 Angle : 0.631 7.308 9650 Z= 0.330 Chirality : 0.046 0.157 1038 Planarity : 0.005 0.051 1276 Dihedral : 4.865 28.003 943 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % 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 : 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: -3.54 (0.26), residues: 876 helix: -1.45 (0.52), residues: 63 sheet: -2.57 (0.34), residues: 176 loop : -2.56 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 983 HIS 0.006 0.001 HIS C 76 PHE 0.032 0.002 PHE A 693 TYR 0.020 0.001 TYR B1004 ARG 0.007 0.001 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 131) hydrogen bonds : angle 7.80731 ( 336) SS BOND : bond 0.00494 ( 12) SS BOND : angle 1.38587 ( 24) covalent geometry : bond 0.00309 ( 7073) covalent geometry : angle 0.62755 ( 9626) *********************** 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 : 0.773 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: 0.9079 (pt) cc_final: 0.8836 (pt) REVERT: A 612 MET cc_start: 0.8012 (mmp) cc_final: 0.7674 (mmm) REVERT: A 615 LEU cc_start: 0.9351 (mm) cc_final: 0.9116 (mm) REVERT: B 867 HIS cc_start: 0.8926 (m-70) cc_final: 0.8668 (t70) REVERT: B 900 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8813 (tm-30) REVERT: B 910 CYS cc_start: 0.7560 (p) cc_final: 0.7339 (p) REVERT: B 1017 PHE cc_start: 0.8681 (m-80) cc_final: 0.8259 (m-80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2328 time to fit residues: 25.0915 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 : 0.807 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.062316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.047884 restraints weight = 77904.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.048652 restraints weight = 68164.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.049269 restraints weight = 61193.701| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7085 Z= 0.218 Angle : 0.726 6.896 9650 Z= 0.383 Chirality : 0.047 0.164 1038 Planarity : 0.005 0.053 1276 Dihedral : 5.584 31.468 943 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 27.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.90 % Favored : 87.10 % 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: -3.67 (0.25), residues: 876 helix: -1.64 (0.56), residues: 56 sheet: -2.64 (0.34), residues: 174 loop : -2.64 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B1013 HIS 0.006 0.001 HIS B1019 PHE 0.017 0.002 PHE A 479 TYR 0.012 0.002 TYR C 37 ARG 0.019 0.001 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 131) hydrogen bonds : angle 7.90505 ( 336) SS BOND : bond 0.00513 ( 12) SS BOND : angle 1.85903 ( 24) covalent geometry : bond 0.00464 ( 7073) covalent geometry : angle 0.72122 ( 9626) *********************** 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 : 0.836 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: 0.8664 (mt) cc_final: 0.8418 (pp) REVERT: A 507 TYR cc_start: 0.9024 (m-80) cc_final: 0.8711 (m-80) REVERT: A 531 TRP cc_start: 0.8917 (m100) cc_final: 0.8556 (m-90) REVERT: B 867 HIS cc_start: 0.8926 (m-70) cc_final: 0.8720 (t70) REVERT: B 900 GLU cc_start: 0.9285 (mm-30) cc_final: 0.9011 (tm-30) REVERT: B 1017 PHE cc_start: 0.8711 (m-80) cc_final: 0.8355 (m-80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2400 time to fit residues: 24.4735 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 : 0.740 ------------------------------------------------------------------------------- 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: 0.2980 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 0.0060 chunk 47 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- 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** ** 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 = 0.3858 r_free = 0.3858 target = 0.065310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.050153 restraints weight = 71183.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.050918 restraints weight = 61980.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.051571 restraints weight = 55838.981| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.6583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7085 Z= 0.122 Angle : 0.623 7.378 9650 Z= 0.322 Chirality : 0.046 0.190 1038 Planarity : 0.005 0.051 1276 Dihedral : 5.053 27.917 943 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % 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: -3.36 (0.26), residues: 876 helix: -1.43 (0.58), residues: 56 sheet: -2.53 (0.35), residues: 178 loop : -2.38 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 796 HIS 0.004 0.001 HIS C 76 PHE 0.011 0.002 PHE A 382 TYR 0.020 0.001 TYR A 458 ARG 0.006 0.001 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.02905 ( 131) hydrogen bonds : angle 7.39065 ( 336) SS BOND : bond 0.00459 ( 12) SS BOND : angle 1.43311 ( 24) covalent geometry : bond 0.00272 ( 7073) covalent geometry : angle 0.61941 ( 9626) *********************** 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 80 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.003 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 351 ASP cc_start: 0.8469 (p0) cc_final: 0.8246 (t70) REVERT: A 506 LEU cc_start: 0.8623 (mt) cc_final: 0.8388 (pp) REVERT: A 507 TYR cc_start: 0.8911 (m-80) cc_final: 0.8661 (m-80) REVERT: A 579 VAL cc_start: 0.8581 (p) cc_final: 0.8241 (p) REVERT: B 952 GLU cc_start: 0.9622 (pp20) cc_final: 0.9405 (pp20) REVERT: B 976 MET cc_start: 0.7160 (ptt) cc_final: 0.6676 (ptp) REVERT: B 1017 PHE cc_start: 0.8634 (m-80) cc_final: 0.8155 (m-80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2840 time to fit residues: 29.7405 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 : 0.750 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 79 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 929 GLN ** 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 = 0.3783 r_free = 0.3783 target = 0.061721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.047644 restraints weight = 76839.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.048440 restraints weight = 67182.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.049041 restraints weight = 60100.912| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.7331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7085 Z= 0.182 Angle : 0.669 6.322 9650 Z= 0.353 Chirality : 0.046 0.157 1038 Planarity : 0.005 0.052 1276 Dihedral : 5.473 30.442 943 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.70 % Favored : 86.30 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: -1.34 (0.60), residues: 56 sheet: -2.45 (0.32), residues: 203 loop : -2.45 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B1013 HIS 0.007 0.002 HIS C 96 PHE 0.020 0.002 PHE A 479 TYR 0.011 0.002 TYR A 458 ARG 0.006 0.001 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 131) hydrogen bonds : angle 7.55102 ( 336) SS BOND : bond 0.00403 ( 12) SS BOND : angle 1.81650 ( 24) covalent geometry : bond 0.00394 ( 7073) covalent geometry : angle 0.66322 ( 9626) *********************** 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 75 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.831 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: A 506 LEU cc_start: 0.8650 (mt) cc_final: 0.8341 (pp) REVERT: A 507 TYR cc_start: 0.9018 (m-80) cc_final: 0.8687 (m-80) REVERT: A 579 VAL cc_start: 0.8898 (p) cc_final: 0.8460 (m) REVERT: A 765 LEU cc_start: 0.9164 (tp) cc_final: 0.8944 (tp) REVERT: B 867 HIS cc_start: 0.8300 (t70) cc_final: 0.7984 (t70) REVERT: B 952 GLU cc_start: 0.9683 (pp20) cc_final: 0.9396 (pp20) REVERT: B 976 MET cc_start: 0.7752 (ptt) cc_final: 0.7266 (ptp) REVERT: B 1017 PHE cc_start: 0.8685 (m-80) cc_final: 0.8327 (m-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2438 time to fit residues: 24.0778 Evaluate side-chains 56 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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: 9.9990 chunk 85 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 48 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.6144 ------------------------------------------------------------------------------- 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 929 GLN ** 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 = 0.3823 r_free = 0.3823 target = 0.063421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.048926 restraints weight = 72582.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.049736 restraints weight = 62805.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.050403 restraints weight = 56067.053| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.7327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7085 Z= 0.126 Angle : 0.615 7.060 9650 Z= 0.320 Chirality : 0.046 0.151 1038 Planarity : 0.005 0.052 1276 Dihedral : 5.241 29.064 943 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -3.33 (0.26), residues: 876 helix: -1.24 (0.62), residues: 56 sheet: -2.19 (0.34), residues: 200 loop : -2.47 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 837 HIS 0.004 0.001 HIS A 384 PHE 0.012 0.002 PHE A 382 TYR 0.013 0.001 TYR B 804 ARG 0.005 0.001 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 131) hydrogen bonds : angle 7.25059 ( 336) SS BOND : bond 0.00301 ( 12) SS BOND : angle 1.45136 ( 24) covalent geometry : bond 0.00280 ( 7073) covalent geometry : angle 0.61198 ( 9626) *********************** 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 77 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.953 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: 0.9462 (mt) cc_final: 0.9023 (mm) REVERT: A 506 LEU cc_start: 0.8664 (mt) cc_final: 0.8377 (pp) REVERT: A 507 TYR cc_start: 0.9047 (m-80) cc_final: 0.8728 (m-80) REVERT: A 579 VAL cc_start: 0.8827 (p) cc_final: 0.8343 (m) REVERT: A 636 HIS cc_start: 0.8867 (m-70) cc_final: 0.8470 (p-80) REVERT: B 867 HIS cc_start: 0.8359 (t70) cc_final: 0.8057 (t70) REVERT: B 945 MET cc_start: 0.3842 (mpp) cc_final: 0.2914 (mpp) REVERT: B 952 GLU cc_start: 0.9656 (pp20) cc_final: 0.9373 (pp20) REVERT: B 976 MET cc_start: 0.7774 (ptt) cc_final: 0.6693 (pmm) REVERT: B 1017 PHE cc_start: 0.8645 (m-80) cc_final: 0.8209 (m-80) REVERT: C 41 LEU cc_start: 0.9101 (mt) cc_final: 0.8896 (mt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2840 time to fit residues: 28.7342 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 : 0.886 ------------------------------------------------------------------------------- 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: 9.9990 chunk 60 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 0.0980 chunk 84 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 929 GLN ** 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 = 0.3796 r_free = 0.3796 target = 0.062061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.047785 restraints weight = 75510.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.048603 restraints weight = 65496.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.049056 restraints weight = 58327.538| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.7655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7085 Z= 0.141 Angle : 0.628 7.506 9650 Z= 0.327 Chirality : 0.046 0.195 1038 Planarity : 0.005 0.052 1276 Dihedral : 5.386 31.234 943 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: -3.23 (0.26), residues: 876 helix: -1.06 (0.63), residues: 56 sheet: -2.26 (0.33), residues: 199 loop : -2.36 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1013 HIS 0.004 0.001 HIS A 384 PHE 0.014 0.002 PHE C 18 TYR 0.017 0.002 TYR B 804 ARG 0.004 0.001 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 131) hydrogen bonds : angle 7.14299 ( 336) SS BOND : bond 0.00385 ( 12) SS BOND : angle 1.66593 ( 24) covalent geometry : bond 0.00310 ( 7073) covalent geometry : angle 0.62358 ( 9626) *********************** 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 : 0.829 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: A 490 ILE cc_start: 0.9442 (mt) cc_final: 0.8953 (mm) REVERT: A 506 LEU cc_start: 0.8643 (mt) cc_final: 0.8319 (pp) REVERT: A 507 TYR cc_start: 0.8942 (m-80) cc_final: 0.8615 (m-80) REVERT: A 579 VAL cc_start: 0.8816 (p) cc_final: 0.8394 (m) REVERT: A 612 MET cc_start: 0.9253 (tpp) cc_final: 0.9043 (tpp) REVERT: A 636 HIS cc_start: 0.8885 (m-70) cc_final: 0.8500 (p-80) REVERT: B 867 HIS cc_start: 0.8278 (t70) cc_final: 0.7932 (t70) REVERT: B 976 MET cc_start: 0.8008 (ptt) cc_final: 0.6642 (pmm) REVERT: B 1017 PHE cc_start: 0.8658 (m-80) cc_final: 0.8227 (m-80) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2635 time to fit residues: 25.3582 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 : 0.797 ------------------------------------------------------------------------------- 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: 8.9990 chunk 58 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.062261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.048018 restraints weight = 76658.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.048776 restraints weight = 66876.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.049382 restraints weight = 60065.580| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.7899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7085 Z= 0.143 Angle : 0.639 8.082 9650 Z= 0.332 Chirality : 0.046 0.172 1038 Planarity : 0.005 0.053 1276 Dihedral : 5.475 30.063 943 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % 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: -3.20 (0.27), residues: 876 helix: -1.12 (0.62), residues: 56 sheet: -2.14 (0.34), residues: 191 loop : -2.38 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 356 HIS 0.007 0.001 HIS A 428 PHE 0.013 0.002 PHE A 382 TYR 0.017 0.002 TYR B 804 ARG 0.005 0.001 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.02964 ( 131) hydrogen bonds : angle 7.06013 ( 336) SS BOND : bond 0.00513 ( 12) SS BOND : angle 1.73601 ( 24) covalent geometry : bond 0.00317 ( 7073) covalent geometry : angle 0.63413 ( 9626) *********************** 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 69 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.943 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: A 506 LEU cc_start: 0.8705 (mt) cc_final: 0.8382 (pp) REVERT: A 507 TYR cc_start: 0.8996 (m-80) cc_final: 0.8666 (m-80) REVERT: A 579 VAL cc_start: 0.8719 (p) cc_final: 0.8270 (m) REVERT: A 636 HIS cc_start: 0.8876 (m-70) cc_final: 0.8480 (p-80) REVERT: B 867 HIS cc_start: 0.8283 (t70) cc_final: 0.7945 (t70) REVERT: B 945 MET cc_start: 0.3902 (mpp) cc_final: 0.3077 (mpp) REVERT: B 976 MET cc_start: 0.8026 (ptt) cc_final: 0.7001 (pmm) REVERT: B 989 THR cc_start: 0.5754 (m) cc_final: 0.5229 (m) REVERT: B 1017 PHE cc_start: 0.8648 (m-80) cc_final: 0.8218 (m-80) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3677 time to fit residues: 34.4014 Evaluate side-chains 56 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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: 3.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** C 98 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.058958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.044826 restraints weight = 78454.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.045568 restraints weight = 68036.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.046191 restraints weight = 60725.600| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.8641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7085 Z= 0.183 Angle : 0.706 7.554 9650 Z= 0.367 Chirality : 0.047 0.172 1038 Planarity : 0.005 0.052 1276 Dihedral : 5.995 31.857 943 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 30.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % 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: -3.34 (0.27), residues: 876 helix: -1.09 (0.62), residues: 56 sheet: -2.40 (0.32), residues: 206 loop : -2.41 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B1013 HIS 0.005 0.002 HIS A 384 PHE 0.022 0.002 PHE A 382 TYR 0.022 0.003 TYR B 804 ARG 0.006 0.001 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 131) hydrogen bonds : angle 7.34794 ( 336) SS BOND : bond 0.00469 ( 12) SS BOND : angle 1.90790 ( 24) covalent geometry : bond 0.00401 ( 7073) covalent geometry : angle 0.70060 ( 9626) ********************** 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 68 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.022 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: 0.9285 (mt) cc_final: 0.8861 (mm) REVERT: A 506 LEU cc_start: 0.8698 (mt) cc_final: 0.8323 (pp) REVERT: A 507 TYR cc_start: 0.9010 (m-80) cc_final: 0.8629 (m-80) REVERT: A 579 VAL cc_start: 0.8826 (p) cc_final: 0.8425 (m) REVERT: A 636 HIS cc_start: 0.8905 (m-70) cc_final: 0.8542 (p-80) REVERT: A 765 LEU cc_start: 0.9131 (tp) cc_final: 0.8847 (tp) REVERT: B 867 HIS cc_start: 0.8257 (t70) cc_final: 0.7934 (t70) REVERT: B 976 MET cc_start: 0.8289 (ptt) cc_final: 0.7809 (ptt) REVERT: B 989 THR cc_start: 0.6035 (m) cc_final: 0.5670 (m) REVERT: B 1017 PHE cc_start: 0.8703 (m-80) cc_final: 0.8304 (m-80) REVERT: C 229 TYR cc_start: 0.8223 (m-80) cc_final: 0.7943 (m-80) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3531 time to fit residues: 32.4718 Evaluate side-chains 52 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.996 ------------------------------------------------------------------------------- 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: 0.4980 chunk 16 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** C 98 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.062808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.048049 restraints weight = 73202.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.048865 restraints weight = 63512.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.049511 restraints weight = 56687.413| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.8350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7085 Z= 0.117 Angle : 0.634 8.223 9650 Z= 0.326 Chirality : 0.046 0.172 1038 Planarity : 0.005 0.053 1276 Dihedral : 5.428 28.718 943 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -3.09 (0.27), residues: 876 helix: -0.82 (0.67), residues: 56 sheet: -2.23 (0.33), residues: 202 loop : -2.24 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 356 HIS 0.009 0.001 HIS A 428 PHE 0.016 0.001 PHE A 452 TYR 0.013 0.001 TYR B 804 ARG 0.003 0.001 ARG B 872 Details of bonding type rmsd hydrogen bonds : bond 0.02577 ( 131) hydrogen bonds : angle 6.70776 ( 336) SS BOND : bond 0.00463 ( 12) SS BOND : angle 2.31944 ( 24) covalent geometry : bond 0.00265 ( 7073) covalent geometry : angle 0.62449 ( 9626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3059.21 seconds wall clock time: 57 minutes 28.39 seconds (3448.39 seconds total)