Starting phenix.real_space_refine on Tue Jan 14 16:22:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3s_32829/01_2025/8h3s_32829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3s_32829/01_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_32829/01_2025/8h3s_32829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3s_32829/01_2025/8h3s_32829.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3s_32829/01_2025/8h3s_32829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3s_32829/01_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-5571/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: 4.23, per 1000 atoms: 0.61 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: 1.57 Conformation dependent library (CDL) restraints added in 1.0 seconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 15 sheets defined 7.4% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 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: 1.85 Time building geometry restraints manager: 1.86 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: 2.870 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.560 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- 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 : 0.639 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: 0.2503 time to fit residues: 59.9483 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 : 0.835 ------------------------------------------------------------------------------- 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 = 71402.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.051941 restraints weight = 61935.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.052619 restraints weight = 55310.820| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 7073 Z= 0.425 Angle : 0.871 8.257 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 : 0.833 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: 0.8318 (m) cc_final: 0.8088 (m) REVERT: B 867 HIS cc_start: 0.8860 (m-70) cc_final: 0.8547 (t70) REVERT: B 874 ASP cc_start: 0.7605 (p0) cc_final: 0.7275 (p0) REVERT: B 1017 PHE cc_start: 0.8700 (m-80) cc_final: 0.8276 (m-80) REVERT: C 30 CYS cc_start: 0.3998 (t) cc_final: 0.3380 (p) REVERT: C 94 ILE cc_start: 0.7486 (tp) cc_final: 0.7244 (tp) REVERT: C 109 MET cc_start: 0.7416 (ttp) cc_final: 0.6941 (ttp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2429 time to fit residues: 32.6267 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 : 0.826 ------------------------------------------------------------------------------- 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: 3.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.067852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.052497 restraints weight = 69183.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.053381 restraints weight = 60118.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.054063 restraints weight = 53741.757| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.5472 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= 0.206 Angle : 0.626 7.068 9626 Z= 0.328 Chirality : 0.046 0.150 1038 Planarity : 0.005 0.052 1276 Dihedral : 4.865 28.042 943 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % 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: -3.55 (0.26), residues: 876 helix: -1.47 (0.52), residues: 63 sheet: -2.57 (0.34), residues: 176 loop : -2.57 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 983 HIS 0.005 0.001 HIS C 76 PHE 0.028 0.002 PHE A 693 TYR 0.019 0.001 TYR B1004 ARG 0.006 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 : 0.747 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: 0.9081 (pt) cc_final: 0.8840 (pt) REVERT: A 612 MET cc_start: 0.8001 (mmp) cc_final: 0.7664 (mmm) REVERT: A 615 LEU cc_start: 0.9347 (mm) cc_final: 0.9109 (mm) REVERT: B 867 HIS cc_start: 0.8934 (m-70) cc_final: 0.8677 (t70) REVERT: B 900 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8817 (tm-30) REVERT: B 910 CYS cc_start: 0.7484 (p) cc_final: 0.7248 (p) REVERT: B 1017 PHE cc_start: 0.8680 (m-80) cc_final: 0.8260 (m-80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2313 time to fit residues: 24.7137 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 : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- 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** ** 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 = 0.3781 r_free = 0.3781 target = 0.062043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.047348 restraints weight = 76168.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.048132 restraints weight = 66182.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.048771 restraints weight = 59229.869| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7073 Z= 0.320 Angle : 0.737 7.411 9626 Z= 0.389 Chirality : 0.047 0.167 1038 Planarity : 0.006 0.054 1276 Dihedral : 5.629 31.488 943 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 28.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % 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: -3.64 (0.26), residues: 876 helix: -1.52 (0.56), residues: 56 sheet: -2.67 (0.34), residues: 174 loop : -2.61 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B1013 HIS 0.007 0.001 HIS B1019 PHE 0.017 0.002 PHE A 479 TYR 0.012 0.002 TYR C 37 ARG 0.006 0.001 ARG A 611 *********************** 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 79 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.858 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 506 LEU cc_start: 0.8661 (mt) cc_final: 0.8369 (pp) REVERT: A 507 TYR cc_start: 0.8992 (m-80) cc_final: 0.8648 (m-80) REVERT: A 531 TRP cc_start: 0.8889 (m100) cc_final: 0.8528 (m-90) REVERT: B 867 HIS cc_start: 0.8925 (m-70) cc_final: 0.8722 (t70) REVERT: B 900 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8997 (tm-30) REVERT: B 976 MET cc_start: 0.7186 (ptt) cc_final: 0.6901 (pmm) REVERT: B 1017 PHE cc_start: 0.8703 (m-80) cc_final: 0.8348 (m-80) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2495 time to fit residues: 25.6712 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 : 0.814 ------------------------------------------------------------------------------- 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: 30.0000 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.059805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.045504 restraints weight = 76296.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.046313 restraints weight = 65822.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.046784 restraints weight = 58432.600| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.7573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7073 Z= 0.309 Angle : 0.723 7.470 9626 Z= 0.384 Chirality : 0.048 0.185 1038 Planarity : 0.006 0.052 1276 Dihedral : 5.948 31.154 943 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 28.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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: -3.69 (0.26), residues: 876 helix: -1.79 (0.58), residues: 56 sheet: -2.53 (0.33), residues: 197 loop : -2.66 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1013 HIS 0.005 0.001 HIS C 96 PHE 0.016 0.002 PHE C 18 TYR 0.023 0.002 TYR A 458 ARG 0.009 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 72 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.807 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: 0.8721 (mt) cc_final: 0.8419 (pp) REVERT: A 507 TYR cc_start: 0.8932 (m-80) cc_final: 0.8629 (m-80) REVERT: A 579 VAL cc_start: 0.8865 (p) cc_final: 0.8436 (m) REVERT: A 765 LEU cc_start: 0.9153 (tp) cc_final: 0.8944 (tp) REVERT: B 976 MET cc_start: 0.8033 (ptt) cc_final: 0.7133 (pmm) REVERT: B 1017 PHE cc_start: 0.8698 (m-80) cc_final: 0.8284 (m-80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2610 time to fit residues: 24.2334 Evaluate side-chains 50 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.6847 > 50: distance: 12 - 80: 17.864 distance: 60 - 61: 11.963 distance: 60 - 66: 5.441 distance: 61 - 62: 19.597 distance: 61 - 64: 9.084 distance: 62 - 63: 10.045 distance: 62 - 67: 6.236 distance: 64 - 65: 14.444 distance: 65 - 66: 6.787 distance: 67 - 68: 7.604 distance: 68 - 69: 9.675 distance: 68 - 71: 12.082 distance: 69 - 70: 6.618 distance: 69 - 75: 11.688 distance: 71 - 72: 11.714 distance: 71 - 73: 27.902 distance: 72 - 74: 17.757 distance: 75 - 76: 12.911 distance: 76 - 77: 6.654 distance: 76 - 79: 19.766 distance: 77 - 78: 8.232 distance: 77 - 81: 22.099 distance: 79 - 80: 13.629 distance: 81 - 82: 22.534 distance: 82 - 83: 19.704 distance: 82 - 85: 10.121 distance: 83 - 84: 9.385 distance: 83 - 89: 3.288 distance: 85 - 86: 19.735 distance: 86 - 87: 7.525 distance: 86 - 88: 10.315 distance: 89 - 90: 15.546 distance: 89 - 95: 13.729 distance: 90 - 91: 14.967 distance: 90 - 93: 16.009 distance: 91 - 92: 7.548 distance: 91 - 96: 3.853 distance: 93 - 94: 14.722 distance: 94 - 95: 5.524 distance: 96 - 97: 11.871 distance: 97 - 98: 7.300 distance: 97 - 100: 10.724 distance: 98 - 99: 20.772 distance: 98 - 105: 16.777 distance: 100 - 101: 20.951 distance: 101 - 102: 11.289 distance: 102 - 103: 10.386 distance: 102 - 104: 8.264 distance: 105 - 106: 7.273 distance: 106 - 107: 16.055 distance: 106 - 109: 17.594 distance: 107 - 108: 14.771 distance: 107 - 114: 17.914 distance: 109 - 110: 24.548 distance: 110 - 111: 22.005 distance: 111 - 112: 8.938 distance: 114 - 115: 9.122 distance: 115 - 116: 8.789 distance: 115 - 118: 8.283 distance: 116 - 117: 13.802 distance: 116 - 122: 10.777 distance: 118 - 119: 17.411 distance: 119 - 120: 8.837 distance: 119 - 121: 12.122 distance: 122 - 123: 10.413 distance: 123 - 124: 25.970 distance: 123 - 126: 14.872 distance: 124 - 125: 24.636 distance: 124 - 131: 17.234 distance: 126 - 127: 16.228 distance: 127 - 128: 11.779 distance: 128 - 129: 7.725 distance: 128 - 130: 9.851 distance: 131 - 132: 5.638 distance: 132 - 133: 7.910 distance: 132 - 135: 10.909 distance: 133 - 134: 5.144 distance: 133 - 138: 11.658 distance: 135 - 136: 11.143 distance: 135 - 137: 11.209