Starting phenix.real_space_refine on Thu Mar 6 00:03:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eme_19818/03_2025/9eme_19818.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eme_19818/03_2025/9eme_19818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eme_19818/03_2025/9eme_19818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eme_19818/03_2025/9eme_19818.map" model { file = "/net/cci-nas-00/data/ceres_data/9eme_19818/03_2025/9eme_19818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eme_19818/03_2025/9eme_19818.cif" } resolution = 2.92 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= 0.002 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 12 5.16 5 C 2562 2.51 5 N 714 2.21 5 O 852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4140 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 690 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.56, per 1000 atoms: 0.62 Number of scatterers: 4140 At special positions: 0 Unit cell: (79.04, 92.56, 52, 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 12 16.00 O 852 8.00 N 714 7.00 C 2562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.02 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: 0.94 Conformation dependent library (CDL) restraints added in 544.3 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23 removed outlier: 6.582A pdb=" N GLN A 16 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG B 19 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 18 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR B 21 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 20 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN B 23 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS A 22 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN B 16 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG C 19 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 18 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR C 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE B 20 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN C 23 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS B 22 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN C 16 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG D 19 " --> pdb=" O GLN C 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 18 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR D 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE C 20 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN D 23 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS C 22 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN D 16 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG E 19 " --> pdb=" O GLN D 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL D 18 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR E 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 20 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN E 23 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS D 22 " --> pdb=" O GLN E 23 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN E 16 " --> pdb=" O THR F 17 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ARG F 19 " --> pdb=" O GLN E 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL E 18 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR F 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE E 20 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN F 23 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS E 22 " --> pdb=" O GLN F 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 30 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.844A pdb=" N LEU A 45 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 45 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 45 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU D 45 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 45 " --> pdb=" O VAL F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 78 removed outlier: 6.757A pdb=" N ALA B 77 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN A 78 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 77 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN B 78 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA D 77 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN C 78 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA E 77 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN D 78 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA F 77 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN E 78 " --> pdb=" O ALA F 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 81 through 83 removed outlier: 8.450A pdb=" N ASP A 81 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP B 81 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP C 81 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP D 81 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP E 81 " --> pdb=" O GLU F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 103 through 106 80 hydrogen bonds defined for protein. 240 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: 1.19 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 690 1.30 - 1.43: 1224 1.43 - 1.55: 2286 1.55 - 1.68: 0 1.68 - 1.81: 12 Bond restraints: 4212 Sorted by residual: bond pdb=" C VAL A 46 " pdb=" O VAL A 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.47e+01 bond pdb=" C VAL F 46 " pdb=" O VAL F 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.46e+01 bond pdb=" C VAL E 46 " pdb=" O VAL E 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.46e+01 bond pdb=" C VAL D 46 " pdb=" O VAL D 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.45e+01 bond pdb=" C VAL B 46 " pdb=" O VAL B 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.45e+01 ... (remaining 4207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 3919 1.92 - 3.84: 1269 3.84 - 5.76: 458 5.76 - 7.68: 60 7.68 - 9.61: 6 Bond angle restraints: 5712 Sorted by residual: angle pdb=" N SER F 64 " pdb=" CA SER F 64 " pdb=" C SER F 64 " ideal model delta sigma weight residual 110.97 120.58 -9.61 1.09e+00 8.42e-01 7.77e+01 angle pdb=" N SER C 64 " pdb=" CA SER C 64 " pdb=" C SER C 64 " ideal model delta sigma weight residual 110.97 120.56 -9.59 1.09e+00 8.42e-01 7.75e+01 angle pdb=" N SER D 64 " pdb=" CA SER D 64 " pdb=" C SER D 64 " ideal model delta sigma weight residual 110.97 120.54 -9.57 1.09e+00 8.42e-01 7.71e+01 angle pdb=" N SER E 64 " pdb=" CA SER E 64 " pdb=" C SER E 64 " ideal model delta sigma weight residual 110.97 120.53 -9.56 1.09e+00 8.42e-01 7.70e+01 angle pdb=" N SER A 64 " pdb=" CA SER A 64 " pdb=" C SER A 64 " ideal model delta sigma weight residual 110.97 120.53 -9.56 1.09e+00 8.42e-01 7.69e+01 ... (remaining 5707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 2160 14.03 - 28.06: 156 28.06 - 42.09: 84 42.09 - 56.12: 24 56.12 - 70.15: 6 Dihedral angle restraints: 2430 sinusoidal: 864 harmonic: 1566 Sorted by residual: dihedral pdb=" C HIS E 95 " pdb=" N HIS E 95 " pdb=" CA HIS E 95 " pdb=" CB HIS E 95 " ideal model delta harmonic sigma weight residual -122.60 -131.87 9.27 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" C HIS F 95 " pdb=" N HIS F 95 " pdb=" CA HIS F 95 " pdb=" CB HIS F 95 " ideal model delta harmonic sigma weight residual -122.60 -131.86 9.26 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C HIS C 95 " pdb=" N HIS C 95 " pdb=" CA HIS C 95 " pdb=" CB HIS C 95 " ideal model delta harmonic sigma weight residual -122.60 -131.86 9.26 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 2427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 228 0.062 - 0.124: 186 0.124 - 0.186: 142 0.186 - 0.248: 62 0.248 - 0.310: 18 Chirality restraints: 636 Sorted by residual: chirality pdb=" CA HIS B 95 " pdb=" N HIS B 95 " pdb=" C HIS B 95 " pdb=" CB HIS B 95 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA HIS A 95 " pdb=" N HIS A 95 " pdb=" C HIS A 95 " pdb=" CB HIS A 95 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA HIS D 95 " pdb=" N HIS D 95 " pdb=" C HIS D 95 " pdb=" CB HIS D 95 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 633 not shown) Planarity restraints: 738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 100 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C GLY E 100 " -0.072 2.00e-02 2.50e+03 pdb=" O GLY E 100 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY E 101 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 100 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C GLY B 100 " -0.072 2.00e-02 2.50e+03 pdb=" O GLY B 100 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY B 101 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 100 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C GLY C 100 " -0.072 2.00e-02 2.50e+03 pdb=" O GLY C 100 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY C 101 " 0.025 2.00e-02 2.50e+03 ... (remaining 735 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 2442 3.03 - 3.50: 3840 3.50 - 3.96: 6802 3.96 - 4.43: 7884 4.43 - 4.90: 15157 Nonbonded interactions: 36125 Sorted by model distance: nonbonded pdb=" N GLY B 100 " pdb=" O GLY B 100 " model vdw 2.562 2.496 nonbonded pdb=" N GLY A 100 " pdb=" O GLY A 100 " model vdw 2.562 2.496 nonbonded pdb=" N GLY C 100 " pdb=" O GLY C 100 " model vdw 2.562 2.496 nonbonded pdb=" N GLY F 100 " pdb=" O GLY F 100 " model vdw 2.562 2.496 nonbonded pdb=" N GLY E 100 " pdb=" O GLY E 100 " model vdw 2.562 2.496 ... (remaining 36120 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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 individual isotropic 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.020 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:15.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 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 : 0.015 0.065 4212 Z= 0.988 Angle : 2.116 9.606 5712 Z= 1.591 Chirality : 0.121 0.310 636 Planarity : 0.012 0.042 738 Dihedral : 14.206 70.153 1428 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % 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: -4.40 (0.21), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.16), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP C 34 HIS 0.007 0.003 HIS B 95 PHE 0.006 0.002 PHE C 61 TYR 0.014 0.002 TYR B 30 ARG 0.007 0.002 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.447 Fit side-chains REVERT: A 23 GLN cc_start: 0.7914 (tt0) cc_final: 0.6979 (tm-30) REVERT: A 89 SER cc_start: 0.6068 (t) cc_final: 0.5827 (t) REVERT: B 23 GLN cc_start: 0.6604 (tt0) cc_final: 0.5670 (tm-30) REVERT: C 19 ARG cc_start: 0.5982 (ttm170) cc_final: 0.5702 (ttm170) REVERT: C 23 GLN cc_start: 0.6797 (tt0) cc_final: 0.5708 (tm-30) REVERT: C 27 LEU cc_start: 0.6638 (tt) cc_final: 0.6275 (mp) REVERT: D 23 GLN cc_start: 0.7023 (tt0) cc_final: 0.5726 (tm-30) REVERT: D 33 SER cc_start: 0.7831 (p) cc_final: 0.7617 (p) REVERT: D 38 LYS cc_start: 0.7392 (mttt) cc_final: 0.7167 (mtpp) REVERT: D 78 GLN cc_start: 0.7055 (mt0) cc_final: 0.6721 (mt0) REVERT: F 23 GLN cc_start: 0.6897 (tt0) cc_final: 0.6431 (tm-30) REVERT: F 78 GLN cc_start: 0.7283 (mt0) cc_final: 0.6979 (mt0) REVERT: F 80 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6218 (tt0) REVERT: F 90 ARG cc_start: 0.6815 (ttt180) cc_final: 0.6035 (tpm170) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 1.0073 time to fit residues: 125.5073 Evaluate side-chains 61 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN A 78 GLN B 52 ASN B 68 ASN B 78 GLN C 68 ASN C 78 GLN D 68 ASN E 16 GLN E 68 ASN ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN F 68 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.119720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.108983 restraints weight = 5626.309| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.00 r_work: 0.3791 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4212 Z= 0.173 Angle : 0.555 6.719 5712 Z= 0.311 Chirality : 0.043 0.119 636 Planarity : 0.002 0.034 738 Dihedral : 4.997 18.169 600 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 3.38 % Allowed : 15.77 % Favored : 80.86 % 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: -3.47 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 34 HIS 0.002 0.001 HIS E 95 PHE 0.002 0.001 PHE A 99 TYR 0.011 0.002 TYR A 31 ARG 0.003 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8539 (mttt) REVERT: D 23 GLN cc_start: 0.7999 (tt0) cc_final: 0.7542 (tm-30) REVERT: E 90 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7321 (ttm-80) REVERT: F 19 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7696 (ttp-110) REVERT: F 80 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7876 (tt0) REVERT: F 90 ARG cc_start: 0.8107 (ttt180) cc_final: 0.6964 (tpm170) outliers start: 15 outliers final: 9 residues processed: 65 average time/residue: 1.6295 time to fit residues: 110.2801 Evaluate side-chains 55 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 49 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 68 ASN D 68 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN F 68 ASN F 78 GLN F 88 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.118334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.107672 restraints weight = 5580.810| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.99 r_work: 0.3783 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4212 Z= 0.193 Angle : 0.526 6.275 5712 Z= 0.294 Chirality : 0.043 0.115 636 Planarity : 0.002 0.022 738 Dihedral : 4.795 17.837 600 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.80 % Allowed : 17.12 % Favored : 81.08 % 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: -3.13 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 34 HIS 0.003 0.001 HIS E 95 PHE 0.003 0.001 PHE A 99 TYR 0.016 0.002 TYR F 86 ARG 0.003 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 1.116 Fit side-chains REVERT: A 38 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8484 (mttt) REVERT: A 90 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7489 (ttp80) REVERT: E 90 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7103 (ttm170) REVERT: F 80 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7895 (tt0) REVERT: F 90 ARG cc_start: 0.7903 (ttt180) cc_final: 0.6838 (tpm170) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 2.2043 time to fit residues: 114.7830 Evaluate side-chains 47 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain E residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.0570 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 16 optimal weight: 7.9990 chunk 25 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.123006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.112207 restraints weight = 5586.552| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.01 r_work: 0.3850 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4212 Z= 0.119 Angle : 0.469 5.028 5712 Z= 0.263 Chirality : 0.043 0.113 636 Planarity : 0.002 0.012 738 Dihedral : 4.347 17.037 600 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.93 % Allowed : 16.44 % Favored : 80.63 % 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: -3.03 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 34 HIS 0.001 0.000 HIS A 95 PHE 0.002 0.001 PHE C 61 TYR 0.016 0.001 TYR B 86 ARG 0.002 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8118 (mm-30) REVERT: A 90 ARG cc_start: 0.7567 (ttp80) cc_final: 0.7320 (ttp80) REVERT: F 80 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7879 (tt0) REVERT: F 90 ARG cc_start: 0.7922 (ttt180) cc_final: 0.6597 (tpm170) outliers start: 13 outliers final: 8 residues processed: 56 average time/residue: 1.2351 time to fit residues: 71.8197 Evaluate side-chains 51 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 22 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 5 optimal weight: 6.9990 chunk 48 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN D 51 ASN D 68 ASN D 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.107555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.097305 restraints weight = 6314.350| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.02 r_work: 0.3647 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.048 4212 Z= 0.656 Angle : 0.741 6.084 5712 Z= 0.414 Chirality : 0.049 0.114 636 Planarity : 0.004 0.032 738 Dihedral : 5.821 19.291 600 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.35 % Allowed : 21.40 % Favored : 77.25 % 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: -3.12 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 34 HIS 0.013 0.004 HIS D 95 PHE 0.014 0.003 PHE B 99 TYR 0.026 0.004 TYR F 30 ARG 0.004 0.001 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: C 82 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7833 (mt-10) REVERT: F 80 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7819 (tt0) REVERT: F 90 ARG cc_start: 0.8018 (ttt180) cc_final: 0.6602 (tpm170) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 1.3271 time to fit residues: 59.3062 Evaluate side-chains 41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain E residue 22 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.114498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.104032 restraints weight = 5803.244| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.98 r_work: 0.3744 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4212 Z= 0.223 Angle : 0.533 5.560 5712 Z= 0.294 Chirality : 0.043 0.112 636 Planarity : 0.002 0.023 738 Dihedral : 4.949 18.054 600 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.13 % Allowed : 22.07 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 34 HIS 0.003 0.001 HIS D 95 PHE 0.003 0.001 PHE E 61 TYR 0.016 0.002 TYR C 35 ARG 0.003 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7530 (ttp80) REVERT: C 82 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7738 (mt-10) REVERT: D 38 LYS cc_start: 0.8864 (mttm) cc_final: 0.8445 (mptt) REVERT: E 90 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7428 (ptm160) REVERT: F 80 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7941 (tt0) REVERT: F 90 ARG cc_start: 0.7942 (ttt180) cc_final: 0.6508 (tpm170) outliers start: 5 outliers final: 5 residues processed: 43 average time/residue: 1.1657 time to fit residues: 52.2981 Evaluate side-chains 44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain E residue 22 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.114795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.104235 restraints weight = 5855.565| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.01 r_work: 0.3746 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4212 Z= 0.228 Angle : 0.533 6.249 5712 Z= 0.293 Chirality : 0.043 0.112 636 Planarity : 0.002 0.019 738 Dihedral : 4.836 17.774 600 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.35 % Allowed : 23.20 % Favored : 75.45 % 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: -3.13 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 34 HIS 0.004 0.001 HIS D 95 PHE 0.004 0.001 PHE A 99 TYR 0.016 0.002 TYR C 35 ARG 0.001 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7745 (mt-10) REVERT: D 38 LYS cc_start: 0.8873 (mttm) cc_final: 0.8462 (mptt) REVERT: E 90 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7460 (ptm160) REVERT: F 80 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7952 (tt0) REVERT: F 90 ARG cc_start: 0.7929 (ttt180) cc_final: 0.6563 (ttm170) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 1.1812 time to fit residues: 54.1585 Evaluate side-chains 43 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 22 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 0.0170 chunk 45 optimal weight: 0.0970 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.120053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.109226 restraints weight = 5620.884| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.06 r_work: 0.3817 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4212 Z= 0.125 Angle : 0.492 7.078 5712 Z= 0.267 Chirality : 0.043 0.113 636 Planarity : 0.002 0.025 738 Dihedral : 4.352 16.223 600 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.13 % Allowed : 24.10 % Favored : 74.77 % 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: -3.03 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 34 HIS 0.002 0.001 HIS A 95 PHE 0.003 0.001 PHE E 61 TYR 0.017 0.001 TYR B 86 ARG 0.005 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7772 (ttm170) cc_final: 0.7491 (ttm110) REVERT: E 90 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7266 (ptm160) REVERT: F 80 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7899 (tt0) REVERT: F 90 ARG cc_start: 0.7874 (ttt180) cc_final: 0.6504 (ttm170) outliers start: 5 outliers final: 5 residues processed: 46 average time/residue: 1.0261 time to fit residues: 49.4125 Evaluate side-chains 45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 22 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 34 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.112597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.101934 restraints weight = 5981.871| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.07 r_work: 0.3717 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4212 Z= 0.313 Angle : 0.579 6.784 5712 Z= 0.317 Chirality : 0.044 0.112 636 Planarity : 0.003 0.024 738 Dihedral : 4.956 17.775 600 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.13 % Allowed : 23.87 % Favored : 75.00 % 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: -3.01 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 34 HIS 0.006 0.002 HIS D 95 PHE 0.006 0.001 PHE B 99 TYR 0.017 0.002 TYR A 30 ARG 0.005 0.001 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7688 (mt-10) REVERT: E 90 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7354 (ptm160) REVERT: F 80 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7875 (tt0) REVERT: F 90 ARG cc_start: 0.7917 (ttt180) cc_final: 0.6496 (ttm170) outliers start: 5 outliers final: 5 residues processed: 44 average time/residue: 1.0915 time to fit residues: 50.2782 Evaluate side-chains 43 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain E residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.116714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.106344 restraints weight = 5866.451| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.97 r_work: 0.3784 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4212 Z= 0.172 Angle : 0.521 6.942 5712 Z= 0.283 Chirality : 0.043 0.112 636 Planarity : 0.002 0.042 738 Dihedral : 4.550 17.194 600 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.13 % Allowed : 24.10 % Favored : 74.77 % 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: -2.97 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 34 HIS 0.003 0.001 HIS A 95 PHE 0.004 0.001 PHE E 61 TYR 0.018 0.001 TYR B 86 ARG 0.008 0.001 ARG F 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7781 (mt-10) REVERT: D 38 LYS cc_start: 0.8727 (mttp) cc_final: 0.8486 (mmtp) REVERT: E 90 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7504 (ptm160) REVERT: F 80 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7904 (tt0) REVERT: F 90 ARG cc_start: 0.7951 (ttt180) cc_final: 0.6605 (ttm170) outliers start: 5 outliers final: 5 residues processed: 43 average time/residue: 1.1223 time to fit residues: 50.4829 Evaluate side-chains 44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain E residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.116991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.106499 restraints weight = 5764.977| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.98 r_work: 0.3788 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4212 Z= 0.178 Angle : 0.527 6.854 5712 Z= 0.286 Chirality : 0.043 0.112 636 Planarity : 0.002 0.038 738 Dihedral : 4.536 16.766 600 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.13 % Allowed : 24.10 % Favored : 74.77 % 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: -2.95 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 34 HIS 0.003 0.001 HIS A 95 PHE 0.003 0.001 PHE E 61 TYR 0.015 0.002 TYR F 86 ARG 0.009 0.001 ARG F 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3247.55 seconds wall clock time: 58 minutes 53.61 seconds (3533.61 seconds total)