Starting phenix.real_space_refine on Wed Sep 17 04:28:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eme_19818/09_2025/9eme_19818.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eme_19818/09_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_19818/09_2025/9eme_19818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eme_19818/09_2025/9eme_19818.map" model { file = "/net/cci-nas-00/data/ceres_data/9eme_19818/09_2025/9eme_19818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eme_19818/09_2025/9eme_19818.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, E, F Time building chain proxies: 0.63, per 1000 atoms: 0.15 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 B 22 " - pdb=" SG CYS B 87 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 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: 0.33 Conformation dependent library (CDL) restraints added in 155.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.17 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: 0.56 Time building geometry restraints manager: 0.39 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.010 Find NCS groups from input model: 0.020 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.240 ------------------------------------------------------------------------------- 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 4218 Z= 1.114 Angle : 2.114 9.606 5724 Z= 1.589 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.002 ARG E 90 TYR 0.014 0.002 TYR B 30 PHE 0.006 0.002 PHE C 61 TRP 0.019 0.005 TRP C 34 HIS 0.007 0.003 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.01474 ( 4212) covalent geometry : angle 2.11604 ( 5712) SS BOND : bond 0.01219 ( 6) SS BOND : angle 1.00173 ( 12) hydrogen bonds : bond 0.17634 ( 80) hydrogen bonds : angle 8.45019 ( 240) *********************** 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 : 0.150 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: 0.5108 time to fit residues: 63.5000 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 : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 A 68 ASN A 78 GLN B 52 ASN B 68 ASN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3966 r_free = 0.3966 target = 0.118457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.107754 restraints weight = 5681.979| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.01 r_work: 0.3774 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4218 Z= 0.128 Angle : 0.566 6.775 5724 Z= 0.318 Chirality : 0.043 0.118 636 Planarity : 0.002 0.032 738 Dihedral : 5.043 18.163 600 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 3.15 % Allowed : 16.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 90 TYR 0.012 0.002 TYR F 30 PHE 0.002 0.001 PHE D 61 TRP 0.015 0.003 TRP D 34 HIS 0.002 0.001 HIS E 95 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4212) covalent geometry : angle 0.56678 ( 5712) SS BOND : bond 0.00373 ( 6) SS BOND : angle 0.28072 ( 12) hydrogen bonds : bond 0.03505 ( 80) hydrogen bonds : angle 5.08623 ( 240) *********************** 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 65 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8464 (mttt) REVERT: B 38 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8486 (mtpp) REVERT: D 23 GLN cc_start: 0.8000 (tt0) cc_final: 0.7555 (tm-30) REVERT: D 90 ARG cc_start: 0.8345 (ttp80) cc_final: 0.8092 (ttp80) REVERT: E 90 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7092 (ttm170) REVERT: F 19 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7716 (ttp-110) REVERT: F 80 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7891 (tt0) REVERT: F 90 ARG cc_start: 0.8083 (ttt180) cc_final: 0.7064 (tpm170) outliers start: 14 outliers final: 7 residues processed: 62 average time/residue: 0.6202 time to fit residues: 39.7591 Evaluate side-chains 53 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 38 LYS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.0270 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN B 78 GLN 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 = 0.3956 r_free = 0.3956 target = 0.116894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.106263 restraints weight = 5683.165| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.00 r_work: 0.3759 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4218 Z= 0.154 Angle : 0.540 6.388 5724 Z= 0.303 Chirality : 0.043 0.114 636 Planarity : 0.002 0.020 738 Dihedral : 4.906 17.796 600 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.25 % Allowed : 17.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.17 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 90 TYR 0.014 0.002 TYR B 86 PHE 0.004 0.001 PHE A 99 TRP 0.014 0.002 TRP D 34 HIS 0.004 0.001 HIS C 95 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4212) covalent geometry : angle 0.54024 ( 5712) SS BOND : bond 0.00365 ( 6) SS BOND : angle 0.39213 ( 12) hydrogen bonds : bond 0.03208 ( 80) hydrogen bonds : angle 4.67303 ( 240) *********************** 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 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8528 (mttt) REVERT: A 90 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7516 (ttp80) REVERT: D 38 LYS cc_start: 0.8777 (mtpp) cc_final: 0.8532 (mtpp) REVERT: D 68 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8851 (m110) REVERT: E 90 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7679 (ttp80) REVERT: F 23 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7950 (tm-30) REVERT: F 80 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7886 (tt0) REVERT: F 90 ARG cc_start: 0.7914 (ttt180) cc_final: 0.6712 (tpm170) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.6615 time to fit residues: 36.9141 Evaluate side-chains 53 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 A residue 62 SER Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain D residue 68 ASN 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 20 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 E 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.112885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.102375 restraints weight = 5811.551| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.99 r_work: 0.3716 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4218 Z= 0.239 Angle : 0.586 5.852 5724 Z= 0.327 Chirality : 0.044 0.114 636 Planarity : 0.003 0.020 738 Dihedral : 5.203 18.174 600 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.25 % Allowed : 17.57 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 28 TYR 0.019 0.002 TYR A 30 PHE 0.005 0.001 PHE A 99 TRP 0.015 0.002 TRP D 34 HIS 0.007 0.002 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 4212) covalent geometry : angle 0.58640 ( 5712) SS BOND : bond 0.00521 ( 6) SS BOND : angle 0.38921 ( 12) hydrogen bonds : bond 0.03491 ( 80) hydrogen bonds : angle 4.59852 ( 240) *********************** 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 54 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8497 (mttt) REVERT: A 90 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7479 (ttp80) REVERT: F 23 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7841 (tm-30) REVERT: F 80 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7845 (tt0) REVERT: F 90 ARG cc_start: 0.7883 (ttt180) cc_final: 0.6496 (tpm170) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 0.6433 time to fit residues: 33.8642 Evaluate side-chains 46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 19 ARG 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 D residue 68 ASN 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 51 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.112938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.102503 restraints weight = 5868.695| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.99 r_work: 0.3722 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4218 Z= 0.210 Angle : 0.557 5.338 5724 Z= 0.310 Chirality : 0.043 0.113 636 Planarity : 0.003 0.028 738 Dihedral : 5.115 18.480 600 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.70 % Allowed : 20.72 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG E 90 TYR 0.016 0.002 TYR A 30 PHE 0.005 0.001 PHE A 99 TRP 0.013 0.002 TRP D 34 HIS 0.005 0.002 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 4212) covalent geometry : angle 0.55698 ( 5712) SS BOND : bond 0.00437 ( 6) SS BOND : angle 0.39800 ( 12) hydrogen bonds : bond 0.03269 ( 80) hydrogen bonds : angle 4.44898 ( 240) *********************** 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 53 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8489 (mttt) REVERT: C 19 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7553 (ttm170) REVERT: C 82 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7864 (mm-30) REVERT: F 80 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7900 (tt0) REVERT: F 90 ARG cc_start: 0.7960 (ttt180) cc_final: 0.6414 (tpm170) outliers start: 12 outliers final: 8 residues processed: 48 average time/residue: 0.6358 time to fit residues: 31.5641 Evaluate side-chains 51 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 B residue 22 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 19 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.109697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.099332 restraints weight = 6089.851| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.02 r_work: 0.3687 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4218 Z= 0.289 Angle : 0.613 5.576 5724 Z= 0.340 Chirality : 0.045 0.112 636 Planarity : 0.003 0.032 738 Dihedral : 5.424 18.884 600 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.80 % Allowed : 22.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG E 90 TYR 0.019 0.002 TYR A 30 PHE 0.008 0.001 PHE B 99 TRP 0.015 0.002 TRP D 34 HIS 0.008 0.003 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00625 ( 4212) covalent geometry : angle 0.61335 ( 5712) SS BOND : bond 0.00555 ( 6) SS BOND : angle 0.53526 ( 12) hydrogen bonds : bond 0.03685 ( 80) hydrogen bonds : angle 4.49367 ( 240) *********************** 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 46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7518 (ttp80) REVERT: C 19 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7575 (ttm170) REVERT: D 81 ASP cc_start: 0.7932 (m-30) cc_final: 0.7726 (m-30) REVERT: F 80 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7848 (tt0) REVERT: F 90 ARG cc_start: 0.8087 (ttt180) cc_final: 0.6534 (tpm170) outliers start: 8 outliers final: 4 residues processed: 41 average time/residue: 0.6710 time to fit residues: 28.4377 Evaluate side-chains 40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 C residue 19 ARG 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 7 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.113205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.102409 restraints weight = 6010.596| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.10 r_work: 0.3726 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4218 Z= 0.194 Angle : 0.555 6.992 5724 Z= 0.304 Chirality : 0.044 0.112 636 Planarity : 0.003 0.034 738 Dihedral : 5.057 18.150 600 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.58 % Allowed : 23.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG C 90 TYR 0.014 0.002 TYR B 86 PHE 0.004 0.001 PHE A 99 TRP 0.012 0.002 TRP D 34 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 4212) covalent geometry : angle 0.55523 ( 5712) SS BOND : bond 0.00378 ( 6) SS BOND : angle 0.44791 ( 12) hydrogen bonds : bond 0.03146 ( 80) hydrogen bonds : angle 4.42971 ( 240) *********************** 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 45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7392 (ttp80) REVERT: C 19 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7520 (ttm170) REVERT: E 90 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7277 (ptm160) REVERT: F 80 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7830 (tt0) REVERT: F 90 ARG cc_start: 0.7921 (ttt180) cc_final: 0.6465 (ttm170) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 0.6491 time to fit residues: 28.2204 Evaluate side-chains 40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 22 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain E residue 22 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.0980 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.116823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.106176 restraints weight = 5784.330| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.01 r_work: 0.3783 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4218 Z= 0.128 Angle : 0.509 7.080 5724 Z= 0.277 Chirality : 0.043 0.111 636 Planarity : 0.002 0.026 738 Dihedral : 4.610 17.334 600 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.58 % Allowed : 23.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 90 TYR 0.017 0.001 TYR B 86 PHE 0.004 0.001 PHE E 61 TRP 0.010 0.002 TRP D 34 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4212) covalent geometry : angle 0.50870 ( 5712) SS BOND : bond 0.00267 ( 6) SS BOND : angle 0.42971 ( 12) hydrogen bonds : bond 0.02706 ( 80) hydrogen bonds : angle 4.37841 ( 240) *********************** 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 48 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7298 (ttp80) REVERT: E 90 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7262 (ptm160) REVERT: F 80 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7883 (tt0) REVERT: F 90 ARG cc_start: 0.7948 (ttt180) cc_final: 0.6604 (ttm170) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.6133 time to fit residues: 29.1657 Evaluate side-chains 45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 45 optimal weight: 0.0040 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.110599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.099961 restraints weight = 6090.242| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.08 r_work: 0.3697 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 4218 Z= 0.262 Angle : 0.600 6.972 5724 Z= 0.330 Chirality : 0.044 0.119 636 Planarity : 0.003 0.042 738 Dihedral : 5.226 18.372 600 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.58 % Allowed : 23.87 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 90 TYR 0.018 0.002 TYR A 30 PHE 0.007 0.001 PHE B 99 TRP 0.014 0.002 TRP D 34 HIS 0.007 0.002 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 4212) covalent geometry : angle 0.59996 ( 5712) SS BOND : bond 0.00497 ( 6) SS BOND : angle 0.57285 ( 12) hydrogen bonds : bond 0.03485 ( 80) hydrogen bonds : angle 4.45296 ( 240) *********************** 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 41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 19 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7534 (ttm170) REVERT: E 90 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7155 (ptm160) REVERT: F 80 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7753 (tt0) REVERT: F 90 ARG cc_start: 0.8022 (ttt180) cc_final: 0.6602 (ttm170) outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 0.6265 time to fit residues: 24.6701 Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 19 ARG 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 4 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.115414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.104891 restraints weight = 5806.490| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.99 r_work: 0.3771 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4218 Z= 0.134 Angle : 0.523 7.137 5724 Z= 0.283 Chirality : 0.043 0.112 636 Planarity : 0.002 0.032 738 Dihedral : 4.701 17.437 600 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.04 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 90 TYR 0.013 0.001 TYR B 86 PHE 0.004 0.001 PHE E 61 TRP 0.010 0.002 TRP D 34 HIS 0.003 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4212) covalent geometry : angle 0.52305 ( 5712) SS BOND : bond 0.00290 ( 6) SS BOND : angle 0.44652 ( 12) hydrogen bonds : bond 0.02763 ( 80) hydrogen bonds : angle 4.40645 ( 240) ********************** 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 43 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7577 (ttm110) REVERT: D 90 ARG cc_start: 0.8433 (ptt90) cc_final: 0.8186 (ptt90) REVERT: E 90 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7250 (ptm160) REVERT: F 80 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7846 (tt0) REVERT: F 90 ARG cc_start: 0.7945 (ttt180) cc_final: 0.6623 (ttm170) outliers start: 5 outliers final: 5 residues processed: 42 average time/residue: 0.6658 time to fit residues: 28.8686 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 : 0.140 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.0770 chunk 2 optimal weight: 0.8980 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.117270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.106407 restraints weight = 5837.400| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.07 r_work: 0.3790 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4218 Z= 0.118 Angle : 0.512 7.160 5724 Z= 0.277 Chirality : 0.043 0.112 636 Planarity : 0.002 0.023 738 Dihedral : 4.486 16.631 600 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.58 % Allowed : 23.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG D 90 TYR 0.015 0.001 TYR F 86 PHE 0.004 0.001 PHE E 61 TRP 0.010 0.002 TRP A 34 HIS 0.002 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4212) covalent geometry : angle 0.51190 ( 5712) SS BOND : bond 0.00256 ( 6) SS BOND : angle 0.40946 ( 12) hydrogen bonds : bond 0.02654 ( 80) hydrogen bonds : angle 4.35209 ( 240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1497.52 seconds wall clock time: 26 minutes 35.47 seconds (1595.47 seconds total)