Starting phenix.real_space_refine on Wed Mar 5 15:54:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwi_60528/03_2025/8zwi_60528.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwi_60528/03_2025/8zwi_60528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zwi_60528/03_2025/8zwi_60528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwi_60528/03_2025/8zwi_60528.map" model { file = "/net/cci-nas-00/data/ceres_data/8zwi_60528/03_2025/8zwi_60528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwi_60528/03_2025/8zwi_60528.cif" } resolution = 3.0 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= 0.003 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: 3 Type Number sf(0) Gaussians C 1590 2.51 5 N 438 2.21 5 O 498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 2526 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.81, per 1000 atoms: 0.72 Number of scatterers: 2526 At special positions: 0 Unit cell: (97.11, 73.87, 30.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 498 8.00 N 438 7.00 C 1590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.60 Conformation dependent library (CDL) restraints added in 338.4 milliseconds 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 51.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 38 through 40 removed outlier: 6.549A pdb=" N TYR A 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 58 removed outlier: 6.792A pdb=" N VAL D 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N HIS D 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY A 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N GLU A 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL E 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N VAL A 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N GLY E 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS A 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N ALA E 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL E 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR A 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLU E 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA A 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 62 through 64 removed outlier: 6.435A pdb=" N VAL A 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL E 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN A 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 70 through 72 removed outlier: 6.342A pdb=" N VAL A 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 75 through 82 removed outlier: 5.710A pdb=" N THR A 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ALA D 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL A 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N LYS D 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN A 79 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL D 82 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR A 81 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA A 76 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 87 through 92 removed outlier: 6.900A pdb=" N ILE D 88 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE A 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA E 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA A 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.549A pdb=" N TYR F 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 58 removed outlier: 6.791A pdb=" N VAL B 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL F 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N HIS B 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY F 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N GLU F 46 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL C 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N VAL F 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 10.280A pdb=" N GLY C 51 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS F 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N ALA C 53 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL F 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL C 55 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR F 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLU C 57 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA F 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.435A pdb=" N VAL F 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL C 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN F 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 70 through 72 removed outlier: 6.343A pdb=" N VAL F 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 82 removed outlier: 5.711A pdb=" N THR F 75 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ALA B 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL F 77 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N LYS B 80 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN F 79 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL B 82 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR F 81 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA F 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 92 removed outlier: 6.900A pdb=" N ILE B 88 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE F 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA C 91 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA F 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 144 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: 0.55 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 432 1.28 - 1.35: 390 1.35 - 1.41: 101 1.41 - 1.48: 451 1.48 - 1.54: 1164 Bond restraints: 2538 Sorted by residual: bond pdb=" C ILE F 88 " pdb=" N ALA F 89 " ideal model delta sigma weight residual 1.331 1.311 0.020 1.29e-02 6.01e+03 2.34e+00 bond pdb=" C ILE A 88 " pdb=" N ALA A 89 " ideal model delta sigma weight residual 1.331 1.311 0.019 1.29e-02 6.01e+03 2.25e+00 bond pdb=" CB GLN C 79 " pdb=" CG GLN C 79 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" CB GLN D 79 " pdb=" CG GLN D 79 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" C ILE D 88 " pdb=" N ALA D 89 " ideal model delta sigma weight residual 1.331 1.311 0.019 1.29e-02 6.01e+03 2.22e+00 ... (remaining 2533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 3019 1.18 - 2.35: 324 2.35 - 3.53: 77 3.53 - 4.71: 0 4.71 - 5.88: 12 Bond angle restraints: 3432 Sorted by residual: angle pdb=" OG1 THR E 44 " pdb=" CB THR E 44 " pdb=" CG2 THR E 44 " ideal model delta sigma weight residual 109.30 103.98 5.32 2.00e+00 2.50e-01 7.09e+00 angle pdb=" OG1 THR F 44 " pdb=" CB THR F 44 " pdb=" CG2 THR F 44 " ideal model delta sigma weight residual 109.30 103.99 5.31 2.00e+00 2.50e-01 7.05e+00 angle pdb=" OG1 THR A 44 " pdb=" CB THR A 44 " pdb=" CG2 THR A 44 " ideal model delta sigma weight residual 109.30 104.00 5.30 2.00e+00 2.50e-01 7.03e+00 angle pdb=" OG1 THR D 44 " pdb=" CB THR D 44 " pdb=" CG2 THR D 44 " ideal model delta sigma weight residual 109.30 104.02 5.28 2.00e+00 2.50e-01 6.96e+00 angle pdb=" OG1 THR C 44 " pdb=" CB THR C 44 " pdb=" CG2 THR C 44 " ideal model delta sigma weight residual 109.30 104.03 5.27 2.00e+00 2.50e-01 6.95e+00 ... (remaining 3427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.96: 1209 8.96 - 17.92: 171 17.92 - 26.88: 72 26.88 - 35.84: 24 35.84 - 44.79: 6 Dihedral angle restraints: 1482 sinusoidal: 492 harmonic: 990 Sorted by residual: dihedral pdb=" CA LYS C 80 " pdb=" CB LYS C 80 " pdb=" CG LYS C 80 " pdb=" CD LYS C 80 " ideal model delta sinusoidal sigma weight residual 180.00 145.26 34.74 3 1.50e+01 4.44e-03 5.91e+00 dihedral pdb=" CA LYS B 80 " pdb=" CB LYS B 80 " pdb=" CG LYS B 80 " pdb=" CD LYS B 80 " ideal model delta sinusoidal sigma weight residual 180.00 145.26 34.74 3 1.50e+01 4.44e-03 5.90e+00 dihedral pdb=" CA LYS E 80 " pdb=" CB LYS E 80 " pdb=" CG LYS E 80 " pdb=" CD LYS E 80 " ideal model delta sinusoidal sigma weight residual 180.00 145.27 34.73 3 1.50e+01 4.44e-03 5.90e+00 ... (remaining 1479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 212 0.037 - 0.074: 104 0.074 - 0.111: 115 0.111 - 0.148: 17 0.148 - 0.186: 8 Chirality restraints: 456 Sorted by residual: chirality pdb=" CB THR F 75 " pdb=" CA THR F 75 " pdb=" OG1 THR F 75 " pdb=" CG2 THR F 75 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CB THR D 75 " pdb=" CA THR D 75 " pdb=" OG1 THR D 75 " pdb=" CG2 THR D 75 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CB THR E 75 " pdb=" CA THR E 75 " pdb=" OG1 THR E 75 " pdb=" CG2 THR E 75 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 453 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 50 " -0.012 2.00e-02 2.50e+03 1.08e-02 1.76e+00 pdb=" CG HIS C 50 " 0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS C 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS C 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 50 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " -0.012 2.00e-02 2.50e+03 1.08e-02 1.74e+00 pdb=" CG HIS F 50 " 0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " -0.012 2.00e-02 2.50e+03 1.08e-02 1.73e+00 pdb=" CG HIS B 50 " 0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " -0.004 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 537 2.79 - 3.32: 2199 3.32 - 3.84: 3791 3.84 - 4.37: 4168 4.37 - 4.90: 8897 Nonbonded interactions: 19592 Sorted by model distance: nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.261 3.120 nonbonded pdb=" OE1 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.261 3.120 nonbonded pdb=" OE1 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.261 3.120 nonbonded pdb=" OE1 GLU B 46 " pdb=" NZ LYS B 80 " model vdw 2.262 3.120 nonbonded pdb=" OE1 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.262 3.120 ... (remaining 19587 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: 0.02 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: 1.980 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.220 Find NCS groups from input model: 0.060 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 : 0.011 0.048 2538 Z= 0.781 Angle : 0.859 5.881 3432 Z= 0.499 Chirality : 0.065 0.186 456 Planarity : 0.003 0.011 420 Dihedral : 11.260 44.795 858 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % 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: -3.70 (0.34), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.26), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.006 HIS C 50 PHE 0.013 0.004 PHE B 94 TYR 0.005 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.292 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 1.4090 time to fit residues: 54.7480 Evaluate side-chains 22 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.0670 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.170227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.142912 restraints weight = 2881.456| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.34 r_work: 0.3966 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3857 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2538 Z= 0.132 Angle : 0.447 4.646 3432 Z= 0.245 Chirality : 0.052 0.126 456 Planarity : 0.001 0.006 420 Dihedral : 3.475 9.489 366 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.16 % Allowed : 8.91 % Favored : 89.92 % 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: -2.79 (0.38), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.006 0.002 PHE B 94 TYR 0.006 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.252 Fit side-chains REVERT: F 75 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8331 (t) REVERT: B 83 GLU cc_start: 0.8303 (tt0) cc_final: 0.8072 (tt0) REVERT: C 60 LYS cc_start: 0.8220 (tttt) cc_final: 0.7928 (tttp) outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 1.3718 time to fit residues: 40.8305 Evaluate side-chains 23 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 0.0980 chunk 1 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.164009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135625 restraints weight = 2825.688| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.35 r_work: 0.3835 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2538 Z= 0.379 Angle : 0.525 3.221 3432 Z= 0.300 Chirality : 0.052 0.124 456 Planarity : 0.002 0.007 420 Dihedral : 4.030 11.308 366 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.33 % Allowed : 11.63 % Favored : 86.05 % 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: -2.57 (0.38), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS D 50 PHE 0.009 0.002 PHE A 94 TYR 0.006 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.289 Fit side-chains REVERT: F 75 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8342 (t) REVERT: B 75 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8281 (t) REVERT: B 83 GLU cc_start: 0.8387 (tt0) cc_final: 0.8185 (tt0) REVERT: C 60 LYS cc_start: 0.8326 (tttt) cc_final: 0.7991 (tttp) outliers start: 6 outliers final: 1 residues processed: 26 average time/residue: 0.9141 time to fit residues: 24.7470 Evaluate side-chains 25 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.0020 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9450 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.170454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.143194 restraints weight = 2875.123| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.36 r_work: 0.3972 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2538 Z= 0.136 Angle : 0.398 2.901 3432 Z= 0.227 Chirality : 0.050 0.122 456 Planarity : 0.001 0.005 420 Dihedral : 3.333 9.164 366 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.16 % Allowed : 12.79 % Favored : 86.05 % 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: -2.17 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS D 50 PHE 0.006 0.002 PHE B 94 TYR 0.004 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.262 Fit side-chains REVERT: F 75 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8286 (t) REVERT: B 75 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8211 (t) REVERT: B 83 GLU cc_start: 0.8294 (tt0) cc_final: 0.8089 (tt0) REVERT: C 60 LYS cc_start: 0.8216 (tttt) cc_final: 0.7876 (tttp) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 1.3219 time to fit residues: 35.3378 Evaluate side-chains 23 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.165564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.137209 restraints weight = 2856.704| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.37 r_work: 0.3852 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2538 Z= 0.324 Angle : 0.482 2.796 3432 Z= 0.279 Chirality : 0.051 0.122 456 Planarity : 0.002 0.006 420 Dihedral : 3.801 9.977 366 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.55 % Allowed : 15.50 % Favored : 82.95 % 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: -2.15 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS D 50 PHE 0.008 0.002 PHE A 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.259 Fit side-chains REVERT: F 75 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8331 (t) REVERT: B 75 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8246 (t) REVERT: B 83 GLU cc_start: 0.8354 (tt0) cc_final: 0.8147 (tt0) REVERT: C 60 LYS cc_start: 0.8291 (tttt) cc_final: 0.7883 (tttp) outliers start: 4 outliers final: 1 residues processed: 25 average time/residue: 1.1174 time to fit residues: 28.8573 Evaluate side-chains 27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.164656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.135308 restraints weight = 2913.123| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.38 r_work: 0.3807 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.036 2538 Z= 0.532 Angle : 0.602 3.174 3432 Z= 0.346 Chirality : 0.053 0.126 456 Planarity : 0.002 0.008 420 Dihedral : 4.406 10.519 366 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.55 % Allowed : 14.73 % Favored : 83.72 % 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: -2.33 (0.39), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS D 50 PHE 0.011 0.003 PHE A 94 TYR 0.006 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.281 Fit side-chains REVERT: D 75 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8459 (t) REVERT: D 83 GLU cc_start: 0.8310 (tt0) cc_final: 0.8052 (tt0) REVERT: F 75 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8346 (t) REVERT: B 75 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8266 (t) REVERT: B 83 GLU cc_start: 0.8345 (tt0) cc_final: 0.8104 (tt0) REVERT: C 60 LYS cc_start: 0.8318 (tttt) cc_final: 0.7998 (tttp) outliers start: 4 outliers final: 0 residues processed: 30 average time/residue: 1.2668 time to fit residues: 39.0629 Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.167154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.138253 restraints weight = 2913.384| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.43 r_work: 0.3860 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2538 Z= 0.284 Angle : 0.478 3.918 3432 Z= 0.276 Chirality : 0.051 0.123 456 Planarity : 0.002 0.006 420 Dihedral : 3.946 10.700 366 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.16 % Allowed : 15.89 % Favored : 82.95 % 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: -2.20 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS D 50 PHE 0.008 0.002 PHE A 94 TYR 0.006 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.253 Fit side-chains REVERT: D 83 GLU cc_start: 0.8317 (tt0) cc_final: 0.8012 (tt0) REVERT: E 60 LYS cc_start: 0.8275 (tttp) cc_final: 0.7963 (tptm) REVERT: F 75 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8321 (t) REVERT: B 75 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8298 (t) REVERT: B 83 GLU cc_start: 0.8329 (tt0) cc_final: 0.8112 (tt0) REVERT: C 60 LYS cc_start: 0.8262 (tttt) cc_final: 0.7851 (tttp) outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 1.3716 time to fit residues: 35.2372 Evaluate side-chains 27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.169240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.141343 restraints weight = 2878.678| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.36 r_work: 0.3944 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2538 Z= 0.168 Angle : 0.422 3.323 3432 Z= 0.243 Chirality : 0.050 0.121 456 Planarity : 0.001 0.006 420 Dihedral : 3.548 9.844 366 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.16 % Allowed : 16.67 % Favored : 82.17 % 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: -1.94 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS D 50 PHE 0.006 0.002 PHE F 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.279 Fit side-chains REVERT: D 83 GLU cc_start: 0.8212 (tt0) cc_final: 0.7911 (tt0) REVERT: F 75 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8257 (t) REVERT: B 75 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8251 (t) REVERT: B 83 GLU cc_start: 0.8250 (tt0) cc_final: 0.8039 (tt0) REVERT: C 60 LYS cc_start: 0.8185 (tttt) cc_final: 0.7761 (tttp) outliers start: 3 outliers final: 1 residues processed: 22 average time/residue: 1.1991 time to fit residues: 27.2127 Evaluate side-chains 23 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.165080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.135385 restraints weight = 2856.981| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.44 r_work: 0.3814 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 2538 Z= 0.475 Angle : 0.585 3.852 3432 Z= 0.335 Chirality : 0.052 0.126 456 Planarity : 0.002 0.012 420 Dihedral : 4.245 11.464 366 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.16 % Allowed : 16.28 % Favored : 82.56 % 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: -2.14 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS D 50 PHE 0.011 0.003 PHE A 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.274 Fit side-chains REVERT: D 75 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8371 (t) REVERT: D 83 GLU cc_start: 0.8271 (tt0) cc_final: 0.7953 (tt0) REVERT: E 60 LYS cc_start: 0.8429 (tptm) cc_final: 0.8222 (tptm) REVERT: F 75 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8207 (t) REVERT: B 75 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8233 (t) REVERT: B 83 GLU cc_start: 0.8352 (tt0) cc_final: 0.8129 (tt0) REVERT: C 60 LYS cc_start: 0.8228 (tttt) cc_final: 0.7888 (tttp) outliers start: 3 outliers final: 0 residues processed: 26 average time/residue: 1.1826 time to fit residues: 31.6956 Evaluate side-chains 28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.169842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.141918 restraints weight = 2857.242| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.34 r_work: 0.3954 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2538 Z= 0.150 Angle : 0.426 2.989 3432 Z= 0.244 Chirality : 0.050 0.120 456 Planarity : 0.001 0.007 420 Dihedral : 3.628 11.847 366 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.55 % Allowed : 16.28 % Favored : 82.17 % 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: -1.92 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 50 PHE 0.006 0.002 PHE F 94 TYR 0.005 0.001 TYR F 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.293 Fit side-chains REVERT: A 60 LYS cc_start: 0.8060 (tttp) cc_final: 0.7600 (tttp) REVERT: D 83 GLU cc_start: 0.8222 (tt0) cc_final: 0.7926 (tt0) REVERT: F 75 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8253 (t) REVERT: B 62 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7408 (mt0) REVERT: B 75 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8304 (t) REVERT: B 83 GLU cc_start: 0.8268 (tt0) cc_final: 0.8049 (tt0) REVERT: C 60 LYS cc_start: 0.8177 (tttt) cc_final: 0.7745 (tttp) outliers start: 4 outliers final: 1 residues processed: 23 average time/residue: 1.3239 time to fit residues: 31.3910 Evaluate side-chains 25 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 0.0980 chunk 17 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.170148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.142132 restraints weight = 2918.109| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.40 r_work: 0.3938 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.189 2538 Z= 0.554 Angle : 1.483 59.157 3432 Z= 0.875 Chirality : 0.054 0.437 456 Planarity : 0.002 0.020 420 Dihedral : 3.620 11.768 366 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.94 % Allowed : 16.28 % Favored : 81.78 % 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: -1.91 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 50 PHE 0.007 0.002 PHE F 94 TYR 0.005 0.001 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2076.59 seconds wall clock time: 36 minutes 25.71 seconds (2185.71 seconds total)