Starting phenix.real_space_refine on Tue Mar 3 11:02:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v47_31702/03_2026/7v47_31702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v47_31702/03_2026/7v47_31702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v47_31702/03_2026/7v47_31702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v47_31702/03_2026/7v47_31702.map" model { file = "/net/cci-nas-00/data/ceres_data/7v47_31702/03_2026/7v47_31702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v47_31702/03_2026/7v47_31702.cif" } resolution = 2.8 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: 3 Type Number sf(0) Gaussians C 1554 2.51 5 N 432 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 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2484 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 414 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 60} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, E, D, F Time building chain proxies: 0.28, per 1000 atoms: 0.11 Number of scatterers: 2484 At special positions: 0 Unit cell: (76.32, 111.3, 33.92, 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 432 7.00 C 1554 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: 0.13 Conformation dependent library (CDL) restraints added in 64.5 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: 612 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 removed outlier: 6.391A pdb=" N TYR A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N SER C 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY A 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N SER D 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY C 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.613A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLY C 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.613A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLY C 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N GLY D 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N HIS C 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA D 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N VAL C 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 10.542A pdb=" N VAL D 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N THR C 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.029A pdb=" N GLU A 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR C 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL A 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL C 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN A 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLU C 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N THR D 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL D 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASN C 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 42 removed outlier: 6.395A pdb=" N TYR B 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER E 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY B 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR E 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N SER F 42 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY E 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 55 removed outlier: 6.609A pdb=" N VAL B 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY E 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N HIS B 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA E 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N VAL B 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N VAL E 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N THR B 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL E 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N GLY F 51 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N HIS E 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA F 53 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N VAL E 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N VAL F 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N THR E 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 66 removed outlier: 6.035A pdb=" N GLU B 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR E 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL B 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL E 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASN B 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLU E 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR F 64 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL E 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL F 66 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN E 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 No hydrogen bonds 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: 0.01 Time building geometry restraints manager: 0.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 432 1.29 - 1.35: 396 1.35 - 1.42: 96 1.42 - 1.48: 421 1.48 - 1.55: 1151 Bond restraints: 2496 Sorted by residual: bond pdb=" N THR D 72 " pdb=" CA THR D 72 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 2.04e+00 bond pdb=" N THR B 72 " pdb=" CA THR B 72 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.94e+00 bond pdb=" N THR E 72 " pdb=" CA THR E 72 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.91e+00 bond pdb=" N THR F 72 " pdb=" CA THR F 72 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.91e+00 bond pdb=" N THR A 72 " pdb=" CA THR A 72 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.90e+00 ... (remaining 2491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 2690 0.83 - 1.66: 569 1.66 - 2.49: 66 2.49 - 3.32: 35 3.32 - 4.15: 18 Bond angle restraints: 3378 Sorted by residual: angle pdb=" CA THR A 72 " pdb=" CB THR A 72 " pdb=" CG2 THR A 72 " ideal model delta sigma weight residual 110.50 114.45 -3.95 1.70e+00 3.46e-01 5.41e+00 angle pdb=" CA THR B 72 " pdb=" CB THR B 72 " pdb=" CG2 THR B 72 " ideal model delta sigma weight residual 110.50 114.42 -3.92 1.70e+00 3.46e-01 5.31e+00 angle pdb=" CA THR D 72 " pdb=" CB THR D 72 " pdb=" CG2 THR D 72 " ideal model delta sigma weight residual 110.50 114.41 -3.91 1.70e+00 3.46e-01 5.28e+00 angle pdb=" CA THR E 72 " pdb=" CB THR E 72 " pdb=" CG2 THR E 72 " ideal model delta sigma weight residual 110.50 114.40 -3.90 1.70e+00 3.46e-01 5.26e+00 angle pdb=" CA THR F 72 " pdb=" CB THR F 72 " pdb=" CG2 THR F 72 " ideal model delta sigma weight residual 110.50 114.39 -3.89 1.70e+00 3.46e-01 5.24e+00 ... (remaining 3373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 1302 15.65 - 31.29: 126 31.29 - 46.94: 6 46.94 - 62.58: 0 62.58 - 78.23: 6 Dihedral angle restraints: 1440 sinusoidal: 462 harmonic: 978 Sorted by residual: dihedral pdb=" CA VAL E 49 " pdb=" C VAL E 49 " pdb=" N HIS E 50 " pdb=" CA HIS E 50 " ideal model delta harmonic sigma weight residual 180.00 165.28 14.72 0 5.00e+00 4.00e-02 8.67e+00 dihedral pdb=" CA VAL C 49 " pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta harmonic sigma weight residual 180.00 165.32 14.68 0 5.00e+00 4.00e-02 8.62e+00 dihedral pdb=" CA VAL D 49 " pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta harmonic sigma weight residual 180.00 165.33 14.67 0 5.00e+00 4.00e-02 8.60e+00 ... (remaining 1437 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.037: 208 0.037 - 0.072: 140 0.072 - 0.108: 63 0.108 - 0.144: 27 0.144 - 0.180: 6 Chirality restraints: 444 Sorted by residual: chirality pdb=" CA THR F 72 " pdb=" N THR F 72 " pdb=" C THR F 72 " pdb=" CB THR F 72 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CA THR C 72 " pdb=" N THR C 72 " pdb=" C THR C 72 " pdb=" CB THR C 72 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA THR A 72 " pdb=" N THR A 72 " pdb=" C THR A 72 " pdb=" CB THR A 72 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 441 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 94 " 0.014 2.00e-02 2.50e+03 1.01e-02 1.79e+00 pdb=" CG PHE A 94 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 94 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 94 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " 0.013 2.00e-02 2.50e+03 9.94e-03 1.73e+00 pdb=" CG PHE C 94 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " 0.013 2.00e-02 2.50e+03 9.93e-03 1.72e+00 pdb=" CG PHE E 94 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE E 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE E 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " 0.003 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 1499 3.03 - 3.50: 2171 3.50 - 3.97: 3296 3.97 - 4.43: 3729 4.43 - 4.90: 6432 Nonbonded interactions: 17127 Sorted by model distance: nonbonded pdb=" OG1 THR C 44 " pdb=" N LYS C 45 " model vdw 2.567 3.120 nonbonded pdb=" OG1 THR D 44 " pdb=" N LYS D 45 " model vdw 2.567 3.120 nonbonded pdb=" OG1 THR F 44 " pdb=" N LYS F 45 " model vdw 2.567 3.120 nonbonded pdb=" OG1 THR A 44 " pdb=" N LYS A 45 " model vdw 2.568 3.120 nonbonded pdb=" OG1 THR E 44 " pdb=" N LYS E 45 " model vdw 2.568 3.120 ... (remaining 17122 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.230 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.810 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:5.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.007 0.030 2496 Z= 0.339 Angle : 0.781 4.148 3378 Z= 0.465 Chirality : 0.060 0.180 444 Planarity : 0.003 0.010 420 Dihedral : 12.908 78.231 828 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.64 % Favored : 81.36 % Rotamer: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.86 (0.28), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.46 (0.21), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR B 39 PHE 0.022 0.007 PHE A 94 HIS 0.003 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00709 ( 2496) covalent geometry : angle 0.78058 ( 3378) *********************** 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 67 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.072 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.3270 time to fit residues: 22.4641 Evaluate side-chains 57 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.0570 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.7502 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.171452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.154154 restraints weight = 3273.416| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.42 r_work: 0.4017 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2496 Z= 0.134 Angle : 0.574 4.978 3378 Z= 0.322 Chirality : 0.056 0.187 444 Planarity : 0.002 0.007 420 Dihedral : 4.756 14.904 366 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 5.69 % Allowed : 22.36 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.16 (0.28), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.21), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR B 39 PHE 0.009 0.002 PHE D 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 2496) covalent geometry : angle 0.57435 ( 3378) *********************** 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 77 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.093 Fit side-chains REVERT: B 83 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: E 43 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8549 (ttpt) REVERT: E 61 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: D 61 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6833 (mt-10) outliers start: 14 outliers final: 4 residues processed: 66 average time/residue: 0.4318 time to fit residues: 29.1832 Evaluate side-chains 66 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.0470 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN C 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.169788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.152574 restraints weight = 3284.373| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.44 r_work: 0.4010 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2496 Z= 0.143 Angle : 0.560 5.067 3378 Z= 0.317 Chirality : 0.056 0.194 444 Planarity : 0.002 0.008 420 Dihedral : 4.598 13.262 366 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % Rotamer: Outliers : 6.91 % Allowed : 24.80 % Favored : 68.29 % 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 are not related in a simple way. whole: -4.73 (0.30), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.23), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR C 39 PHE 0.010 0.003 PHE F 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 2496) covalent geometry : angle 0.56039 ( 3378) *********************** 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 80 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.093 Fit side-chains REVERT: A 83 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: B 61 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6354 (mt-10) REVERT: B 83 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: C 61 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6329 (mt-10) REVERT: D 61 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6899 (mt-10) outliers start: 17 outliers final: 8 residues processed: 66 average time/residue: 0.4687 time to fit residues: 31.6867 Evaluate side-chains 73 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 5 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.165531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.148486 restraints weight = 3339.074| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.42 r_work: 0.3959 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2496 Z= 0.205 Angle : 0.635 5.945 3378 Z= 0.361 Chirality : 0.058 0.220 444 Planarity : 0.002 0.008 420 Dihedral : 5.212 13.431 366 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.95 % Favored : 83.05 % Rotamer: Outliers : 8.13 % Allowed : 26.02 % Favored : 65.85 % 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 are not related in a simple way. whole: -4.65 (0.30), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.23), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR B 39 PHE 0.015 0.004 PHE D 94 HIS 0.003 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 2496) covalent geometry : angle 0.63475 ( 3378) *********************** 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 83 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.148 Fit side-chains REVERT: A 83 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: B 61 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6493 (mt-10) REVERT: B 83 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: C 61 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6551 (mt-10) REVERT: D 61 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6974 (mt-10) REVERT: D 83 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7550 (mt-10) outliers start: 20 outliers final: 9 residues processed: 73 average time/residue: 0.4443 time to fit residues: 33.2769 Evaluate side-chains 73 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.0170 chunk 17 optimal weight: 4.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.172034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.155106 restraints weight = 3267.181| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.42 r_work: 0.4055 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2496 Z= 0.124 Angle : 0.538 4.791 3378 Z= 0.302 Chirality : 0.055 0.180 444 Planarity : 0.001 0.006 420 Dihedral : 4.280 14.090 366 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Rotamer: Outliers : 6.91 % Allowed : 27.24 % Favored : 65.85 % 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 are not related in a simple way. whole: -4.18 (0.31), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.24), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR F 39 PHE 0.007 0.002 PHE C 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2496) covalent geometry : angle 0.53814 ( 3378) *********************** 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 81 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.096 Fit side-chains REVERT: B 61 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6307 (mt-10) REVERT: C 61 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6248 (mt-10) outliers start: 17 outliers final: 8 residues processed: 69 average time/residue: 0.4399 time to fit residues: 31.1058 Evaluate side-chains 69 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.159267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.142394 restraints weight = 3299.191| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.38 r_work: 0.3894 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 2496 Z= 0.350 Angle : 0.807 7.043 3378 Z= 0.456 Chirality : 0.065 0.269 444 Planarity : 0.003 0.012 420 Dihedral : 6.077 15.039 366 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.85 % Allowed : 18.64 % Favored : 80.51 % Rotamer: Outliers : 9.35 % Allowed : 25.61 % Favored : 65.04 % 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 are not related in a simple way. whole: -4.63 (0.31), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.24), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR B 39 PHE 0.026 0.007 PHE F 94 HIS 0.006 0.003 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00753 ( 2496) covalent geometry : angle 0.80684 ( 3378) *********************** 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 84 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.089 Fit side-chains REVERT: A 83 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: B 61 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6664 (mt-10) REVERT: C 61 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6840 (mt-10) REVERT: D 83 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7627 (mt-10) outliers start: 23 outliers final: 9 residues processed: 68 average time/residue: 0.4639 time to fit residues: 32.3173 Evaluate side-chains 72 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 83 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.0670 chunk 1 optimal weight: 0.7980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.168137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.151226 restraints weight = 3241.387| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.37 r_work: 0.4011 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2496 Z= 0.157 Angle : 0.604 5.165 3378 Z= 0.335 Chirality : 0.057 0.199 444 Planarity : 0.002 0.007 420 Dihedral : 4.854 14.414 366 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer: Outliers : 5.69 % Allowed : 29.27 % Favored : 65.04 % 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 are not related in a simple way. whole: -4.25 (0.32), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR F 39 PHE 0.010 0.003 PHE F 94 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2496) covalent geometry : angle 0.60419 ( 3378) *********************** 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 74 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.085 Fit side-chains REVERT: A 83 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: B 61 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6376 (mt-10) REVERT: C 61 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6367 (mt-10) outliers start: 14 outliers final: 5 residues processed: 66 average time/residue: 0.4058 time to fit residues: 27.5202 Evaluate side-chains 67 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.0010 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.171739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.154853 restraints weight = 3285.123| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.40 r_work: 0.4052 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2496 Z= 0.124 Angle : 0.545 4.821 3378 Z= 0.300 Chirality : 0.055 0.197 444 Planarity : 0.001 0.008 420 Dihedral : 4.159 13.954 366 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer: Outliers : 3.66 % Allowed : 32.52 % Favored : 63.82 % 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 are not related in a simple way. whole: -3.83 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR B 39 PHE 0.008 0.002 PHE E 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 2496) covalent geometry : angle 0.54514 ( 3378) *********************** 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 68 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.064 Fit side-chains REVERT: B 61 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6333 (mt-10) REVERT: C 61 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6224 (mt-10) REVERT: F 62 GLN cc_start: 0.8087 (tp-100) cc_final: 0.6904 (tp40) outliers start: 9 outliers final: 5 residues processed: 63 average time/residue: 0.4758 time to fit residues: 30.6876 Evaluate side-chains 65 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 44 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.162628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.146031 restraints weight = 3338.587| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.37 r_work: 0.3929 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 2496 Z= 0.274 Angle : 0.718 6.498 3378 Z= 0.403 Chirality : 0.062 0.247 444 Planarity : 0.003 0.011 420 Dihedral : 5.583 13.738 366 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.80 % Favored : 82.20 % Rotamer: Outliers : 5.69 % Allowed : 30.08 % Favored : 64.23 % 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 are not related in a simple way. whole: -4.23 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR F 39 PHE 0.020 0.005 PHE F 94 HIS 0.005 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 2496) covalent geometry : angle 0.71786 ( 3378) *********************** 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 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.088 Fit side-chains REVERT: A 83 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: B 61 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6694 (mt-10) REVERT: C 61 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6626 (mt-10) outliers start: 14 outliers final: 8 residues processed: 67 average time/residue: 0.4438 time to fit residues: 30.4664 Evaluate side-chains 70 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.0020 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.0010 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.169573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.152678 restraints weight = 3333.962| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.41 r_work: 0.4026 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2496 Z= 0.144 Angle : 0.578 5.052 3378 Z= 0.322 Chirality : 0.056 0.201 444 Planarity : 0.002 0.009 420 Dihedral : 4.586 14.615 366 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 3.66 % Allowed : 31.30 % Favored : 65.04 % 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 are not related in a simple way. whole: -3.90 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR C 39 PHE 0.009 0.002 PHE F 94 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2496) covalent geometry : angle 0.57770 ( 3378) ********************** 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 67 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.074 Fit side-chains REVERT: B 61 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6412 (mt-10) REVERT: C 61 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6287 (mt-10) outliers start: 9 outliers final: 5 residues processed: 62 average time/residue: 0.4334 time to fit residues: 27.6052 Evaluate side-chains 64 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN F 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.170625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.153755 restraints weight = 3321.416| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.41 r_work: 0.4041 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2496 Z= 0.133 Angle : 0.554 5.148 3378 Z= 0.308 Chirality : 0.056 0.205 444 Planarity : 0.002 0.009 420 Dihedral : 4.338 13.591 366 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 4.07 % Allowed : 31.30 % Favored : 64.63 % 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 are not related in a simple way. whole: -3.71 (0.34), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.26), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.001 TYR B 39 PHE 0.008 0.002 PHE D 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2496) covalent geometry : angle 0.55396 ( 3378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1088.74 seconds wall clock time: 19 minutes 29.90 seconds (1169.90 seconds total)