Starting phenix.real_space_refine on Mon Feb 10 20:50:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v47_31702/02_2025/7v47_31702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v47_31702/02_2025/7v47_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_31702/02_2025/7v47_31702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v47_31702/02_2025/7v47_31702.map" model { file = "/net/cci-nas-00/data/ceres_data/7v47_31702/02_2025/7v47_31702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v47_31702/02_2025/7v47_31702.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, E, D, F Time building chain proxies: 1.88, per 1000 atoms: 0.76 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: 0.49 Conformation dependent library (CDL) restraints added in 291.6 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: 0.29 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: 0.07 Time building geometry restraints manager: 0.60 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: 0.06 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: 1.630 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.730 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:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.770 ------------------------------------------------------------------------------- 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 (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: -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 HIS 0.003 0.002 HIS A 50 PHE 0.022 0.007 PHE A 94 TYR 0.006 0.002 TYR B 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 67 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.278 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.9257 time to fit residues: 63.7441 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 : 0.317 ------------------------------------------------------------------------------- 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: 3.9990 chunk 27 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.168315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.151086 restraints weight = 3237.570| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.40 r_work: 0.3974 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2496 Z= 0.170 Angle : 0.619 5.570 3378 Z= 0.349 Chirality : 0.058 0.205 444 Planarity : 0.002 0.008 420 Dihedral : 5.161 14.908 366 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.38 % Favored : 83.62 % 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 (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: -5.28 (0.28), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.22), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 50 PHE 0.012 0.003 PHE D 94 TYR 0.014 0.002 TYR B 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 75 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.299 Fit side-chains REVERT: B 61 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6402 (mt-10) REVERT: B 83 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7701 (mt-10) REVERT: E 43 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8545 (ttpt) REVERT: E 61 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.7004 (mt-10) REVERT: D 61 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6890 (mt-10) outliers start: 14 outliers final: 3 residues processed: 65 average time/residue: 1.0040 time to fit residues: 66.9684 Evaluate side-chains 65 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 21 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- 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 = 0.4244 r_free = 0.4244 target = 0.166056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.148909 restraints weight = 3256.072| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.41 r_work: 0.3952 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2496 Z= 0.192 Angle : 0.626 5.869 3378 Z= 0.356 Chirality : 0.058 0.215 444 Planarity : 0.002 0.009 420 Dihedral : 5.195 14.073 366 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.25 % Favored : 84.75 % Rotamer: Outliers : 7.32 % Allowed : 23.58 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.30), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.23), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.014 0.004 PHE D 94 TYR 0.008 0.002 TYR C 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 81 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.247 Fit side-chains REVERT: A 83 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: B 61 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6597 (mt-10) REVERT: B 83 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: C 61 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6539 (mt-10) REVERT: D 61 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6975 (mt-10) REVERT: F 83 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7517 (mt-10) outliers start: 18 outliers final: 8 residues processed: 70 average time/residue: 1.0235 time to fit residues: 73.5361 Evaluate side-chains 73 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 F residue 83 GLU 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 10 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 0.0020 chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 overall best weight: 1.4992 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.166038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.149091 restraints weight = 3242.406| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.39 r_work: 0.3970 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2496 Z= 0.200 Angle : 0.635 5.829 3378 Z= 0.361 Chirality : 0.058 0.217 444 Planarity : 0.002 0.009 420 Dihedral : 5.229 14.361 366 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.25 % Favored : 84.75 % Rotamer: Outliers : 9.76 % Allowed : 23.17 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.31), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.23), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS F 50 PHE 0.014 0.004 PHE F 94 TYR 0.006 0.001 TYR D 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 87 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.212 Fit side-chains REVERT: A 83 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: B 61 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6598 (mt-10) REVERT: B 83 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: C 61 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6543 (mt-10) REVERT: E 43 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8456 (ttpt) REVERT: D 61 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: D 83 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: F 83 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7567 (mt-10) outliers start: 24 outliers final: 11 residues processed: 74 average time/residue: 0.9714 time to fit residues: 73.7316 Evaluate side-chains 80 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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 42 SER 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 E residue 43 LYS 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 54 THR Chi-restraints excluded: chain F residue 83 GLU 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 20 optimal weight: 7.9990 chunk 5 optimal weight: 0.0670 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.170284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.153309 restraints weight = 3237.255| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.39 r_work: 0.4031 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2496 Z= 0.141 Angle : 0.563 4.993 3378 Z= 0.316 Chirality : 0.056 0.193 444 Planarity : 0.002 0.008 420 Dihedral : 4.553 14.543 366 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 6.10 % Allowed : 28.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.32), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.24), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.008 0.002 PHE F 94 TYR 0.014 0.001 TYR C 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 81 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.258 Fit side-chains REVERT: C 61 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6324 (mt-10) REVERT: E 43 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8389 (ttpt) REVERT: D 61 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6775 (mt-10) outliers start: 15 outliers final: 6 residues processed: 69 average time/residue: 0.9489 time to fit residues: 67.3487 Evaluate side-chains 70 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 54 THR 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 E residue 43 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.170175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.153238 restraints weight = 3253.083| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.39 r_work: 0.4032 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2055 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= 0.141 Angle : 0.564 5.127 3378 Z= 0.314 Chirality : 0.056 0.197 444 Planarity : 0.002 0.007 420 Dihedral : 4.496 13.672 366 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.56 % Favored : 86.44 % Rotamer: Outliers : 7.32 % Allowed : 28.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.009 0.002 PHE F 94 TYR 0.016 0.002 TYR B 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 80 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.279 Fit side-chains REVERT: A 83 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: B 61 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6491 (mt-10) REVERT: C 61 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6339 (mt-10) REVERT: C 83 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: E 43 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8407 (ttpt) REVERT: D 61 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6770 (mt-10) outliers start: 18 outliers final: 9 residues processed: 66 average time/residue: 1.0601 time to fit residues: 71.6886 Evaluate side-chains 75 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 A residue 88 ILE Chi-restraints excluded: chain B residue 38 LEU 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 83 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.166626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.149691 restraints weight = 3382.640| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.41 r_work: 0.3989 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2496 Z= 0.190 Angle : 0.621 5.813 3378 Z= 0.349 Chirality : 0.057 0.218 444 Planarity : 0.002 0.008 420 Dihedral : 5.020 13.534 366 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.97 % Favored : 85.03 % Rotamer: Outliers : 7.32 % Allowed : 27.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS F 50 PHE 0.013 0.004 PHE F 94 TYR 0.015 0.002 TYR C 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 79 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.266 Fit side-chains REVERT: A 83 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: C 61 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6526 (mt-10) REVERT: E 43 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8440 (ttpt) REVERT: D 61 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6898 (mt-10) REVERT: D 83 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7431 (mt-10) outliers start: 18 outliers final: 10 residues processed: 69 average time/residue: 0.9288 time to fit residues: 65.9467 Evaluate side-chains 75 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 42 SER 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 C residue 82 VAL Chi-restraints excluded: chain E residue 43 LYS 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 F residue 82 VAL Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.174684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.157735 restraints weight = 3272.099| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.42 r_work: 0.4082 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2496 Z= 0.113 Angle : 0.534 4.944 3378 Z= 0.295 Chirality : 0.055 0.179 444 Planarity : 0.001 0.008 420 Dihedral : 4.001 14.156 366 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 5.28 % Allowed : 30.08 % 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 (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: -3.63 (0.34), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.26), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.005 0.001 PHE F 94 TYR 0.019 0.001 TYR B 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 73 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.278 Fit side-chains REVERT: C 61 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6098 (mt-10) REVERT: E 43 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8402 (ttpt) REVERT: D 83 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7379 (mt-10) outliers start: 13 outliers final: 7 residues processed: 65 average time/residue: 0.8933 time to fit residues: 59.7974 Evaluate side-chains 66 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 42 SER 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 E residue 43 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 17 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 = 0.4220 r_free = 0.4220 target = 0.162813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.146321 restraints weight = 3288.604| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.33 r_work: 0.3935 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 2496 Z= 0.263 Angle : 0.702 6.371 3378 Z= 0.392 Chirality : 0.061 0.240 444 Planarity : 0.003 0.010 420 Dihedral : 5.503 14.136 366 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.51 % Favored : 82.49 % Rotamer: Outliers : 6.50 % Allowed : 29.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 50 PHE 0.019 0.005 PHE F 94 TYR 0.014 0.003 TYR C 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 79 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.273 Fit side-chains REVERT: A 83 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: C 61 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6625 (mt-10) REVERT: C 83 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7402 (tt0) REVERT: E 43 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8577 (ttpt) REVERT: D 83 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7816 (mt-10) outliers start: 16 outliers final: 8 residues processed: 68 average time/residue: 0.9254 time to fit residues: 64.7939 Evaluate side-chains 73 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 42 SER 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 E residue 43 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain F residue 82 VAL 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: 3.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.163828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.147152 restraints weight = 3293.855| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.37 r_work: 0.3960 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 2496 Z= 0.260 Angle : 0.716 6.477 3378 Z= 0.400 Chirality : 0.061 0.240 444 Planarity : 0.003 0.011 420 Dihedral : 5.576 13.552 366 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.25 % Favored : 84.75 % Rotamer: Outliers : 6.10 % Allowed : 29.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 50 PHE 0.019 0.005 PHE F 94 TYR 0.009 0.002 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 75 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.238 Fit side-chains REVERT: C 61 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6579 (mt-10) REVERT: E 38 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8023 (tp) REVERT: E 43 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8477 (ttpt) REVERT: D 83 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7575 (mt-10) outliers start: 15 outliers final: 10 residues processed: 66 average time/residue: 0.8865 time to fit residues: 60.1910 Evaluate side-chains 73 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 44 THR 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 C residue 88 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain F residue 82 VAL 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 35 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN E 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.162248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.145627 restraints weight = 3341.304| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.38 r_work: 0.3945 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1933 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= 0.272 Angle : 0.737 6.818 3378 Z= 0.413 Chirality : 0.062 0.251 444 Planarity : 0.003 0.011 420 Dihedral : 5.789 13.653 366 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.51 % Favored : 82.49 % Rotamer: Outliers : 6.10 % Allowed : 29.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.020 0.006 PHE F 94 TYR 0.009 0.002 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2174.76 seconds wall clock time: 38 minutes 57.64 seconds (2337.64 seconds total)