Starting phenix.real_space_refine on Wed Mar 5 15:46:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v47_31702/03_2025/7v47_31702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v47_31702/03_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_31702/03_2025/7v47_31702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v47_31702/03_2025/7v47_31702.map" model { file = "/net/cci-nas-00/data/ceres_data/7v47_31702/03_2025/7v47_31702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v47_31702/03_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-5624/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: 1.64, per 1000 atoms: 0.66 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: 0.60 Conformation dependent library (CDL) restraints added in 340.8 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: 0.28 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: 0.08 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.470 Find NCS groups from input model: 0.050 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:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- 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 : 0.287 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.9169 time to fit residues: 63.1645 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 : 0.259 ------------------------------------------------------------------------------- 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 : 0.302 Fit side-chains REVERT: B 61 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6403 (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: 0.8544 (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: 0.6891 (mt-10) outliers start: 14 outliers final: 3 residues processed: 65 average time/residue: 1.0241 time to fit residues: 68.4182 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 : 0.290 ------------------------------------------------------------------------------- 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: 4.9990 chunk 2 optimal weight: 0.0870 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.166708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.149679 restraints weight = 3246.076| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.38 r_work: 0.3962 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2496 Z= 0.184 Angle : 0.617 5.792 3378 Z= 0.350 Chirality : 0.058 0.212 444 Planarity : 0.002 0.009 420 Dihedral : 5.117 14.140 366 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % Rotamer: Outliers : 7.32 % Allowed : 23.17 % Favored : 69.51 % 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: -4.87 (0.30), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.23), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.013 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 82 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.286 Fit side-chains REVERT: A 83 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: B 61 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6573 (mt-10) REVERT: B 83 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: C 61 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6498 (mt-10) REVERT: D 61 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6871 (mt-10) outliers start: 18 outliers final: 9 residues processed: 70 average time/residue: 1.0260 time to fit residues: 73.6808 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 : 0.293 ------------------------------------------------------------------------------- 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 C residue 88 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 61 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: 3.9990 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.161801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.144995 restraints weight = 3270.477| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.36 r_work: 0.3914 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2496 Z= 0.285 Angle : 0.740 6.965 3378 Z= 0.421 Chirality : 0.062 0.249 444 Planarity : 0.003 0.011 420 Dihedral : 5.859 13.760 366 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.08 % Favored : 81.92 % Rotamer: Outliers : 9.35 % Allowed : 23.98 % Favored : 66.67 % 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: -4.83 (0.31), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.24), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 50 PHE 0.021 0.006 PHE F 94 TYR 0.008 0.002 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 84 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.239 Fit side-chains REVERT: A 83 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: B 61 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: B 83 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: C 61 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6659 (mt-10) REVERT: D 61 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: D 83 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7757 (mt-10) outliers start: 23 outliers final: 8 residues processed: 72 average time/residue: 1.0125 time to fit residues: 74.7525 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 : 0.281 ------------------------------------------------------------------------------- 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 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 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 54 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 0.0020 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.168673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.151824 restraints weight = 3273.965| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.38 r_work: 0.4009 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1790 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= 0.154 Angle : 0.594 5.065 3378 Z= 0.332 Chirality : 0.057 0.194 444 Planarity : 0.002 0.008 420 Dihedral : 4.898 15.072 366 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.15 % Favored : 87.85 % Rotamer: Outliers : 6.50 % Allowed : 27.64 % 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 (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: -4.49 (0.31), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.24), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.010 0.003 PHE E 94 TYR 0.013 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 80 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.286 Fit side-chains REVERT: A 83 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: B 83 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: C 61 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6359 (mt-10) outliers start: 16 outliers final: 8 residues processed: 69 average time/residue: 1.0086 time to fit residues: 71.4817 Evaluate side-chains 72 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 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 1 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.170389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.153614 restraints weight = 3259.501| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.38 r_work: 0.4042 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2496 Z= 0.138 Angle : 0.566 5.132 3378 Z= 0.315 Chirality : 0.056 0.197 444 Planarity : 0.002 0.009 420 Dihedral : 4.503 14.014 366 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 7.72 % Allowed : 27.64 % 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: -4.17 (0.32), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (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 0.017 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 82 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.285 Fit side-chains REVERT: B 61 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6496 (mt-10) REVERT: C 61 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6336 (mt-10) REVERT: D 61 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6765 (mt-10) outliers start: 19 outliers final: 8 residues processed: 68 average time/residue: 0.9873 time to fit residues: 68.9237 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 : 0.285 ------------------------------------------------------------------------------- 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 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 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: 0.1980 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 11 optimal weight: 0.4980 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 0.0060 chunk 27 optimal weight: 4.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.175556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.158397 restraints weight = 3283.384| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.45 r_work: 0.4098 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2447 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= 0.110 Angle : 0.528 4.869 3378 Z= 0.290 Chirality : 0.054 0.178 444 Planarity : 0.001 0.008 420 Dihedral : 3.911 14.032 366 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % 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: -3.66 (0.34), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.26), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.005 0.001 PHE F 94 TYR 0.018 0.001 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 73 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.295 Fit side-chains REVERT: C 61 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6205 (mt-10) REVERT: D 83 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: F 62 GLN cc_start: 0.8106 (tp-100) cc_final: 0.6850 (tp40) outliers start: 13 outliers final: 6 residues processed: 63 average time/residue: 0.9871 time to fit residues: 63.9194 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 : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR 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 83 GLU Chi-restraints excluded: chain F residue 54 THR 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: 3.9990 chunk 24 optimal weight: 0.0370 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 35 optimal weight: 0.0970 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4373 r_free = 0.4373 target = 0.176453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.159447 restraints weight = 3248.184| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.43 r_work: 0.4109 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2496 Z= 0.106 Angle : 0.511 4.961 3378 Z= 0.280 Chirality : 0.054 0.173 444 Planarity : 0.001 0.008 420 Dihedral : 3.695 12.524 366 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer: Outliers : 4.47 % Allowed : 30.89 % 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: -3.39 (0.35), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.006 0.001 PHE D 94 TYR 0.018 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 68 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.293 Fit side-chains REVERT: B 61 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6419 (mt-10) REVERT: C 61 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6110 (mt-10) REVERT: D 83 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: F 62 GLN cc_start: 0.8056 (tp-100) cc_final: 0.6774 (tp40) outliers start: 11 outliers final: 6 residues processed: 60 average time/residue: 1.1117 time to fit residues: 68.3799 Evaluate side-chains 66 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 D residue 83 GLU Chi-restraints excluded: chain F residue 54 THR 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: 0.0270 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: 1.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.163472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.146675 restraints weight = 3293.423| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.38 r_work: 0.3949 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1987 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= 0.268 Angle : 0.709 6.452 3378 Z= 0.397 Chirality : 0.061 0.238 444 Planarity : 0.003 0.011 420 Dihedral : 5.507 14.594 366 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.51 % Favored : 82.49 % Rotamer: Outliers : 4.47 % Allowed : 31.30 % 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: -3.98 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.020 0.005 PHE F 94 TYR 0.015 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 74 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.310 Fit side-chains REVERT: C 61 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6575 (mt-10) REVERT: D 83 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7570 (mt-10) outliers start: 11 outliers final: 6 residues processed: 66 average time/residue: 0.9226 time to fit residues: 62.6658 Evaluate side-chains 69 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 42 SER 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 83 GLU 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 28 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.170315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.153273 restraints weight = 3278.025| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.43 r_work: 0.4039 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2266 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= 0.140 Angle : 0.576 4.969 3378 Z= 0.320 Chirality : 0.056 0.193 444 Planarity : 0.002 0.009 420 Dihedral : 4.494 14.023 366 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.15 % Favored : 87.85 % Rotamer: Outliers : 3.66 % Allowed : 32.11 % 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: -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 0.010 0.002 PHE F 94 TYR 0.004 0.001 TYR D 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 68 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.284 Fit side-chains REVERT: C 61 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6303 (mt-10) REVERT: D 83 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7476 (mt-10) outliers start: 9 outliers final: 5 residues processed: 62 average time/residue: 1.0002 time to fit residues: 63.6954 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 : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain C residue 42 SER 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 83 GLU 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: 5.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.0670 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.167585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.150807 restraints weight = 3327.585| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.40 r_work: 0.4001 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2496 Z= 0.187 Angle : 0.620 5.803 3378 Z= 0.345 Chirality : 0.058 0.222 444 Planarity : 0.002 0.009 420 Dihedral : 4.919 13.402 366 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % Rotamer: Outliers : 4.88 % Allowed : 31.30 % 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: -3.77 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.25), 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 0.015 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2297.65 seconds wall clock time: 39 minutes 55.06 seconds (2395.06 seconds total)