Starting phenix.real_space_refine on Fri Dec 27 05:04:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v47_31702/12_2024/7v47_31702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v47_31702/12_2024/7v47_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_31702/12_2024/7v47_31702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v47_31702/12_2024/7v47_31702.map" model { file = "/net/cci-nas-00/data/ceres_data/7v47_31702/12_2024/7v47_31702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v47_31702/12_2024/7v47_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-5532/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: 1.98, per 1000 atoms: 0.80 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: 0.63 Conformation dependent library (CDL) restraints added in 365.7 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: 0.27 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: 0.13 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 432 1.29 - 1.35: 396 1.35 - 1.42: 96 1.42 - 1.48: 421 1.48 - 1.55: 1151 Bond restraints: 2496 Sorted by residual: bond pdb=" N THR D 72 " pdb=" CA THR D 72 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 2.04e+00 bond pdb=" N THR B 72 " pdb=" CA THR B 72 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.94e+00 bond pdb=" N THR E 72 " pdb=" CA THR E 72 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.91e+00 bond pdb=" N THR F 72 " pdb=" CA THR F 72 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.91e+00 bond pdb=" N THR A 72 " pdb=" CA THR A 72 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.90e+00 ... (remaining 2491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 2690 0.83 - 1.66: 569 1.66 - 2.49: 66 2.49 - 3.32: 35 3.32 - 4.15: 18 Bond angle restraints: 3378 Sorted by residual: angle pdb=" CA THR A 72 " pdb=" CB THR A 72 " pdb=" CG2 THR A 72 " ideal model delta sigma weight residual 110.50 114.45 -3.95 1.70e+00 3.46e-01 5.41e+00 angle pdb=" CA THR B 72 " pdb=" CB THR B 72 " pdb=" CG2 THR B 72 " ideal model delta sigma weight residual 110.50 114.42 -3.92 1.70e+00 3.46e-01 5.31e+00 angle pdb=" CA THR D 72 " pdb=" CB THR D 72 " pdb=" CG2 THR D 72 " ideal model delta sigma weight residual 110.50 114.41 -3.91 1.70e+00 3.46e-01 5.28e+00 angle pdb=" CA THR E 72 " pdb=" CB THR E 72 " pdb=" CG2 THR E 72 " ideal model delta sigma weight residual 110.50 114.40 -3.90 1.70e+00 3.46e-01 5.26e+00 angle pdb=" CA THR F 72 " pdb=" CB THR F 72 " pdb=" CG2 THR F 72 " ideal model delta sigma weight residual 110.50 114.39 -3.89 1.70e+00 3.46e-01 5.24e+00 ... (remaining 3373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 1302 15.65 - 31.29: 126 31.29 - 46.94: 6 46.94 - 62.58: 0 62.58 - 78.23: 6 Dihedral angle restraints: 1440 sinusoidal: 462 harmonic: 978 Sorted by residual: dihedral pdb=" CA VAL E 49 " pdb=" C VAL E 49 " pdb=" N HIS E 50 " pdb=" CA HIS E 50 " ideal model delta harmonic sigma weight residual 180.00 165.28 14.72 0 5.00e+00 4.00e-02 8.67e+00 dihedral pdb=" CA VAL C 49 " pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta harmonic sigma weight residual 180.00 165.32 14.68 0 5.00e+00 4.00e-02 8.62e+00 dihedral pdb=" CA VAL D 49 " pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta harmonic sigma weight residual 180.00 165.33 14.67 0 5.00e+00 4.00e-02 8.60e+00 ... (remaining 1437 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.037: 208 0.037 - 0.072: 140 0.072 - 0.108: 63 0.108 - 0.144: 27 0.144 - 0.180: 6 Chirality restraints: 444 Sorted by residual: chirality pdb=" CA THR F 72 " pdb=" N THR F 72 " pdb=" C THR F 72 " pdb=" CB THR F 72 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CA THR C 72 " pdb=" N THR C 72 " pdb=" C THR C 72 " pdb=" CB THR C 72 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA THR A 72 " pdb=" N THR A 72 " pdb=" C THR A 72 " pdb=" CB THR A 72 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 441 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 94 " 0.014 2.00e-02 2.50e+03 1.01e-02 1.79e+00 pdb=" CG PHE A 94 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 94 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 94 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " 0.013 2.00e-02 2.50e+03 9.94e-03 1.73e+00 pdb=" CG PHE C 94 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " 0.013 2.00e-02 2.50e+03 9.93e-03 1.72e+00 pdb=" CG PHE E 94 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE E 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE E 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " 0.003 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 1499 3.03 - 3.50: 2171 3.50 - 3.97: 3296 3.97 - 4.43: 3729 4.43 - 4.90: 6432 Nonbonded interactions: 17127 Sorted by model distance: nonbonded pdb=" OG1 THR C 44 " pdb=" N LYS C 45 " model vdw 2.567 3.120 nonbonded pdb=" OG1 THR D 44 " pdb=" N LYS D 45 " model vdw 2.567 3.120 nonbonded pdb=" OG1 THR F 44 " pdb=" N LYS F 45 " model vdw 2.567 3.120 nonbonded pdb=" OG1 THR A 44 " pdb=" N LYS A 45 " model vdw 2.568 3.120 nonbonded pdb=" OG1 THR E 44 " pdb=" N LYS E 45 " model vdw 2.568 3.120 ... (remaining 17122 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 10.950 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 26.000 ------------------------------------------------------------------------------- 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 : 0.275 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.9418 time to fit residues: 64.8540 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 : 0.246 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 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 : 0.283 Fit side-chains REVERT: B 61 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6276 (mt-10) REVERT: B 83 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7524 (mt-10) REVERT: E 43 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8188 (ttpt) REVERT: E 61 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6830 (mt-10) REVERT: D 61 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6631 (mt-10) outliers start: 14 outliers final: 3 residues processed: 65 average time/residue: 1.0087 time to fit residues: 67.3167 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 : 0.281 ------------------------------------------------------------------------------- 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 18 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1451 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 5.756 3378 Z= 0.351 Chirality : 0.058 0.212 444 Planarity : 0.002 0.009 420 Dihedral : 5.118 14.126 366 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % Rotamer: Outliers : 7.72 % Allowed : 22.76 % 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 0.014 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 83 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.282 Fit side-chains REVERT: A 83 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: B 61 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6411 (mt-10) REVERT: B 83 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: C 61 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6365 (mt-10) REVERT: D 61 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6618 (mt-10) REVERT: F 83 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7284 (mt-10) outliers start: 19 outliers final: 9 residues processed: 71 average time/residue: 0.9905 time to fit residues: 72.1577 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 : 0.253 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.0670 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2496 Z= 0.130 Angle : 0.552 4.821 3378 Z= 0.310 Chirality : 0.055 0.186 444 Planarity : 0.001 0.008 420 Dihedral : 4.449 14.722 366 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Rotamer: Outliers : 6.50 % Allowed : 28.05 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.39 (0.31), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (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 0.003 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 81 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.261 Fit side-chains REVERT: C 61 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6150 (mt-10) REVERT: D 61 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6485 (mt-10) outliers start: 16 outliers final: 8 residues processed: 70 average time/residue: 0.9302 time to fit residues: 66.9055 Evaluate side-chains 71 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1634 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= 0.270 Angle : 0.708 6.565 3378 Z= 0.400 Chirality : 0.061 0.244 444 Planarity : 0.003 0.009 420 Dihedral : 5.634 13.544 366 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.08 % Favored : 81.92 % Rotamer: Outliers : 7.72 % Allowed : 26.83 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.58 (0.31), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.24), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.019 0.005 PHE F 94 TYR 0.014 0.002 TYR B 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: 19 poor density : 61 time to evaluate : 0.260 Fit side-chains REVERT: A 83 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: C 61 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6500 (mt-10) REVERT: D 83 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: F 83 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7342 (mt-10) outliers start: 19 outliers final: 8 residues processed: 66 average time/residue: 1.0006 time to fit residues: 67.7634 Evaluate side-chains 70 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 81 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain F residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.0030 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.4028 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2189 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= 0.118 Angle : 0.549 4.657 3378 Z= 0.304 Chirality : 0.055 0.176 444 Planarity : 0.001 0.008 420 Dihedral : 4.189 15.012 366 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 5.69 % Allowed : 28.86 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.01 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.007 0.002 PHE F 94 TYR 0.014 0.001 TYR C 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 77 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.258 Fit side-chains REVERT: C 61 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6137 (mt-10) REVERT: D 83 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7047 (mt-10) outliers start: 14 outliers final: 4 residues processed: 67 average time/residue: 0.9417 time to fit residues: 64.8186 Evaluate side-chains 65 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 82 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 2496 Z= 0.322 Angle : 0.773 6.820 3378 Z= 0.435 Chirality : 0.063 0.248 444 Planarity : 0.003 0.011 420 Dihedral : 5.866 14.239 366 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.56 % Allowed : 18.64 % Favored : 80.79 % Rotamer: Outliers : 8.13 % Allowed : 26.42 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.46 (0.32), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 50 PHE 0.024 0.007 PHE F 94 TYR 0.014 0.003 TYR B 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: 20 poor density : 59 time to evaluate : 0.278 Fit side-chains REVERT: A 83 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: C 61 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6589 (mt-10) REVERT: D 83 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7212 (mt-10) outliers start: 20 outliers final: 11 residues processed: 65 average time/residue: 1.0177 time to fit residues: 67.8931 Evaluate side-chains 72 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 B residue 44 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.0050 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.0270 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.4452 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2235 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= 0.125 Angle : 0.565 4.773 3378 Z= 0.312 Chirality : 0.055 0.176 444 Planarity : 0.001 0.008 420 Dihedral : 4.410 15.324 366 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 4.07 % Allowed : 30.89 % 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: -3.90 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.007 0.002 PHE F 94 TYR 0.020 0.001 TYR C 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: 10 poor density : 63 time to evaluate : 0.278 Fit side-chains REVERT: A 83 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: C 61 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6162 (mt-10) REVERT: D 83 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7210 (mt-10) outliers start: 10 outliers final: 5 residues processed: 66 average time/residue: 0.9538 time to fit residues: 64.7265 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 : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 83 GLU 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 29 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 0.0000 chunk 28 optimal weight: 2.9990 overall best weight: 1.4390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2003 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= 0.197 Angle : 0.626 5.816 3378 Z= 0.349 Chirality : 0.058 0.225 444 Planarity : 0.002 0.010 420 Dihedral : 4.993 13.722 366 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.82 % Favored : 84.18 % Rotamer: Outliers : 5.69 % Allowed : 30.08 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.05 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 50 PHE 0.013 0.004 PHE F 94 TYR 0.016 0.002 TYR B 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 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.259 Fit side-chains REVERT: A 83 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: C 61 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6406 (mt-10) REVERT: D 83 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7330 (mt-10) outliers start: 14 outliers final: 8 residues processed: 64 average time/residue: 0.9007 time to fit residues: 59.2846 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 : 0.321 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain 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 22 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2186 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= 0.148 Angle : 0.589 5.303 3378 Z= 0.325 Chirality : 0.056 0.205 444 Planarity : 0.002 0.009 420 Dihedral : 4.542 14.463 366 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % 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: -3.80 (0.34), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (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 0.018 0.002 TYR C 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 72 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.342 Fit side-chains REVERT: A 83 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: C 61 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6201 (mt-10) REVERT: D 61 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.5981 (mp0) REVERT: D 83 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7241 (mt-10) outliers start: 12 outliers final: 6 residues processed: 61 average time/residue: 0.9762 time to fit residues: 61.1646 Evaluate side-chains 69 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 44 THR 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 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 3 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 0.0570 chunk 1 optimal weight: 0.3980 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.4100 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.166950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.150115 restraints weight = 3273.557| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.40 r_work: 0.3994 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2496 Z= 0.195 Angle : 0.632 5.987 3378 Z= 0.352 Chirality : 0.058 0.229 444 Planarity : 0.002 0.010 420 Dihedral : 5.041 13.766 366 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.10 % Favored : 83.90 % Rotamer: Outliers : 5.28 % Allowed : 30.89 % 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: -3.92 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 50 PHE 0.014 0.004 PHE D 94 TYR 0.016 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1701.14 seconds wall clock time: 31 minutes 10.31 seconds (1870.31 seconds total)