Starting phenix.real_space_refine on Mon Feb 10 21:16:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yng_33961/02_2025/7yng_33961.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yng_33961/02_2025/7yng_33961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yng_33961/02_2025/7yng_33961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yng_33961/02_2025/7yng_33961.map" model { file = "/net/cci-nas-00/data/ceres_data/7yng_33961/02_2025/7yng_33961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yng_33961/02_2025/7yng_33961.cif" } resolution = 3.1 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 1644 2.51 5 N 456 2.21 5 O 528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2628 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.49, per 1000 atoms: 0.57 Number of scatterers: 2628 At special positions: 0 Unit cell: (115.54, 102.82, 31.8, 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 528 8.00 N 456 7.00 C 1644 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: 0.62 Conformation dependent library (CDL) restraints added in 352.1 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 50.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41 removed outlier: 6.491A pdb=" N VAL A 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 58 removed outlier: 8.372A pdb=" N GLU A 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL B 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N GLU B 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL F 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N HIS F 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 66 removed outlier: 6.350A pdb=" N GLN A 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ASN F 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR A 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.478A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 82 removed outlier: 6.841A pdb=" N VAL A 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 78 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLN A 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS B 80 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 82 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 74 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL F 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA A 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N GLN F 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ALA A 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR F 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LYS A 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 89 through 92 removed outlier: 6.707A pdb=" N ALA A 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR F 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA A 91 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.490A pdb=" N VAL C 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 45 through 58 removed outlier: 6.840A pdb=" N VAL D 48 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS D 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY C 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N GLU C 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL E 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N VAL C 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N GLY E 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N HIS C 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ALA E 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL C 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL E 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR C 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLU E 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA C 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 66 removed outlier: 6.354A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASN D 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR C 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.478A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 74 through 82 removed outlier: 6.283A pdb=" N VAL C 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL D 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N GLN D 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ALA C 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR D 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LYS C 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL C 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA E 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLN C 79 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS E 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL E 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 89 through 92 removed outlier: 6.708A pdb=" N ALA C 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR D 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA C 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.55 Time building geometry restraints manager: 0.73 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: 462 1.29 - 1.35: 408 1.35 - 1.42: 108 1.42 - 1.48: 450 1.48 - 1.55: 1212 Bond restraints: 2640 Sorted by residual: bond pdb=" CA SER D 87 " pdb=" C SER D 87 " ideal model delta sigma weight residual 1.528 1.509 0.019 1.35e-02 5.49e+03 2.00e+00 bond pdb=" CA SER A 87 " pdb=" C SER A 87 " ideal model delta sigma weight residual 1.528 1.509 0.019 1.35e-02 5.49e+03 2.00e+00 bond pdb=" CA SER F 87 " pdb=" C SER F 87 " ideal model delta sigma weight residual 1.528 1.509 0.019 1.35e-02 5.49e+03 1.91e+00 bond pdb=" CA SER E 87 " pdb=" C SER E 87 " ideal model delta sigma weight residual 1.528 1.509 0.019 1.35e-02 5.49e+03 1.89e+00 bond pdb=" CA SER B 87 " pdb=" C SER B 87 " ideal model delta sigma weight residual 1.528 1.510 0.018 1.35e-02 5.49e+03 1.83e+00 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 2914 0.91 - 1.82: 472 1.82 - 2.73: 130 2.73 - 3.64: 36 3.64 - 4.55: 18 Bond angle restraints: 3570 Sorted by residual: angle pdb=" C THR A 92 " pdb=" N GLY A 93 " pdb=" CA GLY A 93 " ideal model delta sigma weight residual 119.99 123.07 -3.08 1.13e+00 7.83e-01 7.42e+00 angle pdb=" C THR B 92 " pdb=" N GLY B 93 " pdb=" CA GLY B 93 " ideal model delta sigma weight residual 119.99 123.05 -3.06 1.13e+00 7.83e-01 7.34e+00 angle pdb=" C THR D 92 " pdb=" N GLY D 93 " pdb=" CA GLY D 93 " ideal model delta sigma weight residual 119.99 123.05 -3.06 1.13e+00 7.83e-01 7.33e+00 angle pdb=" C THR C 92 " pdb=" N GLY C 93 " pdb=" CA GLY C 93 " ideal model delta sigma weight residual 119.99 123.04 -3.05 1.13e+00 7.83e-01 7.31e+00 angle pdb=" C THR F 92 " pdb=" N GLY F 93 " pdb=" CA GLY F 93 " ideal model delta sigma weight residual 119.99 123.04 -3.05 1.13e+00 7.83e-01 7.28e+00 ... (remaining 3565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 1368 14.86 - 29.73: 138 29.73 - 44.59: 36 44.59 - 59.46: 0 59.46 - 74.32: 6 Dihedral angle restraints: 1548 sinusoidal: 522 harmonic: 1026 Sorted by residual: dihedral pdb=" CA GLY F 93 " pdb=" C GLY F 93 " pdb=" N PHE F 94 " pdb=" CA PHE F 94 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY A 93 " pdb=" C GLY A 93 " pdb=" N PHE A 94 " pdb=" CA PHE A 94 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY D 93 " pdb=" C GLY D 93 " pdb=" N PHE D 94 " pdb=" CA PHE D 94 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 156 0.025 - 0.050: 144 0.050 - 0.075: 68 0.075 - 0.100: 59 0.100 - 0.125: 41 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA VAL C 95 " pdb=" N VAL C 95 " pdb=" C VAL C 95 " pdb=" CB VAL C 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL E 95 " pdb=" N VAL E 95 " pdb=" C VAL E 95 " pdb=" CB VAL E 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 465 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 83 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C GLU F 83 " -0.017 2.00e-02 2.50e+03 pdb=" O GLU F 83 " 0.007 2.00e-02 2.50e+03 pdb=" N GLY F 84 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 83 " 0.005 2.00e-02 2.50e+03 1.00e-02 1.01e+00 pdb=" C GLU B 83 " -0.017 2.00e-02 2.50e+03 pdb=" O GLU B 83 " 0.007 2.00e-02 2.50e+03 pdb=" N GLY B 84 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 83 " -0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C GLU C 83 " 0.017 2.00e-02 2.50e+03 pdb=" O GLU C 83 " -0.007 2.00e-02 2.50e+03 pdb=" N GLY C 84 " -0.006 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 156 2.73 - 3.28: 2535 3.28 - 3.82: 4208 3.82 - 4.36: 4429 4.36 - 4.90: 9232 Nonbonded interactions: 20560 Sorted by model distance: nonbonded pdb=" NZ LYS B 60 " pdb=" OE1 GLN B 62 " model vdw 2.192 3.120 nonbonded pdb=" NZ LYS E 60 " pdb=" OE1 GLN E 62 " model vdw 2.192 3.120 nonbonded pdb=" NZ LYS A 60 " pdb=" OE1 GLN A 62 " model vdw 2.192 3.120 nonbonded pdb=" NZ LYS F 60 " pdb=" OE1 GLN F 62 " model vdw 2.192 3.120 nonbonded pdb=" NZ LYS C 60 " pdb=" OE1 GLN C 62 " model vdw 2.193 3.120 ... (remaining 20555 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.460 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 : 0.009 0.042 2640 Z= 0.627 Angle : 0.851 4.552 3570 Z= 0.495 Chirality : 0.057 0.125 468 Planarity : 0.003 0.010 444 Dihedral : 13.706 74.320 900 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.31), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS D 50 PHE 0.011 0.004 PHE D 94 TYR 0.003 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.303 Fit side-chains REVERT: A 45 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8261 (mttt) REVERT: F 45 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8415 (mttm) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2877 time to fit residues: 8.1865 Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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: 0.1980 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.231832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.196690 restraints weight = 2584.440| |-----------------------------------------------------------------------------| r_work (start): 0.4651 rms_B_bonded: 2.73 r_work: 0.4541 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2640 Z= 0.139 Angle : 0.470 4.163 3570 Z= 0.257 Chirality : 0.052 0.131 468 Planarity : 0.002 0.010 444 Dihedral : 4.485 14.411 378 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % 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: -3.06 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.005 0.001 PHE F 94 TYR 0.004 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.273 Fit side-chains REVERT: B 79 GLN cc_start: 0.8770 (tt0) cc_final: 0.8569 (tt0) REVERT: F 45 LYS cc_start: 0.8555 (mtpp) cc_final: 0.8259 (mttm) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2587 time to fit residues: 8.2789 Evaluate side-chains 26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.0970 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 0.0040 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.0060 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.4210 ------------------------------------------------------------------------------- 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 = 0.4958 r_free = 0.4958 target = 0.227342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.190768 restraints weight = 2567.384| |-----------------------------------------------------------------------------| r_work (start): 0.4578 rms_B_bonded: 2.77 r_work: 0.4469 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2640 Z= 0.204 Angle : 0.450 3.376 3570 Z= 0.251 Chirality : 0.051 0.123 468 Planarity : 0.002 0.009 444 Dihedral : 4.367 13.060 378 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.37 % Allowed : 10.00 % Favored : 89.63 % 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: -2.65 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.007 0.002 PHE F 94 TYR 0.008 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.289 Fit side-chains REVERT: F 45 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8224 (mttt) outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.2560 time to fit residues: 7.1112 Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4965 r_free = 0.4965 target = 0.228191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.191281 restraints weight = 2597.092| |-----------------------------------------------------------------------------| r_work (start): 0.4618 rms_B_bonded: 2.87 r_work: 0.4503 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2640 Z= 0.162 Angle : 0.416 3.273 3570 Z= 0.231 Chirality : 0.051 0.124 468 Planarity : 0.002 0.008 444 Dihedral : 4.057 11.367 378 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.37 % Allowed : 9.63 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.007 0.002 PHE F 94 TYR 0.006 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.289 Fit side-chains REVERT: F 45 LYS cc_start: 0.8515 (mtpp) cc_final: 0.8290 (mttt) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.2268 time to fit residues: 6.6762 Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.4877 r_free = 0.4877 target = 0.220279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.183188 restraints weight = 2618.485| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 2.83 r_work: 0.4414 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2640 Z= 0.285 Angle : 0.504 5.138 3570 Z= 0.280 Chirality : 0.052 0.125 468 Planarity : 0.002 0.020 444 Dihedral : 4.497 12.598 378 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.008 0.002 PHE F 94 TYR 0.010 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.258 Fit side-chains REVERT: F 45 LYS cc_start: 0.8540 (mtpp) cc_final: 0.8310 (mttt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2148 time to fit residues: 5.1281 Evaluate side-chains 17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4887 r_free = 0.4887 target = 0.220818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.184685 restraints weight = 2631.661| |-----------------------------------------------------------------------------| r_work (start): 0.4555 rms_B_bonded: 2.71 r_work: 0.4443 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.4303 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2640 Z= 0.232 Angle : 0.462 4.733 3570 Z= 0.256 Chirality : 0.051 0.128 468 Planarity : 0.002 0.014 444 Dihedral : 4.323 12.500 378 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.003 HIS A 50 PHE 0.007 0.002 PHE F 94 TYR 0.009 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.289 Fit side-chains REVERT: F 45 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8339 (mttt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1930 time to fit residues: 4.5194 Evaluate side-chains 19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4980 r_free = 0.4980 target = 0.229105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.193152 restraints weight = 2646.573| |-----------------------------------------------------------------------------| r_work (start): 0.4639 rms_B_bonded: 2.73 r_work: 0.4528 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2640 Z= 0.127 Angle : 0.392 4.811 3570 Z= 0.217 Chirality : 0.050 0.125 468 Planarity : 0.001 0.010 444 Dihedral : 3.714 10.678 378 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.37 % Allowed : 12.22 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.005 0.002 PHE F 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.282 Fit side-chains REVERT: F 45 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8211 (mttt) outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.2190 time to fit residues: 6.1087 Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.0970 chunk 30 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.2780 ------------------------------------------------------------------------------- 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 = 0.4946 r_free = 0.4946 target = 0.225829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.189760 restraints weight = 2572.906| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 2.71 r_work: 0.4486 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.4351 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2640 Z= 0.180 Angle : 0.417 4.693 3570 Z= 0.231 Chirality : 0.050 0.125 468 Planarity : 0.002 0.008 444 Dihedral : 3.864 10.770 378 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % 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: -2.12 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.006 0.002 PHE F 94 TYR 0.007 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.274 Fit side-chains REVERT: F 45 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8287 (mttt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2077 time to fit residues: 4.8379 Evaluate side-chains 19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4963 r_free = 0.4963 target = 0.227452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.191314 restraints weight = 2572.368| |-----------------------------------------------------------------------------| r_work (start): 0.4632 rms_B_bonded: 2.73 r_work: 0.4526 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.4392 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2640 Z= 0.136 Angle : 0.397 4.679 3570 Z= 0.219 Chirality : 0.050 0.125 468 Planarity : 0.001 0.007 444 Dihedral : 3.653 10.215 378 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.37 % Allowed : 13.70 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.006 0.002 PHE D 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.262 Fit side-chains REVERT: F 45 LYS cc_start: 0.8486 (mtpp) cc_final: 0.8263 (mttt) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.1820 time to fit residues: 4.2918 Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 9.9990 chunk 18 optimal weight: 0.0000 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.4893 r_free = 0.4893 target = 0.220823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.184400 restraints weight = 2592.866| |-----------------------------------------------------------------------------| r_work (start): 0.4544 rms_B_bonded: 2.72 r_work: 0.4435 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.4299 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2640 Z= 0.252 Angle : 0.463 4.922 3570 Z= 0.256 Chirality : 0.051 0.125 468 Planarity : 0.002 0.006 444 Dihedral : 4.121 11.503 378 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.37 % Allowed : 13.70 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.007 0.002 PHE C 94 TYR 0.009 0.002 TYR E 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.270 Fit side-chains REVERT: F 45 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8325 (mttt) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.2066 time to fit residues: 5.0837 Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4928 r_free = 0.4928 target = 0.223761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.187741 restraints weight = 2591.611| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 2.70 r_work: 0.4459 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.4322 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2640 Z= 0.209 Angle : 0.440 4.917 3570 Z= 0.243 Chirality : 0.050 0.127 468 Planarity : 0.002 0.006 444 Dihedral : 4.053 11.734 378 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.37 % Allowed : 13.70 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.006 0.002 PHE C 94 TYR 0.008 0.002 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.15 seconds wall clock time: 32 minutes 0.92 seconds (1920.92 seconds total)