Starting phenix.real_space_refine on Wed Mar 5 16:21:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwd_38733/03_2025/8xwd_38733.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwd_38733/03_2025/8xwd_38733.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/8xwd_38733/03_2025/8xwd_38733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwd_38733/03_2025/8xwd_38733.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwd_38733/03_2025/8xwd_38733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwd_38733/03_2025/8xwd_38733.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 1686 2.51 5 N 426 2.21 5 O 558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2670 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "D" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "E" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "A" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "F" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "B" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 412 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KDH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.86, per 1000 atoms: 1.07 Number of scatterers: 2670 At special positions: 0 Unit cell: (97.11, 98.77, 31.54, 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 558 8.00 N 426 7.00 C 1686 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: 0.78 Conformation dependent library (CDL) restraints added in 347.0 milliseconds 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 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 8 sheets defined 0.0% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 46 through 56 removed outlier: 6.858A pdb=" N GLY C 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL E 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA C 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR E 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA E 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLY C 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N HIS F 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N VAL C 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N VAL F 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY C 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR F 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA F 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL C 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 69 through 71 removed outlier: 6.532A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 77 removed outlier: 8.643A pdb=" N THR C 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL F 77 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 80 through 82 removed outlier: 6.499A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 56 removed outlier: 6.831A pdb=" N VAL D 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N HIS D 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY A 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU D 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N VAL B 49 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL D 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLY B 51 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N HIS D 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ALA B 53 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL D 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N VAL B 55 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N THR D 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.538A pdb=" N VAL D 70 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 77 removed outlier: 8.656A pdb=" N THR D 75 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 80 through 82 removed outlier: 6.516A pdb=" N LYS D 80 " --> pdb=" O THR A 81 " (cutoff:3.500A) 20 hydrogen bonds defined for protein. 60 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: 0.53 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.27: 432 1.27 - 1.34: 384 1.34 - 1.41: 270 1.41 - 1.48: 444 1.48 - 1.55: 1170 Bond restraints: 2700 Sorted by residual: bond pdb=" CB VAL D 40 " pdb=" CG1 VAL D 40 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 bond pdb=" CB VAL A 40 " pdb=" CG1 VAL A 40 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 bond pdb=" CB VAL F 40 " pdb=" CG1 VAL F 40 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CB VAL E 40 " pdb=" CG1 VAL E 40 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.80e+00 bond pdb=" CB VAL B 40 " pdb=" CG1 VAL B 40 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.80e+00 ... (remaining 2695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 2879 0.94 - 1.89: 524 1.89 - 2.83: 179 2.83 - 3.77: 71 3.77 - 4.71: 37 Bond angle restraints: 3690 Sorted by residual: angle pdb=" N GLY D 73 " pdb=" CA GLY D 73 " pdb=" C GLY D 73 " ideal model delta sigma weight residual 114.10 118.21 -4.11 1.51e+00 4.39e-01 7.42e+00 angle pdb=" N GLY C 73 " pdb=" CA GLY C 73 " pdb=" C GLY C 73 " ideal model delta sigma weight residual 114.10 118.21 -4.11 1.51e+00 4.39e-01 7.40e+00 angle pdb=" N GLY B 73 " pdb=" CA GLY B 73 " pdb=" C GLY B 73 " ideal model delta sigma weight residual 114.10 118.20 -4.10 1.51e+00 4.39e-01 7.39e+00 angle pdb=" N GLY E 73 " pdb=" CA GLY E 73 " pdb=" C GLY E 73 " ideal model delta sigma weight residual 114.10 118.20 -4.10 1.51e+00 4.39e-01 7.38e+00 angle pdb=" N GLY A 73 " pdb=" CA GLY A 73 " pdb=" C GLY A 73 " ideal model delta sigma weight residual 114.10 118.18 -4.08 1.51e+00 4.39e-01 7.31e+00 ... (remaining 3685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.89: 1476 25.89 - 51.77: 60 51.77 - 77.66: 6 77.66 - 103.54: 0 103.54 - 129.43: 6 Dihedral angle restraints: 1548 sinusoidal: 576 harmonic: 972 Sorted by residual: dihedral pdb=" C33 KDH D 501 " pdb=" C36 KDH D 501 " pdb=" O35 KDH D 501 " pdb=" C38 KDH D 501 " ideal model delta sinusoidal sigma weight residual 166.64 -63.93 -129.43 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C33 KDH A 501 " pdb=" C36 KDH A 501 " pdb=" O35 KDH A 501 " pdb=" C38 KDH A 501 " ideal model delta sinusoidal sigma weight residual 166.64 -64.00 -129.36 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C33 KDH B 501 " pdb=" C36 KDH B 501 " pdb=" O35 KDH B 501 " pdb=" C38 KDH B 501 " ideal model delta sinusoidal sigma weight residual 166.64 -64.02 -129.34 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 203 0.037 - 0.074: 139 0.074 - 0.111: 74 0.111 - 0.148: 34 0.148 - 0.185: 12 Chirality restraints: 462 Sorted by residual: chirality pdb=" CB VAL D 40 " pdb=" CA VAL D 40 " pdb=" CG1 VAL D 40 " pdb=" CG2 VAL D 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CB VAL F 40 " pdb=" CA VAL F 40 " pdb=" CG1 VAL F 40 " pdb=" CG2 VAL F 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CB VAL C 40 " pdb=" CA VAL C 40 " pdb=" CG1 VAL C 40 " pdb=" CG2 VAL C 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 459 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " 0.012 2.00e-02 2.50e+03 1.05e-02 1.64e+00 pdb=" CG HIS B 50 " -0.022 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.012 2.00e-02 2.50e+03 1.03e-02 1.60e+00 pdb=" CG HIS A 50 " -0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " -0.012 2.00e-02 2.50e+03 1.03e-02 1.58e+00 pdb=" CG HIS F 50 " 0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " -0.005 2.00e-02 2.50e+03 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 493 2.76 - 3.29: 2485 3.29 - 3.83: 3858 3.83 - 4.36: 4344 4.36 - 4.90: 9687 Nonbonded interactions: 20867 Sorted by model distance: nonbonded pdb=" NE2 GLN C 79 " pdb=" O GLY E 86 " model vdw 2.222 3.120 nonbonded pdb=" O GLY D 86 " pdb=" NE2 GLN B 79 " model vdw 2.228 3.120 nonbonded pdb=" O GLY C 86 " pdb=" NE2 GLN F 79 " model vdw 2.229 3.120 nonbonded pdb=" NE2 GLN D 79 " pdb=" O GLY A 86 " model vdw 2.237 3.120 nonbonded pdb=" C4 KDH C 501 " pdb=" O37 KDH F 501 " model vdw 2.425 3.340 ... (remaining 20862 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: 0.03 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.400 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 : 0.010 0.056 2700 Z= 0.627 Angle : 1.016 4.713 3690 Z= 0.530 Chirality : 0.066 0.185 462 Planarity : 0.003 0.010 438 Dihedral : 17.290 129.429 936 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.41 % Favored : 77.59 % Rotamer: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % 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: -4.55 (0.39), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS B 50 PHE 0.008 0.003 PHE E 94 TYR 0.017 0.004 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.284 Fit side-chains REVERT: C 43 LYS cc_start: 0.7848 (ptpp) cc_final: 0.7591 (ptpp) REVERT: E 43 LYS cc_start: 0.8258 (ptpp) cc_final: 0.7936 (ptpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2023 time to fit residues: 7.0562 Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.138173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.099193 restraints weight = 3146.941| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.12 r_work: 0.3428 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2700 Z= 0.139 Angle : 0.653 4.994 3690 Z= 0.339 Chirality : 0.058 0.159 462 Planarity : 0.002 0.006 438 Dihedral : 15.586 86.818 468 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 2.38 % Allowed : 7.94 % Favored : 89.68 % 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: -3.28 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.008 0.002 PHE D 94 TYR 0.007 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.281 Fit side-chains REVERT: B 46 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8220 (mt-10) outliers start: 6 outliers final: 6 residues processed: 26 average time/residue: 0.2108 time to fit residues: 6.4989 Evaluate side-chains 25 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.125981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085351 restraints weight = 3429.411| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.37 r_work: 0.3240 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2700 Z= 0.164 Angle : 0.548 3.774 3690 Z= 0.297 Chirality : 0.054 0.137 462 Planarity : 0.002 0.007 438 Dihedral : 13.763 87.868 468 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 3.57 % Allowed : 7.54 % Favored : 88.89 % 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: -2.74 (0.46), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.007 0.001 PHE D 94 TYR 0.005 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.267 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 30 average time/residue: 0.1798 time to fit residues: 6.4761 Evaluate side-chains 31 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.129843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.090611 restraints weight = 3257.053| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.16 r_work: 0.3270 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2700 Z= 0.405 Angle : 0.675 4.051 3690 Z= 0.372 Chirality : 0.056 0.137 462 Planarity : 0.002 0.009 438 Dihedral : 14.140 82.596 468 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.66 % Favored : 85.34 % Rotamer: Outliers : 6.35 % Allowed : 4.76 % Favored : 88.89 % 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: -2.76 (0.45), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS D 50 PHE 0.010 0.003 PHE D 94 TYR 0.004 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 26 time to evaluate : 0.257 Fit side-chains REVERT: C 43 LYS cc_start: 0.7503 (ptpp) cc_final: 0.7141 (ptpp) REVERT: E 43 LYS cc_start: 0.7967 (ptpp) cc_final: 0.7678 (ptpp) outliers start: 16 outliers final: 16 residues processed: 38 average time/residue: 0.1769 time to fit residues: 7.9065 Evaluate side-chains 41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.126493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.086385 restraints weight = 3428.082| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.38 r_work: 0.3261 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2700 Z= 0.140 Angle : 0.517 3.831 3690 Z= 0.282 Chirality : 0.053 0.129 462 Planarity : 0.001 0.006 438 Dihedral : 13.010 80.284 468 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 3.57 % Allowed : 8.73 % Favored : 87.70 % 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: -2.24 (0.47), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.007 0.001 PHE D 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.288 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 29 average time/residue: 0.1933 time to fit residues: 6.7108 Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.0270 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.9242 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.127018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.087632 restraints weight = 3508.215| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.48 r_work: 0.3276 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2700 Z= 0.124 Angle : 0.471 3.494 3690 Z= 0.261 Chirality : 0.052 0.127 462 Planarity : 0.001 0.006 438 Dihedral : 12.337 77.568 468 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Rotamer: Outliers : 3.97 % Allowed : 8.33 % Favored : 87.70 % 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: -1.96 (0.48), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 50 PHE 0.005 0.001 PHE D 94 TYR 0.004 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.278 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 27 average time/residue: 0.1777 time to fit residues: 5.7788 Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.0000 chunk 27 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.123059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.082506 restraints weight = 3506.672| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.48 r_work: 0.3377 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2700 Z= 0.199 Angle : 0.507 3.512 3690 Z= 0.283 Chirality : 0.052 0.130 462 Planarity : 0.002 0.008 438 Dihedral : 12.308 76.088 468 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 5.95 % Allowed : 6.35 % Favored : 87.70 % 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: -1.85 (0.48), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS E 50 PHE 0.008 0.002 PHE D 94 TYR 0.004 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.288 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 30 average time/residue: 0.1690 time to fit residues: 6.2209 Evaluate side-chains 33 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.123471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.083251 restraints weight = 3410.006| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.45 r_work: 0.3395 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2700 Z= 0.184 Angle : 0.500 3.703 3690 Z= 0.279 Chirality : 0.052 0.130 462 Planarity : 0.002 0.008 438 Dihedral : 12.144 74.788 468 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 5.95 % Allowed : 6.35 % Favored : 87.70 % 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: -1.82 (0.48), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS E 50 PHE 0.008 0.002 PHE D 94 TYR 0.004 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 21 time to evaluate : 0.275 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 33 average time/residue: 0.1597 time to fit residues: 6.4106 Evaluate side-chains 36 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 21 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.129495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.087944 restraints weight = 3288.722| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.52 r_work: 0.3166 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2700 Z= 0.351 Angle : 0.601 3.893 3690 Z= 0.337 Chirality : 0.053 0.135 462 Planarity : 0.002 0.009 438 Dihedral : 12.508 74.687 468 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.23 % Favored : 84.77 % Rotamer: Outliers : 6.35 % Allowed : 6.35 % Favored : 87.30 % 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: -2.03 (0.47), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS D 50 PHE 0.012 0.003 PHE D 94 TYR 0.003 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 21 time to evaluate : 0.256 Fit side-chains outliers start: 16 outliers final: 16 residues processed: 34 average time/residue: 0.1574 time to fit residues: 6.5236 Evaluate side-chains 37 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 21 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.133652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.089249 restraints weight = 3134.558| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.64 r_work: 0.3292 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2700 Z= 0.144 Angle : 0.486 3.861 3690 Z= 0.270 Chirality : 0.052 0.131 462 Planarity : 0.001 0.006 438 Dihedral : 12.002 74.573 468 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 4.76 % Allowed : 7.94 % Favored : 87.30 % 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: -1.83 (0.48), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 50 PHE 0.006 0.001 PHE D 94 TYR 0.005 0.001 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 20 time to evaluate : 0.263 Fit side-chains REVERT: B 46 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8406 (mt-10) outliers start: 12 outliers final: 12 residues processed: 30 average time/residue: 0.1679 time to fit residues: 6.0922 Evaluate side-chains 32 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 20 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 chunk 35 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.131895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.090588 restraints weight = 3221.704| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.52 r_work: 0.3220 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2700 Z= 0.236 Angle : 0.526 3.782 3690 Z= 0.294 Chirality : 0.052 0.130 462 Planarity : 0.002 0.008 438 Dihedral : 12.132 74.406 468 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.66 % Favored : 85.34 % Rotamer: Outliers : 6.35 % Allowed : 6.75 % Favored : 86.90 % 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: -1.86 (0.48), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS E 50 PHE 0.009 0.002 PHE D 94 TYR 0.003 0.001 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2285.13 seconds wall clock time: 40 minutes 0.73 seconds (2400.73 seconds total)