Starting phenix.real_space_refine on Wed Sep 17 03:24:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e9x_47820/09_2025/9e9x_47820.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e9x_47820/09_2025/9e9x_47820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e9x_47820/09_2025/9e9x_47820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e9x_47820/09_2025/9e9x_47820.map" model { file = "/net/cci-nas-00/data/ceres_data/9e9x_47820/09_2025/9e9x_47820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e9x_47820/09_2025/9e9x_47820.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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 1953 2.51 5 N 547 2.21 5 O 643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3143 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 583 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 86} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "B" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 583 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 86} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "C" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 583 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 86} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "E" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "F" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.20, per 1000 atoms: 0.38 Number of scatterers: 3143 At special positions: 0 Unit cell: (123.6, 82.4, 37.08, 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 643 8.00 N 547 7.00 C 1953 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: 0.29 Conformation dependent library (CDL) restraints added in 92.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 800 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.520A pdb=" N VAL A 26 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 34 removed outlier: 7.011A pdb=" N THR A 33 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR B 33 " --> pdb=" O LYS C 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.435A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.343A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 90 removed outlier: 8.869A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ILE B 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 94 through 96 Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 65 Processing sheet with id=AB1, first strand: chain 'D' and resid 39 through 42 removed outlier: 7.160A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR E 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N SER F 42 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY E 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 55 removed outlier: 6.777A pdb=" N GLU E 46 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY D 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL E 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA D 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR E 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL D 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU F 46 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY E 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL F 52 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA E 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 60 through 63 Processing sheet with id=AB4, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.356A pdb=" N VAL E 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 75 through 82 removed outlier: 6.372A pdb=" N ALA E 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLN F 79 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA E 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N THR F 81 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS E 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 95 through 96 40 hydrogen bonds defined for protein. 117 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: 0.48 Time building geometry restraints manager: 0.37 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: 571 1.29 - 1.36: 502 1.36 - 1.43: 110 1.43 - 1.50: 574 1.50 - 1.57: 1395 Bond restraints: 3152 Sorted by residual: bond pdb=" CB VAL B 66 " pdb=" CG2 VAL B 66 " ideal model delta sigma weight residual 1.521 1.569 -0.048 3.30e-02 9.18e+02 2.13e+00 bond pdb=" CA THR C 72 " pdb=" C THR C 72 " ideal model delta sigma weight residual 1.525 1.545 -0.020 1.40e-02 5.10e+03 1.94e+00 bond pdb=" CB GLU B 83 " pdb=" CG GLU B 83 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.82e+00 bond pdb=" C ALA B 30 " pdb=" N GLY B 31 " ideal model delta sigma weight residual 1.331 1.322 0.009 6.60e-03 2.30e+04 1.72e+00 bond pdb=" CA THR A 72 " pdb=" C THR A 72 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.61e-02 3.86e+03 1.72e+00 ... (remaining 3147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 3981 1.61 - 3.22: 236 3.22 - 4.84: 32 4.84 - 6.45: 12 6.45 - 8.06: 9 Bond angle restraints: 4270 Sorted by residual: angle pdb=" CA TYR D 39 " pdb=" CB TYR D 39 " pdb=" CG TYR D 39 " ideal model delta sigma weight residual 113.90 121.03 -7.13 1.80e+00 3.09e-01 1.57e+01 angle pdb=" CA TYR F 39 " pdb=" CB TYR F 39 " pdb=" CG TYR F 39 " ideal model delta sigma weight residual 113.90 120.97 -7.07 1.80e+00 3.09e-01 1.54e+01 angle pdb=" OG1 THR C 72 " pdb=" CB THR C 72 " pdb=" CG2 THR C 72 " ideal model delta sigma weight residual 109.30 101.94 7.36 2.00e+00 2.50e-01 1.35e+01 angle pdb=" OG1 THR A 72 " pdb=" CB THR A 72 " pdb=" CG2 THR A 72 " ideal model delta sigma weight residual 109.30 101.95 7.35 2.00e+00 2.50e-01 1.35e+01 angle pdb=" CA GLU B 83 " pdb=" CB GLU B 83 " pdb=" CG GLU B 83 " ideal model delta sigma weight residual 114.10 121.10 -7.00 2.00e+00 2.50e-01 1.23e+01 ... (remaining 4265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 1608 16.84 - 33.68: 173 33.68 - 50.51: 42 50.51 - 67.35: 16 67.35 - 84.19: 3 Dihedral angle restraints: 1842 sinusoidal: 579 harmonic: 1263 Sorted by residual: dihedral pdb=" CA THR C 44 " pdb=" C THR C 44 " pdb=" N LYS C 45 " pdb=" CA LYS C 45 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA ALA C 29 " pdb=" C ALA C 29 " pdb=" N ALA C 30 " pdb=" CA ALA C 30 " ideal model delta harmonic sigma weight residual -180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA HIS C 50 " pdb=" C HIS C 50 " pdb=" N GLY C 51 " pdb=" CA GLY C 51 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 1839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 488 0.105 - 0.209: 71 0.209 - 0.314: 1 0.314 - 0.418: 1 0.418 - 0.523: 1 Chirality restraints: 562 Sorted by residual: chirality pdb=" CB VAL B 66 " pdb=" CA VAL B 66 " pdb=" CG1 VAL B 66 " pdb=" CG2 VAL B 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.83e+00 chirality pdb=" CB VAL C 66 " pdb=" CA VAL C 66 " pdb=" CG1 VAL C 66 " pdb=" CG2 VAL C 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB ILE C 88 " pdb=" CA ILE C 88 " pdb=" CG1 ILE C 88 " pdb=" CG2 ILE C 88 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 559 not shown) Planarity restraints: 541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 83 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" CD GLU A 83 " -0.057 2.00e-02 2.50e+03 pdb=" OE1 GLU A 83 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU A 83 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " -0.021 2.00e-02 2.50e+03 1.84e-02 5.95e+00 pdb=" CG PHE E 94 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE E 94 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE E 94 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE E 94 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 72 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C THR A 72 " 0.041 2.00e-02 2.50e+03 pdb=" O THR A 72 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 73 " -0.013 2.00e-02 2.50e+03 ... (remaining 538 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 839 2.81 - 3.34: 2643 3.34 - 3.86: 5205 3.86 - 4.38: 5614 4.38 - 4.90: 10423 Nonbonded interactions: 24724 Sorted by model distance: nonbonded pdb=" OG1 THR E 54 " pdb=" CG2 VAL E 74 " model vdw 2.294 3.460 nonbonded pdb=" OE2 GLU D 61 " pdb=" OG1 THR D 72 " model vdw 2.334 3.040 nonbonded pdb=" N ILE E 88 " pdb=" O ILE E 88 " model vdw 2.626 2.496 nonbonded pdb=" N THR C 75 " pdb=" OG1 THR C 75 " model vdw 2.633 2.496 nonbonded pdb=" O GLY B 25 " pdb=" CG2 VAL B 26 " model vdw 2.641 3.460 ... (remaining 24719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' } 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.750 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 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 : 0.005 0.048 3152 Z= 0.234 Angle : 0.938 8.059 4270 Z= 0.541 Chirality : 0.069 0.523 562 Planarity : 0.004 0.033 541 Dihedral : 16.563 84.188 1042 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 24.33 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.29 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.005 TYR D 39 PHE 0.043 0.005 PHE E 94 HIS 0.009 0.004 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 3152) covalent geometry : angle 0.93780 ( 4270) hydrogen bonds : bond 0.14231 ( 40) hydrogen bonds : angle 8.82930 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.123 Fit side-chains REVERT: A 83 GLU cc_start: 0.6565 (pm20) cc_final: 0.5641 (mm-30) REVERT: B 83 GLU cc_start: 0.7292 (tm-30) cc_final: 0.7036 (tm-30) REVERT: C 83 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7399 (tt0) REVERT: D 58 LYS cc_start: 0.8517 (mmtp) cc_final: 0.7187 (pttp) REVERT: E 62 GLN cc_start: 0.7087 (mt0) cc_final: 0.6863 (mt0) REVERT: F 43 LYS cc_start: 0.7552 (mttt) cc_final: 0.7230 (mtpt) REVERT: F 58 LYS cc_start: 0.7857 (ptmt) cc_final: 0.7496 (mmpt) REVERT: F 83 GLU cc_start: 0.5020 (tp30) cc_final: 0.4405 (pt0) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0519 time to fit residues: 3.7128 Evaluate side-chains 44 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN E 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.199849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.166007 restraints weight = 3457.882| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 1.76 r_work: 0.4326 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4233 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3152 Z= 0.110 Angle : 0.529 4.232 4270 Z= 0.305 Chirality : 0.052 0.201 562 Planarity : 0.002 0.009 541 Dihedral : 5.465 20.004 463 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.00 % Allowed : 23.33 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR E 39 PHE 0.008 0.002 PHE C 94 HIS 0.006 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3152) covalent geometry : angle 0.52880 ( 4270) hydrogen bonds : bond 0.02511 ( 40) hydrogen bonds : angle 7.06239 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.117 Fit side-chains REVERT: C 80 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6506 (mttt) REVERT: D 46 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6282 (mt-10) REVERT: D 58 LYS cc_start: 0.8141 (mmtp) cc_final: 0.7054 (pttp) REVERT: F 43 LYS cc_start: 0.7596 (mttt) cc_final: 0.7305 (mtpt) REVERT: F 58 LYS cc_start: 0.7746 (ptmt) cc_final: 0.7480 (mmpt) outliers start: 18 outliers final: 11 residues processed: 46 average time/residue: 0.0625 time to fit residues: 3.6508 Evaluate side-chains 46 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.187275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.154226 restraints weight = 3562.240| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 1.77 r_work: 0.4186 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4085 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 3152 Z= 0.293 Angle : 0.733 6.952 4270 Z= 0.412 Chirality : 0.055 0.161 562 Planarity : 0.003 0.014 541 Dihedral : 6.603 24.736 463 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 8.33 % Allowed : 26.00 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.39 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR D 39 PHE 0.013 0.003 PHE E 94 HIS 0.012 0.005 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00675 ( 3152) covalent geometry : angle 0.73270 ( 4270) hydrogen bonds : bond 0.02974 ( 40) hydrogen bonds : angle 7.34672 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 40 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.5503 (pt0) cc_final: 0.4147 (tp-100) REVERT: D 39 TYR cc_start: 0.6418 (OUTLIER) cc_final: 0.5429 (t80) REVERT: D 58 LYS cc_start: 0.8640 (mmtp) cc_final: 0.7527 (pttp) REVERT: F 43 LYS cc_start: 0.7605 (mttt) cc_final: 0.7310 (mtpt) REVERT: F 46 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.5908 (mp0) REVERT: F 58 LYS cc_start: 0.7952 (ptmt) cc_final: 0.7526 (mmpt) outliers start: 25 outliers final: 17 residues processed: 59 average time/residue: 0.0525 time to fit residues: 4.0171 Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4712 r_free = 0.4712 target = 0.193829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.159509 restraints weight = 3463.849| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 1.81 r_work: 0.4251 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4144 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3152 Z= 0.144 Angle : 0.569 4.528 4270 Z= 0.325 Chirality : 0.051 0.158 562 Planarity : 0.002 0.010 541 Dihedral : 5.740 21.921 463 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 9.33 % Allowed : 23.67 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR E 39 PHE 0.008 0.002 PHE C 94 HIS 0.008 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3152) covalent geometry : angle 0.56911 ( 4270) hydrogen bonds : bond 0.02480 ( 40) hydrogen bonds : angle 6.94933 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 37 time to evaluate : 0.069 Fit side-chains REVERT: A 24 GLN cc_start: 0.5662 (pt0) cc_final: 0.4046 (tp40) REVERT: A 83 GLU cc_start: 0.6648 (pm20) cc_final: 0.5114 (mm-30) REVERT: B 88 ILE cc_start: 0.6121 (mm) cc_final: 0.5820 (mt) REVERT: C 28 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5630 (pt0) REVERT: C 35 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7048 (mt-10) REVERT: C 52 VAL cc_start: 0.0246 (OUTLIER) cc_final: -0.0025 (t) REVERT: C 75 THR cc_start: 0.3471 (OUTLIER) cc_final: 0.3183 (m) REVERT: C 98 ASP cc_start: 0.4331 (m-30) cc_final: 0.4114 (m-30) REVERT: D 46 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6394 (mt-10) REVERT: D 58 LYS cc_start: 0.8520 (mmtp) cc_final: 0.7256 (pttp) REVERT: F 43 LYS cc_start: 0.7634 (mttt) cc_final: 0.7215 (mtpt) REVERT: F 58 LYS cc_start: 0.7832 (ptmt) cc_final: 0.7405 (mmpt) outliers start: 28 outliers final: 17 residues processed: 59 average time/residue: 0.0520 time to fit residues: 3.9532 Evaluate side-chains 58 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 36 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.0370 chunk 31 optimal weight: 0.9980 overall best weight: 0.9860 ------------------------------------------------------------------------------- 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 = 0.4684 r_free = 0.4684 target = 0.190913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4346 r_free = 0.4346 target = 0.158427 restraints weight = 3463.344| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 1.69 r_work: 0.4252 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4158 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3152 Z= 0.176 Angle : 0.589 4.818 4270 Z= 0.337 Chirality : 0.051 0.141 562 Planarity : 0.002 0.011 541 Dihedral : 5.770 22.109 463 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 9.67 % Allowed : 25.33 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.29 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR B 39 PHE 0.009 0.002 PHE E 94 HIS 0.009 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 3152) covalent geometry : angle 0.58937 ( 4270) hydrogen bonds : bond 0.02390 ( 40) hydrogen bonds : angle 6.81579 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 37 time to evaluate : 0.138 Fit side-chains REVERT: A 24 GLN cc_start: 0.5999 (pt0) cc_final: 0.4148 (tp40) REVERT: A 83 GLU cc_start: 0.6422 (pm20) cc_final: 0.5094 (mm-30) REVERT: C 28 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5888 (pt0) REVERT: C 35 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: C 52 VAL cc_start: 0.0180 (OUTLIER) cc_final: -0.0110 (t) REVERT: D 46 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6377 (mt-10) REVERT: D 58 LYS cc_start: 0.8545 (mmtp) cc_final: 0.7369 (pttp) REVERT: F 43 LYS cc_start: 0.7569 (mttt) cc_final: 0.7185 (mtpt) REVERT: F 58 LYS cc_start: 0.7892 (ptmt) cc_final: 0.7463 (mmpt) outliers start: 29 outliers final: 21 residues processed: 59 average time/residue: 0.0488 time to fit residues: 3.7458 Evaluate side-chains 60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 35 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.0010 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 41 optimal weight: 0.0570 chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 overall best weight: 0.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.192722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.161036 restraints weight = 3506.030| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 1.74 r_work: 0.4251 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4150 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3152 Z= 0.143 Angle : 0.548 4.242 4270 Z= 0.315 Chirality : 0.051 0.131 562 Planarity : 0.002 0.012 541 Dihedral : 5.439 20.784 463 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 9.00 % Allowed : 26.33 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.008 0.002 PHE F 94 HIS 0.008 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3152) covalent geometry : angle 0.54845 ( 4270) hydrogen bonds : bond 0.02323 ( 40) hydrogen bonds : angle 6.67752 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 36 time to evaluate : 0.084 Fit side-chains REVERT: A 24 GLN cc_start: 0.6241 (pt0) cc_final: 0.4214 (tp-100) REVERT: A 83 GLU cc_start: 0.6456 (pm20) cc_final: 0.5135 (mm-30) REVERT: C 35 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: C 52 VAL cc_start: 0.0431 (OUTLIER) cc_final: 0.0210 (t) REVERT: C 75 THR cc_start: 0.3052 (OUTLIER) cc_final: 0.2746 (m) REVERT: D 46 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6417 (mt-10) REVERT: D 58 LYS cc_start: 0.8501 (mmtp) cc_final: 0.7256 (pttp) REVERT: E 60 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7074 (tttt) REVERT: F 43 LYS cc_start: 0.7588 (mttt) cc_final: 0.7184 (mtpt) REVERT: F 46 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.5933 (mp0) REVERT: F 58 LYS cc_start: 0.7866 (ptmt) cc_final: 0.7427 (mmpt) outliers start: 27 outliers final: 18 residues processed: 56 average time/residue: 0.0533 time to fit residues: 3.8023 Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 33 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 0.0020 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.9192 ------------------------------------------------------------------------------- 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 = 0.4682 r_free = 0.4682 target = 0.190150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.159155 restraints weight = 3582.236| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 1.62 r_work: 0.4257 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4161 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3152 Z= 0.166 Angle : 0.575 4.290 4270 Z= 0.328 Chirality : 0.051 0.131 562 Planarity : 0.002 0.015 541 Dihedral : 5.571 21.532 463 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 10.00 % Allowed : 26.00 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.17 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.008 0.002 PHE F 94 HIS 0.008 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3152) covalent geometry : angle 0.57480 ( 4270) hydrogen bonds : bond 0.02321 ( 40) hydrogen bonds : angle 6.72431 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 36 time to evaluate : 0.089 Fit side-chains REVERT: A 24 GLN cc_start: 0.6315 (pt0) cc_final: 0.4231 (tp-100) REVERT: A 83 GLU cc_start: 0.6340 (pm20) cc_final: 0.5345 (mm-30) REVERT: C 35 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6987 (mt-10) REVERT: C 52 VAL cc_start: 0.0505 (OUTLIER) cc_final: 0.0277 (t) REVERT: D 39 TYR cc_start: 0.6180 (OUTLIER) cc_final: 0.5308 (t80) REVERT: D 46 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6315 (mt-10) REVERT: D 58 LYS cc_start: 0.8509 (mmtp) cc_final: 0.7328 (pttp) REVERT: E 60 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7129 (tttt) REVERT: F 43 LYS cc_start: 0.7591 (mttt) cc_final: 0.7198 (mtpt) REVERT: F 46 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5956 (mp0) REVERT: F 58 LYS cc_start: 0.7876 (ptmt) cc_final: 0.7476 (mmpt) outliers start: 30 outliers final: 20 residues processed: 59 average time/residue: 0.0486 time to fit residues: 3.6627 Evaluate side-chains 62 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 36 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 9.9990 chunk 39 optimal weight: 0.0070 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.190560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.158814 restraints weight = 3600.119| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 1.67 r_work: 0.4256 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4159 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3152 Z= 0.164 Angle : 0.574 4.800 4270 Z= 0.328 Chirality : 0.051 0.130 562 Planarity : 0.002 0.014 541 Dihedral : 5.517 21.044 463 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 9.00 % Allowed : 27.67 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.15 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.009 0.002 PHE C 94 HIS 0.008 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 3152) covalent geometry : angle 0.57357 ( 4270) hydrogen bonds : bond 0.02315 ( 40) hydrogen bonds : angle 6.68121 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 34 time to evaluate : 0.131 Fit side-chains REVERT: A 24 GLN cc_start: 0.6329 (pt0) cc_final: 0.4235 (tp-100) REVERT: A 83 GLU cc_start: 0.6338 (pm20) cc_final: 0.5425 (mm-30) REVERT: C 35 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6898 (mt-10) REVERT: D 46 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6295 (mt-10) REVERT: D 58 LYS cc_start: 0.8493 (mmtp) cc_final: 0.7301 (pttp) REVERT: E 60 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7081 (tttt) REVERT: F 43 LYS cc_start: 0.7601 (mttt) cc_final: 0.7201 (mtpt) REVERT: F 46 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.5953 (mp0) REVERT: F 58 LYS cc_start: 0.7885 (ptmt) cc_final: 0.7475 (mmpt) outliers start: 27 outliers final: 21 residues processed: 55 average time/residue: 0.0544 time to fit residues: 3.8279 Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 32 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.0010 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.192533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.161416 restraints weight = 3601.473| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 1.62 r_work: 0.4283 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4191 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3152 Z= 0.134 Angle : 0.535 4.502 4270 Z= 0.308 Chirality : 0.051 0.127 562 Planarity : 0.002 0.016 541 Dihedral : 5.260 20.086 463 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 8.33 % Allowed : 28.67 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.06 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 39 PHE 0.007 0.002 PHE F 94 HIS 0.007 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3152) covalent geometry : angle 0.53477 ( 4270) hydrogen bonds : bond 0.02236 ( 40) hydrogen bonds : angle 6.55070 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 35 time to evaluate : 0.142 Fit side-chains REVERT: A 24 GLN cc_start: 0.6276 (pt0) cc_final: 0.4267 (tp-100) REVERT: A 83 GLU cc_start: 0.6230 (pm20) cc_final: 0.5399 (mm-30) REVERT: D 46 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6366 (mt-10) REVERT: D 58 LYS cc_start: 0.8468 (mmtp) cc_final: 0.7282 (pttp) REVERT: E 60 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7096 (tttt) REVERT: F 43 LYS cc_start: 0.7570 (mttt) cc_final: 0.7339 (mtpt) REVERT: F 58 LYS cc_start: 0.7752 (ptmt) cc_final: 0.7360 (mmpt) outliers start: 25 outliers final: 20 residues processed: 54 average time/residue: 0.0598 time to fit residues: 4.1198 Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 0.3980 chunk 16 optimal weight: 0.0870 chunk 19 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.193794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.159987 restraints weight = 3519.694| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 1.82 r_work: 0.4263 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4162 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3152 Z= 0.116 Angle : 0.516 4.870 4270 Z= 0.298 Chirality : 0.050 0.127 562 Planarity : 0.002 0.014 541 Dihedral : 5.022 19.205 463 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.67 % Allowed : 30.33 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR D 39 PHE 0.007 0.001 PHE C 94 HIS 0.006 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3152) covalent geometry : angle 0.51627 ( 4270) hydrogen bonds : bond 0.02120 ( 40) hydrogen bonds : angle 6.47616 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.124 Fit side-chains REVERT: A 24 GLN cc_start: 0.6390 (pt0) cc_final: 0.4362 (tp40) REVERT: A 83 GLU cc_start: 0.6199 (pm20) cc_final: 0.5361 (mm-30) REVERT: D 46 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6412 (mt-10) REVERT: D 58 LYS cc_start: 0.8468 (mmtp) cc_final: 0.7214 (pttp) REVERT: E 60 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7061 (tttt) REVERT: F 43 LYS cc_start: 0.7636 (mttt) cc_final: 0.7339 (mtpt) REVERT: F 58 LYS cc_start: 0.7768 (ptmt) cc_final: 0.7365 (mmpt) outliers start: 20 outliers final: 17 residues processed: 50 average time/residue: 0.0577 time to fit residues: 3.7075 Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4658 r_free = 0.4658 target = 0.188247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.157306 restraints weight = 3608.047| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 1.65 r_work: 0.4240 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4146 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3152 Z= 0.188 Angle : 0.591 4.590 4270 Z= 0.337 Chirality : 0.051 0.135 562 Planarity : 0.002 0.017 541 Dihedral : 5.505 21.863 463 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 7.67 % Allowed : 29.67 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 39 PHE 0.009 0.002 PHE E 94 HIS 0.009 0.004 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 3152) covalent geometry : angle 0.59103 ( 4270) hydrogen bonds : bond 0.02316 ( 40) hydrogen bonds : angle 6.69158 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1243.07 seconds wall clock time: 22 minutes 2.66 seconds (1322.66 seconds total)