Starting phenix.real_space_refine on Wed Jul 23 10:38:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e9x_47820/07_2025/9e9x_47820.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e9x_47820/07_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_47820/07_2025/9e9x_47820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e9x_47820/07_2025/9e9x_47820.map" model { file = "/net/cci-nas-00/data/ceres_data/9e9x_47820/07_2025/9e9x_47820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e9x_47820/07_2025/9e9x_47820.cif" } resolution = 3.2 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= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 2.95, per 1000 atoms: 0.94 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: 0.70 Conformation dependent library (CDL) restraints added in 400.6 milliseconds 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: 0.43 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: 0.69 Time building geometry restraints manager: 0.85 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: 1.320 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: 0.030 Process input model: 12.650 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.230 ------------------------------------------------------------------------------- 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 (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: -3.29 (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 HIS 0.009 0.004 HIS B 50 PHE 0.043 0.005 PHE E 94 TYR 0.025 0.005 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.14231 ( 40) hydrogen bonds : angle 8.82930 ( 117) covalent geometry : bond 0.00482 ( 3152) covalent geometry : angle 0.93780 ( 4270) *********************** 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 : 0.313 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: 0.4458 (pt0) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1193 time to fit residues: 8.3714 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 : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.191416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.159170 restraints weight = 3465.584| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 1.69 r_work: 0.4251 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4157 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 3152 Z= 0.220 Angle : 0.667 6.354 4270 Z= 0.377 Chirality : 0.054 0.187 562 Planarity : 0.003 0.012 541 Dihedral : 6.252 23.362 463 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 8.67 % Allowed : 23.67 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS B 50 PHE 0.012 0.003 PHE C 94 TYR 0.012 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 40) hydrogen bonds : angle 7.38212 ( 117) covalent geometry : bond 0.00506 ( 3152) covalent geometry : angle 0.66682 ( 4270) *********************** 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 66 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.357 Fit side-chains REVERT: A 24 GLN cc_start: 0.5139 (pt0) cc_final: 0.3758 (tp-100) REVERT: C 80 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6641 (mttt) REVERT: D 46 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6205 (mt-10) REVERT: D 58 LYS cc_start: 0.8503 (mmtp) cc_final: 0.7262 (pttp) REVERT: F 43 LYS cc_start: 0.7567 (mttt) cc_final: 0.7322 (mtpt) REVERT: F 58 LYS cc_start: 0.7850 (ptmt) cc_final: 0.7513 (mmpt) outliers start: 26 outliers final: 18 residues processed: 59 average time/residue: 0.1298 time to fit residues: 9.7460 Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 48 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 C residue 15 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 80 LYS 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.0010 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.184814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.152575 restraints weight = 3513.564| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 1.69 r_work: 0.4178 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4078 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 3152 Z= 0.317 Angle : 0.787 5.858 4270 Z= 0.443 Chirality : 0.057 0.163 562 Planarity : 0.004 0.014 541 Dihedral : 7.024 27.424 463 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 11.00 % Allowed : 24.33 % 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 (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: -3.64 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.005 HIS B 50 PHE 0.016 0.003 PHE E 94 TYR 0.010 0.003 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 40) hydrogen bonds : angle 7.24110 ( 117) covalent geometry : bond 0.00733 ( 3152) covalent geometry : angle 0.78736 ( 4270) *********************** 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 74 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 41 time to evaluate : 0.304 Fit side-chains REVERT: A 24 GLN cc_start: 0.5554 (pt0) cc_final: 0.4175 (tp-100) REVERT: A 83 GLU cc_start: 0.6785 (pm20) cc_final: 0.5852 (mm-30) REVERT: A 100 LEU cc_start: 0.5676 (OUTLIER) cc_final: 0.5462 (mm) REVERT: B 88 ILE cc_start: 0.7133 (mm) cc_final: 0.6602 (mt) REVERT: C 35 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7118 (mt-10) REVERT: C 98 ASP cc_start: 0.4600 (m-30) cc_final: 0.4393 (m-30) REVERT: D 58 LYS cc_start: 0.8649 (mmtp) cc_final: 0.7385 (pttp) REVERT: F 43 LYS cc_start: 0.7663 (mttt) cc_final: 0.7230 (mtpt) REVERT: F 46 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6061 (mp0) REVERT: F 58 LYS cc_start: 0.8002 (ptmt) cc_final: 0.7507 (mmpt) outliers start: 33 outliers final: 24 residues processed: 66 average time/residue: 0.1235 time to fit residues: 10.1869 Evaluate side-chains 65 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 38 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 A residue 100 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 64 THR 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 49 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 Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.0000 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 = 0.4734 r_free = 0.4734 target = 0.195885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.161728 restraints weight = 3444.235| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 1.79 r_work: 0.4276 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4173 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3152 Z= 0.110 Angle : 0.532 4.536 4270 Z= 0.307 Chirality : 0.051 0.155 562 Planarity : 0.002 0.008 541 Dihedral : 5.582 20.762 463 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 7.67 % Allowed : 29.00 % 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 (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: -3.36 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS B 50 PHE 0.008 0.002 PHE F 94 TYR 0.006 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02392 ( 40) hydrogen bonds : angle 6.74664 ( 117) covalent geometry : bond 0.00242 ( 3152) covalent geometry : angle 0.53223 ( 4270) *********************** 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 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 34 time to evaluate : 0.317 Fit side-chains REVERT: A 24 GLN cc_start: 0.5799 (pt0) cc_final: 0.3972 (tp40) REVERT: B 88 ILE cc_start: 0.5994 (mm) cc_final: 0.5525 (mt) REVERT: C 38 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8402 (mp) REVERT: C 75 THR cc_start: 0.3533 (OUTLIER) cc_final: 0.3172 (m) REVERT: D 46 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6386 (mt-10) REVERT: D 58 LYS cc_start: 0.8430 (mmtp) cc_final: 0.7190 (pttp) REVERT: F 43 LYS cc_start: 0.7636 (mttt) cc_final: 0.7325 (mtpt) REVERT: F 58 LYS cc_start: 0.7792 (ptmt) cc_final: 0.7365 (mmpt) outliers start: 23 outliers final: 14 residues processed: 50 average time/residue: 0.1233 time to fit residues: 7.9829 Evaluate side-chains 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A 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 15 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 50 HIS 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 46 GLU 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 88 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.0020 chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- 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 = 0.4681 r_free = 0.4681 target = 0.190653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.156368 restraints weight = 3514.712| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 1.82 r_work: 0.4222 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3152 Z= 0.175 Angle : 0.579 4.619 4270 Z= 0.333 Chirality : 0.051 0.147 562 Planarity : 0.002 0.012 541 Dihedral : 5.724 21.809 463 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 7.67 % Allowed : 28.67 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS B 50 PHE 0.009 0.002 PHE F 94 TYR 0.007 0.002 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02390 ( 40) hydrogen bonds : angle 6.80998 ( 117) covalent geometry : bond 0.00405 ( 3152) covalent geometry : angle 0.57887 ( 4270) *********************** 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 59 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 36 time to evaluate : 0.280 Fit side-chains REVERT: A 24 GLN cc_start: 0.6031 (pt0) cc_final: 0.4088 (tp40) REVERT: A 83 GLU cc_start: 0.6520 (pm20) cc_final: 0.4962 (mm-30) REVERT: A 100 LEU cc_start: 0.5448 (OUTLIER) cc_final: 0.5233 (mm) REVERT: B 83 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6759 (tm-30) REVERT: B 88 ILE cc_start: 0.6401 (mm) cc_final: 0.6160 (mt) REVERT: C 38 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8516 (mp) REVERT: C 52 VAL cc_start: 0.0283 (OUTLIER) cc_final: -0.0008 (t) REVERT: D 39 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.5406 (t80) REVERT: D 58 LYS cc_start: 0.8512 (mmtp) cc_final: 0.7269 (pttp) REVERT: F 43 LYS cc_start: 0.7633 (mttt) cc_final: 0.7361 (mtpt) REVERT: F 46 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6001 (mp0) REVERT: F 58 LYS cc_start: 0.7930 (ptmt) cc_final: 0.7446 (mmpt) outliers start: 23 outliers final: 14 residues processed: 53 average time/residue: 0.1183 time to fit residues: 8.0447 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 100 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 38 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 0.0370 overall best weight: 0.7262 ------------------------------------------------------------------------------- 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 = 0.4701 r_free = 0.4701 target = 0.192985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.159671 restraints weight = 3600.565| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 1.92 r_work: 0.4241 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4141 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3152 Z= 0.137 Angle : 0.543 4.368 4270 Z= 0.313 Chirality : 0.051 0.136 562 Planarity : 0.002 0.012 541 Dihedral : 5.418 20.438 463 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 7.33 % Allowed : 29.67 % 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 (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: -3.25 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS B 50 PHE 0.008 0.002 PHE F 94 TYR 0.006 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02275 ( 40) hydrogen bonds : angle 6.60392 ( 117) covalent geometry : bond 0.00310 ( 3152) covalent geometry : angle 0.54253 ( 4270) *********************** 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 58 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 36 time to evaluate : 0.343 Fit side-chains REVERT: A 24 GLN cc_start: 0.6148 (pt0) cc_final: 0.4184 (tp-100) REVERT: A 83 GLU cc_start: 0.6352 (pm20) cc_final: 0.4965 (mm-30) REVERT: A 100 LEU cc_start: 0.5358 (OUTLIER) cc_final: 0.5143 (mp) REVERT: B 83 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6774 (tm-30) REVERT: B 88 ILE cc_start: 0.6463 (mm) cc_final: 0.6207 (mt) REVERT: D 46 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6320 (mt-10) REVERT: D 58 LYS cc_start: 0.8460 (mmtp) cc_final: 0.7257 (pttp) REVERT: F 43 LYS cc_start: 0.7661 (mttt) cc_final: 0.7414 (mtpt) REVERT: F 46 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5923 (mp0) REVERT: F 58 LYS cc_start: 0.7891 (ptmt) cc_final: 0.7452 (mmpt) outliers start: 22 outliers final: 16 residues processed: 51 average time/residue: 0.1210 time to fit residues: 7.9172 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 100 LEU 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 46 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 74 VAL 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 12 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4646 r_free = 0.4646 target = 0.186902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.153556 restraints weight = 3523.200| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 1.79 r_work: 0.4195 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4090 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3152 Z= 0.226 Angle : 0.637 4.606 4270 Z= 0.363 Chirality : 0.053 0.137 562 Planarity : 0.003 0.015 541 Dihedral : 5.923 22.772 463 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % 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 (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: -3.38 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS B 50 PHE 0.010 0.002 PHE C 94 TYR 0.009 0.002 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02468 ( 40) hydrogen bonds : angle 6.85714 ( 117) covalent geometry : bond 0.00521 ( 3152) covalent geometry : angle 0.63673 ( 4270) *********************** 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 68 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 38 time to evaluate : 0.316 Fit side-chains REVERT: A 24 GLN cc_start: 0.6373 (pt0) cc_final: 0.4354 (tp-100) REVERT: A 83 GLU cc_start: 0.6430 (pm20) cc_final: 0.5182 (mm-30) REVERT: C 52 VAL cc_start: 0.0339 (OUTLIER) cc_final: 0.0068 (t) REVERT: D 39 TYR cc_start: 0.6404 (OUTLIER) cc_final: 0.5428 (t80) REVERT: D 58 LYS cc_start: 0.8587 (mmtp) cc_final: 0.7318 (pttp) REVERT: F 43 LYS cc_start: 0.7672 (mttt) cc_final: 0.7362 (mtpt) REVERT: F 46 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6036 (mp0) REVERT: F 58 LYS cc_start: 0.7948 (ptmt) cc_final: 0.7442 (mmpt) outliers start: 30 outliers final: 20 residues processed: 61 average time/residue: 0.1251 time to fit residues: 9.7680 Evaluate side-chains 59 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 36 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 88 ILE 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 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 59 THR 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 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 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 chunk 4 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.192634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.158462 restraints weight = 3505.045| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 1.84 r_work: 0.4249 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4147 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3229 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= 0.127 Angle : 0.549 5.679 4270 Z= 0.316 Chirality : 0.051 0.125 562 Planarity : 0.002 0.013 541 Dihedral : 5.402 20.171 463 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 6.67 % Allowed : 30.67 % 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 (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: -3.21 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS B 50 PHE 0.007 0.002 PHE F 94 TYR 0.006 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02212 ( 40) hydrogen bonds : angle 6.58745 ( 117) covalent geometry : bond 0.00284 ( 3152) covalent geometry : angle 0.54856 ( 4270) *********************** 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 58 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.315 Fit side-chains REVERT: A 24 GLN cc_start: 0.6404 (pt0) cc_final: 0.4249 (tp-100) REVERT: A 83 GLU cc_start: 0.6260 (pm20) cc_final: 0.5078 (mm-30) REVERT: C 97 LYS cc_start: 0.6557 (mttt) cc_final: 0.5294 (mmtt) REVERT: D 46 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6475 (mt-10) REVERT: D 58 LYS cc_start: 0.8469 (mmtp) cc_final: 0.7216 (pttp) REVERT: F 43 LYS cc_start: 0.7618 (mttt) cc_final: 0.7326 (mtpt) REVERT: F 58 LYS cc_start: 0.7852 (ptmt) cc_final: 0.7411 (mmpt) outliers start: 20 outliers final: 17 residues processed: 51 average time/residue: 0.1510 time to fit residues: 9.4385 Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL 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 15 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.0670 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.192532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.161694 restraints weight = 3519.718| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 1.60 r_work: 0.4300 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.4208 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3152 Z= 0.130 Angle : 0.543 5.203 4270 Z= 0.312 Chirality : 0.051 0.132 562 Planarity : 0.002 0.016 541 Dihedral : 5.274 20.011 463 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 6.67 % Allowed : 30.00 % 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 (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: -3.13 (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 HIS 0.007 0.003 HIS B 50 PHE 0.007 0.002 PHE E 94 TYR 0.006 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02140 ( 40) hydrogen bonds : angle 6.56302 ( 117) covalent geometry : bond 0.00296 ( 3152) covalent geometry : angle 0.54319 ( 4270) *********************** 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 58 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.283 Fit side-chains REVERT: A 24 GLN cc_start: 0.6349 (pt0) cc_final: 0.4278 (tp-100) REVERT: A 83 GLU cc_start: 0.6173 (pm20) cc_final: 0.5090 (mm-30) REVERT: D 46 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6367 (mt-10) REVERT: D 58 LYS cc_start: 0.8465 (mmtp) cc_final: 0.7240 (pttp) REVERT: F 43 LYS cc_start: 0.7565 (mttt) cc_final: 0.7327 (mtpt) REVERT: F 46 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.5893 (mp0) REVERT: F 58 LYS cc_start: 0.7743 (ptmt) cc_final: 0.7326 (mmpt) outliers start: 20 outliers final: 17 residues processed: 50 average time/residue: 0.1199 time to fit residues: 7.7128 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL 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 74 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.0020 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN E 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.189156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.155644 restraints weight = 3459.051| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 1.81 r_work: 0.4223 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3152 Z= 0.177 Angle : 0.593 4.811 4270 Z= 0.339 Chirality : 0.051 0.132 562 Planarity : 0.002 0.015 541 Dihedral : 5.558 21.353 463 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 7.00 % Allowed : 30.33 % 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 (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: -3.22 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS B 50 PHE 0.008 0.002 PHE E 94 TYR 0.008 0.002 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02302 ( 40) hydrogen bonds : angle 6.72878 ( 117) covalent geometry : bond 0.00404 ( 3152) covalent geometry : angle 0.59278 ( 4270) ********************** 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 58 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 37 time to evaluate : 0.361 Fit side-chains REVERT: A 24 GLN cc_start: 0.6576 (pt0) cc_final: 0.4555 (tp40) REVERT: A 83 GLU cc_start: 0.6227 (pm20) cc_final: 0.5435 (mm-30) REVERT: B 98 ASP cc_start: 0.4572 (m-30) cc_final: 0.4354 (m-30) REVERT: C 97 LYS cc_start: 0.6590 (mttt) cc_final: 0.5345 (mmtt) REVERT: D 58 LYS cc_start: 0.8539 (mmtp) cc_final: 0.7256 (pttp) REVERT: F 43 LYS cc_start: 0.7662 (mttt) cc_final: 0.7354 (mtpt) REVERT: F 46 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.5935 (mp0) REVERT: F 58 LYS cc_start: 0.7862 (ptmt) cc_final: 0.7445 (mmpt) outliers start: 21 outliers final: 19 residues processed: 51 average time/residue: 0.1344 time to fit residues: 8.6858 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 : 0.262 ------------------------------------------------------------------------------- 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 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 81 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 74 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 0.0370 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.4702 r_free = 0.4702 target = 0.192374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.158648 restraints weight = 3538.908| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 1.81 r_work: 0.4249 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4145 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3152 Z= 0.127 Angle : 0.536 4.665 4270 Z= 0.310 Chirality : 0.051 0.129 562 Planarity : 0.002 0.015 541 Dihedral : 5.229 20.304 463 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.67 % Allowed : 31.00 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.10 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.007 0.002 PHE E 94 TYR 0.006 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02140 ( 40) hydrogen bonds : angle 6.55244 ( 117) covalent geometry : bond 0.00289 ( 3152) covalent geometry : angle 0.53647 ( 4270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2492.40 seconds wall clock time: 43 minutes 22.71 seconds (2602.71 seconds total)