Starting phenix.real_space_refine on Wed Sep 17 06:13:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jij_61507/09_2025/9jij_61507.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jij_61507/09_2025/9jij_61507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jij_61507/09_2025/9jij_61507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jij_61507/09_2025/9jij_61507.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jij_61507/09_2025/9jij_61507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jij_61507/09_2025/9jij_61507.map" } resolution = 2.64 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= 0.001 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 3630 2.51 5 N 982 2.21 5 O 1140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 5768 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1106 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 7, 'TRANS': 139} Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 821 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 957 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "B" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1106 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 7, 'TRANS': 139} Chain: "F" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 821 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "E" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 957 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Time building chain proxies: 1.80, per 1000 atoms: 0.31 Number of scatterers: 5768 At special positions: 0 Unit cell: (111.15, 66.95, 78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 1140 8.00 N 982 7.00 C 3630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=1.86 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 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: 0.50 Conformation dependent library (CDL) restraints added in 241.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 18 sheets defined 3.7% alpha, 47.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.651A pdb=" N ASP L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 510 removed outlier: 4.341A pdb=" N SER A 497 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER A 582 " --> pdb=" O GLN A 568 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLN A 568 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510 removed outlier: 4.341A pdb=" N SER A 497 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 477 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL A 593 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A 547 " --> pdb=" O GLY A 556 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.265A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.617A pdb=" N LEU L 98 " --> pdb=" O ASP L 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 20 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.878A pdb=" N GLY H 33 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.684A pdb=" N CYS H 96 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TRP H 115 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG H 98 " --> pdb=" O ASP H 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=AB2, first strand: chain 'B' and resid 508 through 510 removed outlier: 4.277A pdb=" N SER B 497 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER B 582 " --> pdb=" O GLN B 568 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLN B 568 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 508 through 510 removed outlier: 4.277A pdb=" N SER B 497 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 477 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL B 593 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE B 547 " --> pdb=" O GLY B 556 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.121A pdb=" N GLN F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU F 47 " --> pdb=" O GLN F 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.624A pdb=" N LEU F 98 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 18 through 20 Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.865A pdb=" N GLY E 33 " --> pdb=" O GLU E 99 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.717A pdb=" N CYS E 96 " --> pdb=" O TRP E 115 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TRP E 115 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG E 98 " --> pdb=" O ASP E 113 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP E 113 " --> pdb=" O ARG E 98 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 579 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: 1.02 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1862 1.34 - 1.46: 1482 1.46 - 1.58: 2532 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 5900 Sorted by residual: bond pdb=" CB ASP A 496 " pdb=" CG ASP A 496 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.07e+00 bond pdb=" CB GLU H 89 " pdb=" CG GLU H 89 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CB ASP F 61 " pdb=" CG ASP F 61 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 8.02e-01 bond pdb=" CA VAL E 105 " pdb=" CB VAL E 105 " ideal model delta sigma weight residual 1.539 1.552 -0.012 1.38e-02 5.25e+03 7.75e-01 bond pdb=" CA VAL E 123 " pdb=" CB VAL E 123 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 7.11e-01 ... (remaining 5895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 7938 1.88 - 3.77: 112 3.77 - 5.65: 6 5.65 - 7.54: 3 7.54 - 9.42: 1 Bond angle restraints: 8060 Sorted by residual: angle pdb=" N VAL E 104 " pdb=" CA VAL E 104 " pdb=" C VAL E 104 " ideal model delta sigma weight residual 112.43 109.30 3.13 9.20e-01 1.18e+00 1.16e+01 angle pdb=" CA GLU H 89 " pdb=" CB GLU H 89 " pdb=" CG GLU H 89 " ideal model delta sigma weight residual 114.10 120.62 -6.52 2.00e+00 2.50e-01 1.06e+01 angle pdb=" N VAL H 104 " pdb=" CA VAL H 104 " pdb=" C VAL H 104 " ideal model delta sigma weight residual 112.43 109.53 2.90 9.20e-01 1.18e+00 9.93e+00 angle pdb=" C ASP F 51 " pdb=" N ASN F 52 " pdb=" CA ASN F 52 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 8.99e+00 angle pdb=" C ASP L 51 " pdb=" N ASN L 52 " pdb=" CA ASN L 52 " ideal model delta sigma weight residual 121.54 127.21 -5.67 1.91e+00 2.74e-01 8.81e+00 ... (remaining 8055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 2991 15.99 - 31.98: 360 31.98 - 47.98: 74 47.98 - 63.97: 22 63.97 - 79.96: 3 Dihedral angle restraints: 3450 sinusoidal: 1260 harmonic: 2190 Sorted by residual: dihedral pdb=" CA GLU E 106 " pdb=" C GLU E 106 " pdb=" N PRO E 107 " pdb=" CA PRO E 107 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLU H 106 " pdb=" C GLU H 106 " pdb=" N PRO H 107 " pdb=" CA PRO H 107 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -53.99 -32.01 1 1.00e+01 1.00e-02 1.46e+01 ... (remaining 3447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 517 0.028 - 0.055: 248 0.055 - 0.083: 76 0.083 - 0.111: 62 0.111 - 0.138: 23 Chirality restraints: 926 Sorted by residual: chirality pdb=" CA ILE H 59 " pdb=" N ILE H 59 " pdb=" C ILE H 59 " pdb=" CB ILE H 59 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA VAL E 105 " pdb=" N VAL E 105 " pdb=" C VAL E 105 " pdb=" CB VAL E 105 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA VAL H 105 " pdb=" N VAL H 105 " pdb=" C VAL H 105 " pdb=" CB VAL H 105 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 923 not shown) Planarity restraints: 1026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 38 " 0.272 9.50e-02 1.11e+02 1.22e-01 9.15e+00 pdb=" NE ARG E 38 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG E 38 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG E 38 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 38 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 460 " -0.207 9.50e-02 1.11e+02 9.26e-02 5.27e+00 pdb=" NE ARG A 460 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 460 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 460 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 460 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 62 " 0.200 9.50e-02 1.11e+02 8.98e-02 4.95e+00 pdb=" NE ARG F 62 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG F 62 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 62 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 62 " 0.007 2.00e-02 2.50e+03 ... (remaining 1023 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1004 2.77 - 3.30: 5118 3.30 - 3.83: 9841 3.83 - 4.37: 11876 4.37 - 4.90: 20480 Nonbonded interactions: 48319 Sorted by model distance: nonbonded pdb=" O PRO L 7 " pdb=" OG1 THR L 105 " model vdw 2.235 3.040 nonbonded pdb=" O SER B 513 " pdb=" OG SER B 513 " model vdw 2.249 3.040 nonbonded pdb=" O PRO F 7 " pdb=" OG1 THR F 105 " model vdw 2.255 3.040 nonbonded pdb=" N VAL F 34 " pdb=" OD1 ASN F 52 " model vdw 2.265 3.120 nonbonded pdb=" N VAL L 34 " pdb=" OD1 ASN L 52 " model vdw 2.284 3.120 ... (remaining 48314 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'L' } 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: 6.280 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.910 Find NCS groups from input model: 0.080 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:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.004 0.170 5904 Z= 0.200 Angle : 0.625 23.699 8068 Z= 0.332 Chirality : 0.044 0.138 926 Planarity : 0.007 0.122 1026 Dihedral : 14.805 79.962 2046 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.80 % Allowed : 19.55 % Favored : 79.65 % 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: -1.23 (0.31), residues: 752 helix: None (None), residues: 0 sheet: -0.49 (0.28), residues: 342 loop : -1.05 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 512 TYR 0.011 0.001 TYR H 60 PHE 0.006 0.001 PHE E 64 TRP 0.013 0.001 TRP L 92 HIS 0.003 0.001 HIS L 86 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 5900) covalent geometry : angle 0.56271 ( 8060) SS BOND : bond 0.08521 ( 4) SS BOND : angle 8.69073 ( 8) hydrogen bonds : bond 0.24898 ( 199) hydrogen bonds : angle 10.26178 ( 579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.217 Fit side-chains REVERT: L 62 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7798 (mtm-85) REVERT: L 106 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6792 (tpt) REVERT: H 81 MET cc_start: 0.7430 (tmm) cc_final: 0.6935 (tmt) REVERT: F 87 TYR cc_start: 0.8105 (m-80) cc_final: 0.7851 (m-80) REVERT: F 109 VAL cc_start: 0.7341 (OUTLIER) cc_final: 0.7125 (m) outliers start: 5 outliers final: 2 residues processed: 113 average time/residue: 0.3381 time to fit residues: 41.2633 Evaluate side-chains 90 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain L residue 106 MET Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 109 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.142090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.133226 restraints weight = 7045.058| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.52 r_work: 0.3773 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5904 Z= 0.255 Angle : 0.667 6.339 8068 Z= 0.353 Chirality : 0.048 0.148 926 Planarity : 0.006 0.047 1026 Dihedral : 6.286 59.532 840 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 6.57 % Allowed : 17.95 % Favored : 75.48 % 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: -1.10 (0.30), residues: 752 helix: None (None), residues: 0 sheet: -0.05 (0.29), residues: 336 loop : -1.32 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 542 TYR 0.019 0.002 TYR E 60 PHE 0.013 0.002 PHE A 537 TRP 0.013 0.002 TRP H 47 HIS 0.005 0.002 HIS F 86 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 5900) covalent geometry : angle 0.66473 ( 8060) SS BOND : bond 0.00930 ( 4) SS BOND : angle 1.94796 ( 8) hydrogen bonds : bond 0.05075 ( 199) hydrogen bonds : angle 6.78569 ( 579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.251 Fit side-chains REVERT: F 109 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7137 (m) outliers start: 41 outliers final: 21 residues processed: 120 average time/residue: 0.2632 time to fit residues: 34.8582 Evaluate side-chains 111 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 110 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 29 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.143312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.134513 restraints weight = 6938.764| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.50 r_work: 0.3792 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5904 Z= 0.157 Angle : 0.586 7.596 8068 Z= 0.308 Chirality : 0.045 0.137 926 Planarity : 0.005 0.041 1026 Dihedral : 5.370 37.344 836 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.97 % Allowed : 19.39 % Favored : 75.64 % 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: -0.93 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.08 (0.28), residues: 346 loop : -1.25 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 542 TYR 0.017 0.002 TYR L 37 PHE 0.011 0.002 PHE A 547 TRP 0.012 0.002 TRP H 47 HIS 0.004 0.001 HIS F 86 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5900) covalent geometry : angle 0.58370 ( 8060) SS BOND : bond 0.00544 ( 4) SS BOND : angle 1.88458 ( 8) hydrogen bonds : bond 0.04343 ( 199) hydrogen bonds : angle 6.24463 ( 579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.235 Fit side-chains REVERT: A 518 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7264 (mttp) REVERT: A 572 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6447 (tt0) REVERT: H 78 THR cc_start: 0.7942 (t) cc_final: 0.7571 (m) REVERT: H 112 MET cc_start: 0.7965 (mtm) cc_final: 0.7614 (mtm) outliers start: 31 outliers final: 18 residues processed: 116 average time/residue: 0.2826 time to fit residues: 35.9087 Evaluate side-chains 113 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 110 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 GLN F 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.142477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.133676 restraints weight = 7133.439| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.51 r_work: 0.3779 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5904 Z= 0.201 Angle : 0.624 6.756 8068 Z= 0.327 Chirality : 0.046 0.143 926 Planarity : 0.005 0.042 1026 Dihedral : 5.556 37.844 835 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 6.73 % Allowed : 19.23 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.95 (0.30), residues: 752 helix: None (None), residues: 0 sheet: 0.18 (0.29), residues: 334 loop : -1.35 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 38 TYR 0.016 0.002 TYR E 60 PHE 0.011 0.002 PHE A 547 TRP 0.014 0.002 TRP H 47 HIS 0.005 0.001 HIS F 86 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 5900) covalent geometry : angle 0.62120 ( 8060) SS BOND : bond 0.00578 ( 4) SS BOND : angle 1.99319 ( 8) hydrogen bonds : bond 0.04346 ( 199) hydrogen bonds : angle 6.18019 ( 579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.209 Fit side-chains REVERT: A 518 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7294 (mttp) REVERT: A 572 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6452 (tt0) REVERT: H 78 THR cc_start: 0.7847 (t) cc_final: 0.7501 (m) REVERT: H 112 MET cc_start: 0.8011 (mtm) cc_final: 0.7698 (mtm) outliers start: 42 outliers final: 28 residues processed: 124 average time/residue: 0.2534 time to fit residues: 34.7582 Evaluate side-chains 126 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 110 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.142554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.133627 restraints weight = 7170.490| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.53 r_work: 0.3782 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5904 Z= 0.182 Angle : 0.603 6.492 8068 Z= 0.317 Chirality : 0.045 0.145 926 Planarity : 0.005 0.042 1026 Dihedral : 5.476 37.063 835 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.93 % Allowed : 20.51 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.90 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.18 (0.29), residues: 336 loop : -1.28 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 38 TYR 0.015 0.002 TYR L 37 PHE 0.010 0.002 PHE A 547 TRP 0.014 0.002 TRP H 47 HIS 0.004 0.001 HIS F 86 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5900) covalent geometry : angle 0.59981 ( 8060) SS BOND : bond 0.00556 ( 4) SS BOND : angle 1.95644 ( 8) hydrogen bonds : bond 0.04041 ( 199) hydrogen bonds : angle 6.08026 ( 579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.247 Fit side-chains REVERT: A 518 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7345 (mttp) REVERT: A 572 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6466 (tt0) REVERT: H 78 THR cc_start: 0.7871 (t) cc_final: 0.7546 (m) REVERT: H 112 MET cc_start: 0.7999 (mtm) cc_final: 0.7710 (mtm) REVERT: E 84 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6708 (mtt-85) outliers start: 37 outliers final: 27 residues processed: 118 average time/residue: 0.2392 time to fit residues: 31.3620 Evaluate side-chains 123 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 2 optimal weight: 0.0030 chunk 41 optimal weight: 0.0570 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 overall best weight: 0.3108 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.145071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.136206 restraints weight = 7163.554| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.55 r_work: 0.3831 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5904 Z= 0.114 Angle : 0.529 6.232 8068 Z= 0.280 Chirality : 0.044 0.139 926 Planarity : 0.005 0.040 1026 Dihedral : 5.001 28.125 835 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.01 % Allowed : 22.44 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.80 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.28 (0.29), residues: 334 loop : -1.24 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 38 TYR 0.016 0.001 TYR L 37 PHE 0.009 0.001 PHE A 547 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.000 HIS F 86 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5900) covalent geometry : angle 0.52686 ( 8060) SS BOND : bond 0.00460 ( 4) SS BOND : angle 1.57859 ( 8) hydrogen bonds : bond 0.03414 ( 199) hydrogen bonds : angle 5.72640 ( 579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.222 Fit side-chains REVERT: A 518 LYS cc_start: 0.7520 (mmtp) cc_final: 0.7315 (mttp) REVERT: A 572 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6482 (tt0) REVERT: H 78 THR cc_start: 0.7775 (t) cc_final: 0.7453 (m) REVERT: H 112 MET cc_start: 0.7900 (mtm) cc_final: 0.7634 (mtm) outliers start: 25 outliers final: 20 residues processed: 113 average time/residue: 0.2518 time to fit residues: 31.5526 Evaluate side-chains 117 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 27 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.143420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.134586 restraints weight = 7115.511| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.53 r_work: 0.3801 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5904 Z= 0.165 Angle : 0.584 7.608 8068 Z= 0.305 Chirality : 0.045 0.147 926 Planarity : 0.005 0.041 1026 Dihedral : 5.239 29.077 835 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.61 % Allowed : 21.15 % Favored : 73.24 % 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: -0.79 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.28 (0.29), residues: 336 loop : -1.23 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 38 TYR 0.014 0.002 TYR H 60 PHE 0.010 0.002 PHE A 547 TRP 0.014 0.002 TRP H 47 HIS 0.003 0.001 HIS F 86 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 5900) covalent geometry : angle 0.58182 ( 8060) SS BOND : bond 0.00512 ( 4) SS BOND : angle 1.83595 ( 8) hydrogen bonds : bond 0.03780 ( 199) hydrogen bonds : angle 5.81974 ( 579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.270 Fit side-chains REVERT: A 572 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6489 (tt0) REVERT: H 43 GLN cc_start: 0.7568 (mp10) cc_final: 0.7305 (mp10) REVERT: E 84 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6660 (mtt-85) REVERT: E 89 GLU cc_start: 0.7317 (tm-30) cc_final: 0.7092 (mm-30) outliers start: 35 outliers final: 26 residues processed: 117 average time/residue: 0.2716 time to fit residues: 34.9628 Evaluate side-chains 122 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.142494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.133816 restraints weight = 7114.508| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.49 r_work: 0.3791 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5904 Z= 0.206 Angle : 0.614 7.428 8068 Z= 0.322 Chirality : 0.046 0.155 926 Planarity : 0.005 0.047 1026 Dihedral : 5.518 35.008 835 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.25 % Allowed : 21.15 % Favored : 72.60 % 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: -0.76 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.37 (0.29), residues: 332 loop : -1.26 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 84 TYR 0.016 0.002 TYR H 60 PHE 0.010 0.002 PHE B 536 TRP 0.015 0.002 TRP H 47 HIS 0.004 0.001 HIS L 86 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 5900) covalent geometry : angle 0.61177 ( 8060) SS BOND : bond 0.00517 ( 4) SS BOND : angle 1.92996 ( 8) hydrogen bonds : bond 0.04011 ( 199) hydrogen bonds : angle 5.95971 ( 579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.266 Fit side-chains REVERT: A 572 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6471 (tt0) REVERT: H 43 GLN cc_start: 0.7589 (mp10) cc_final: 0.7357 (mp10) REVERT: H 78 THR cc_start: 0.7793 (t) cc_final: 0.7504 (m) outliers start: 39 outliers final: 31 residues processed: 121 average time/residue: 0.2661 time to fit residues: 35.4537 Evaluate side-chains 130 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.142660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.133894 restraints weight = 7149.514| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.51 r_work: 0.3792 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5904 Z= 0.193 Angle : 0.602 7.356 8068 Z= 0.315 Chirality : 0.046 0.154 926 Planarity : 0.005 0.045 1026 Dihedral : 5.483 35.968 835 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.45 % Allowed : 22.28 % Favored : 72.28 % 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: -0.77 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.39 (0.29), residues: 332 loop : -1.29 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 84 TYR 0.015 0.002 TYR H 60 PHE 0.010 0.002 PHE A 547 TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS L 86 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 5900) covalent geometry : angle 0.59945 ( 8060) SS BOND : bond 0.00507 ( 4) SS BOND : angle 1.81744 ( 8) hydrogen bonds : bond 0.03912 ( 199) hydrogen bonds : angle 5.91011 ( 579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.218 Fit side-chains REVERT: A 572 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6467 (tt0) REVERT: H 43 GLN cc_start: 0.7614 (mp10) cc_final: 0.7369 (mp10) REVERT: H 78 THR cc_start: 0.7791 (t) cc_final: 0.7490 (m) outliers start: 34 outliers final: 31 residues processed: 117 average time/residue: 0.2676 time to fit residues: 34.4600 Evaluate side-chains 129 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 69 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.144605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.135830 restraints weight = 7239.143| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.54 r_work: 0.3820 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5904 Z= 0.122 Angle : 0.538 7.510 8068 Z= 0.283 Chirality : 0.044 0.144 926 Planarity : 0.005 0.041 1026 Dihedral : 5.028 27.340 835 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.49 % Allowed : 22.92 % Favored : 72.60 % 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: -0.67 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.39 (0.29), residues: 334 loop : -1.17 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 542 TYR 0.014 0.001 TYR E 60 PHE 0.010 0.002 PHE A 547 TRP 0.015 0.001 TRP H 47 HIS 0.002 0.001 HIS E 110 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5900) covalent geometry : angle 0.53606 ( 8060) SS BOND : bond 0.00416 ( 4) SS BOND : angle 1.50019 ( 8) hydrogen bonds : bond 0.03367 ( 199) hydrogen bonds : angle 5.60112 ( 579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.242 Fit side-chains REVERT: A 572 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6491 (tt0) REVERT: H 43 GLN cc_start: 0.7601 (mp10) cc_final: 0.7372 (mp10) outliers start: 28 outliers final: 25 residues processed: 113 average time/residue: 0.2607 time to fit residues: 32.4940 Evaluate side-chains 123 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.143920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.135274 restraints weight = 7108.507| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.50 r_work: 0.3800 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5904 Z= 0.153 Angle : 0.568 7.167 8068 Z= 0.298 Chirality : 0.045 0.151 926 Planarity : 0.005 0.042 1026 Dihedral : 5.185 26.611 835 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.49 % Allowed : 22.92 % Favored : 72.60 % 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: -0.68 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.42 (0.29), residues: 332 loop : -1.22 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 542 TYR 0.013 0.001 TYR H 60 PHE 0.010 0.002 PHE A 547 TRP 0.016 0.002 TRP H 47 HIS 0.003 0.001 HIS F 86 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 5900) covalent geometry : angle 0.56537 ( 8060) SS BOND : bond 0.00450 ( 4) SS BOND : angle 1.82635 ( 8) hydrogen bonds : bond 0.03613 ( 199) hydrogen bonds : angle 5.70173 ( 579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.84 seconds wall clock time: 42 minutes 14.82 seconds (2534.82 seconds total)