Starting phenix.real_space_refine on Sun Oct 25 02:05:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pfv_13381/10_2026/7pfv_13381.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pfv_13381/10_2026/7pfv_13381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pfv_13381/10_2026/7pfv_13381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pfv_13381/10_2026/7pfv_13381.map" model { file = "/net/cci-nas-00/data/ceres_data/7pfv_13381/10_2026/7pfv_13381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pfv_13381/10_2026/7pfv_13381.cif" } resolution = 4.4 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 354 5.49 5 S 10 5.16 5 C 7612 2.51 5 N 2606 2.21 5 O 3298 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-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13880 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3647 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "I" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3610 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 2.75, per 1000 atoms: 0.20 Number of scatterers: 13880 At special positions: 0 Unit cell: (137.55, 90.3, 139.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 354 15.00 O 3298 8.00 N 2606 7.00 C 7612 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: 1.15 Conformation dependent library (CDL) restraints added in 363.8 milliseconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 11 sheets defined 70.0% alpha, 3.3% beta 173 base pairs and 312 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.769A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.704A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.950A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.279A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.534A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.643A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.621A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.125A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.279A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.508A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 49 removed outlier: 3.951A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 69 Processing helix chain 'U' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.746A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.221A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.967A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.490A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.777A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.408A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'U' and resid 56 through 57 437 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 445 hydrogen bonds 890 hydrogen bond angles 0 basepair planarities 173 basepair parallelities 312 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2439 1.33 - 1.45: 5131 1.45 - 1.57: 6550 1.57 - 1.69: 706 1.69 - 1.81: 20 Bond restraints: 14846 Sorted by residual: bond pdb=" C3' DT J 779 " pdb=" C2' DT J 779 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C3' DA J 711 " pdb=" C2' DA J 711 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DG I 158 " pdb=" O3' DG I 158 " ideal model delta sigma weight residual 1.435 1.480 -0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" C3' DT I 134 " pdb=" C2' DT I 134 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DC I 140 " pdb=" C2' DC I 140 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 ... (remaining 14841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 20411 2.16 - 4.31: 1073 4.31 - 6.47: 55 6.47 - 8.62: 21 8.62 - 10.78: 3 Bond angle restraints: 21563 Sorted by residual: angle pdb=" O4' DG I 130 " pdb=" C4' DG I 130 " pdb=" C3' DG I 130 " ideal model delta sigma weight residual 106.00 101.47 4.53 6.00e-01 2.78e+00 5.69e+01 angle pdb=" O4' DG I 151 " pdb=" C4' DG I 151 " pdb=" C3' DG I 151 " ideal model delta sigma weight residual 106.00 102.05 3.95 6.00e-01 2.78e+00 4.33e+01 angle pdb=" O4' DC I 110 " pdb=" C4' DC I 110 " pdb=" C3' DC I 110 " ideal model delta sigma weight residual 106.00 102.39 3.61 6.00e-01 2.78e+00 3.61e+01 angle pdb=" O4' DC J 777 " pdb=" C4' DC J 777 " pdb=" C3' DC J 777 " ideal model delta sigma weight residual 106.00 102.74 3.26 6.00e-01 2.78e+00 2.96e+01 angle pdb=" CA GLU A 97 " pdb=" CB GLU A 97 " pdb=" CG GLU A 97 " ideal model delta sigma weight residual 114.10 124.88 -10.78 2.00e+00 2.50e-01 2.90e+01 ... (remaining 21558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 6021 35.35 - 70.70: 1934 70.70 - 106.05: 48 106.05 - 141.40: 2 141.40 - 176.75: 2 Dihedral angle restraints: 8007 sinusoidal: 5576 harmonic: 2431 Sorted by residual: dihedral pdb=" CA PHE A 84 " pdb=" C PHE A 84 " pdb=" N GLN A 85 " pdb=" CA GLN A 85 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ILE F 50 " pdb=" C ILE F 50 " pdb=" N TYR F 51 " pdb=" CA TYR F 51 " ideal model delta harmonic sigma weight residual -180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 8004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1749 0.051 - 0.101: 583 0.101 - 0.152: 114 0.152 - 0.202: 6 0.202 - 0.253: 4 Chirality restraints: 2456 Sorted by residual: chirality pdb=" C3' DG I 158 " pdb=" C4' DG I 158 " pdb=" O3' DG I 158 " pdb=" C2' DG I 158 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ARG B 23 " pdb=" N ARG B 23 " pdb=" C ARG B 23 " pdb=" CB ARG B 23 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLU H 71 " pdb=" N GLU H 71 " pdb=" C GLU H 71 " pdb=" CB GLU H 71 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2453 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 101 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C VAL A 101 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL A 101 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY A 102 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 70 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C VAL B 70 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL B 70 " 0.019 2.00e-02 2.50e+03 pdb=" N THR B 71 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 61 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" CD GLU C 61 " 0.049 2.00e-02 2.50e+03 pdb=" OE1 GLU C 61 " -0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU C 61 " -0.018 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2905 2.78 - 3.31: 12957 3.31 - 3.84: 30777 3.84 - 4.37: 34193 4.37 - 4.90: 46781 Nonbonded interactions: 127613 Sorted by model distance: nonbonded pdb=" NH1 ARG B 23 " pdb=" OD1 ASP B 24 " model vdw 2.249 3.120 nonbonded pdb=" OD1 ASP A 123 " pdb=" NE2 HIS E 113 " model vdw 2.265 3.120 nonbonded pdb=" OG SER G 40 " pdb=" O ARG G 42 " model vdw 2.273 3.040 nonbonded pdb=" OP1 DT J 649 " pdb=" NH1 ARG U 53 " model vdw 2.277 3.120 nonbonded pdb=" OG SER C 40 " pdb=" O ARG C 42 " model vdw 2.307 3.040 ... (remaining 127608 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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 group one per residue 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 14.540 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 : 0.007 0.051 14846 Z= 0.649 Angle : 1.006 10.776 21563 Z= 0.820 Chirality : 0.050 0.253 2456 Planarity : 0.007 0.091 1498 Dihedral : 30.434 176.752 6441 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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 are not related in a simple way. whole: 0.36 (0.26), residues: 825 helix: 0.67 (0.20), residues: 575 sheet: -2.49 (1.47), residues: 10 loop : -0.45 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 23 TYR 0.021 0.003 TYR C 39 PHE 0.020 0.002 PHE E 104 HIS 0.011 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.65 (14846) covalent geometry : angle 1.00617 / 0.82 (21563) hydrogen bonds : bond 0.11251 / 7.77 ( 882) hydrogen bonds : angle 4.69223 / 3.35 ( 2177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9120 (t80) cc_final: 0.8848 (t80) REVERT: A 90 MET cc_start: 0.9710 (mmp) cc_final: 0.9504 (mmm) REVERT: A 94 GLU cc_start: 0.9479 (mp0) cc_final: 0.8979 (pm20) REVERT: A 120 MET cc_start: 0.8394 (mtm) cc_final: 0.7748 (mpp) REVERT: B 53 GLU cc_start: 0.9319 (tm-30) cc_final: 0.9011 (tm-30) REVERT: B 63 GLU cc_start: 0.9195 (pt0) cc_final: 0.8861 (pp20) REVERT: B 97 LEU cc_start: 0.8864 (tp) cc_final: 0.8591 (tt) REVERT: C 61 GLU cc_start: 0.9394 (mt-10) cc_final: 0.9109 (mt-10) REVERT: D 82 HIS cc_start: 0.9669 (t-90) cc_final: 0.9348 (t-90) REVERT: D 105 GLU cc_start: 0.9551 (pp20) cc_final: 0.9336 (pp20) REVERT: D 109 HIS cc_start: 0.9850 (m-70) cc_final: 0.9645 (m90) REVERT: F 62 LEU cc_start: 0.9856 (mt) cc_final: 0.9621 (pp) REVERT: F 74 GLU cc_start: 0.9632 (tm-30) cc_final: 0.9366 (mt-10) REVERT: H 62 MET cc_start: 0.9525 (mmp) cc_final: 0.9296 (tmm) REVERT: H 105 GLU cc_start: 0.9527 (pm20) cc_final: 0.9311 (pm20) REVERT: H 106 LEU cc_start: 0.9869 (mt) cc_final: 0.9622 (mt) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1147 time to fit residues: 16.9092 Evaluate side-chains 68 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN E 76 GLN E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.029659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.022549 restraints weight = 215481.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.023257 restraints weight = 104226.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.023707 restraints weight = 63251.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.024083 restraints weight = 45440.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.024313 restraints weight = 35106.701| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14846 Z= 0.168 Angle : 0.724 7.566 21563 Z= 0.418 Chirality : 0.050 0.296 2456 Planarity : 0.005 0.045 1498 Dihedral : 33.993 172.629 4789 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.14 % Allowed : 3.17 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.27), residues: 825 helix: 1.75 (0.21), residues: 566 sheet: -2.44 (1.46), residues: 10 loop : -0.58 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.015 0.002 TYR G 39 PHE 0.034 0.002 PHE G 25 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.17 (14846) covalent geometry : angle 0.72424 / 0.42 (21563) hydrogen bonds : bond 0.06266 / 4.25 ( 882) hydrogen bonds : angle 3.63018 / 2.58 ( 2177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9657 (mmp) cc_final: 0.9446 (mmp) REVERT: A 93 GLN cc_start: 0.9187 (tp40) cc_final: 0.8881 (tp-100) REVERT: A 120 MET cc_start: 0.8524 (mtm) cc_final: 0.7908 (mpp) REVERT: B 63 GLU cc_start: 0.9298 (pt0) cc_final: 0.8827 (pp20) REVERT: D 59 MET cc_start: 0.9125 (tpt) cc_final: 0.8703 (tpt) REVERT: D 62 MET cc_start: 0.9267 (mmp) cc_final: 0.9042 (mmp) REVERT: D 82 HIS cc_start: 0.9599 (t-90) cc_final: 0.9286 (t-90) REVERT: D 105 GLU cc_start: 0.9421 (pp20) cc_final: 0.9150 (pp20) REVERT: D 109 HIS cc_start: 0.9763 (m-70) cc_final: 0.9543 (m90) REVERT: E 104 PHE cc_start: 0.9660 (m-10) cc_final: 0.9395 (m-80) REVERT: F 62 LEU cc_start: 0.9834 (mt) cc_final: 0.9595 (pp) REVERT: F 74 GLU cc_start: 0.9598 (tm-30) cc_final: 0.9320 (tm-30) REVERT: H 62 MET cc_start: 0.9444 (mmp) cc_final: 0.9221 (mmm) REVERT: H 68 ASP cc_start: 0.9549 (t0) cc_final: 0.9290 (t0) REVERT: H 105 GLU cc_start: 0.9523 (pm20) cc_final: 0.9295 (pm20) REVERT: H 106 LEU cc_start: 0.9877 (mt) cc_final: 0.9515 (mt) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.1202 time to fit residues: 17.4215 Evaluate side-chains 65 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [49, 97, 60, 104, 65, 106, 38, 111, 78, 82, 22] chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 104 optimal weight: 30.0000 chunk 65 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 78 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS D 109 HIS E 76 GLN E 93 GLN E 108 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.028124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.021355 restraints weight = 229800.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.021996 restraints weight = 111684.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.022470 restraints weight = 68377.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.022737 restraints weight = 48096.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.022935 restraints weight = 38038.844| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14846 Z= 0.252 Angle : 0.770 8.548 21563 Z= 0.438 Chirality : 0.049 0.290 2456 Planarity : 0.005 0.046 1498 Dihedral : 33.917 174.602 4789 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.29 % Allowed : 3.03 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.28), residues: 825 helix: 1.85 (0.21), residues: 570 sheet: -1.67 (1.80), residues: 10 loop : -0.43 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 23 TYR 0.017 0.002 TYR G 39 PHE 0.017 0.002 PHE D 65 HIS 0.008 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.25 (14846) covalent geometry : angle 0.76974 / 0.44 (21563) hydrogen bonds : bond 0.10823 / 7.28 ( 882) hydrogen bonds : angle 3.68400 / 2.66 ( 2177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9657 (mmp) cc_final: 0.9360 (mmm) REVERT: A 93 GLN cc_start: 0.9364 (tp40) cc_final: 0.9037 (tp-100) REVERT: A 94 GLU cc_start: 0.9422 (mp0) cc_final: 0.9070 (mp0) REVERT: A 105 GLU cc_start: 0.9351 (mp0) cc_final: 0.9126 (mp0) REVERT: A 120 MET cc_start: 0.8582 (mtm) cc_final: 0.7953 (mpp) REVERT: D 59 MET cc_start: 0.8866 (tpt) cc_final: 0.8449 (tpt) REVERT: D 82 HIS cc_start: 0.9607 (t-90) cc_final: 0.9291 (t-90) REVERT: E 105 GLU cc_start: 0.9578 (mm-30) cc_final: 0.9165 (mm-30) REVERT: E 120 MET cc_start: 0.9335 (tpp) cc_final: 0.9037 (tpp) REVERT: F 74 GLU cc_start: 0.9624 (tm-30) cc_final: 0.9378 (tm-30) REVERT: H 62 MET cc_start: 0.9447 (mmp) cc_final: 0.9196 (mmm) REVERT: H 105 GLU cc_start: 0.9500 (pm20) cc_final: 0.9243 (pm20) REVERT: H 106 LEU cc_start: 0.9864 (mt) cc_final: 0.9505 (mt) outliers start: 2 outliers final: 2 residues processed: 84 average time/residue: 0.1153 time to fit residues: 14.2168 Evaluate side-chains 64 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [97, 37, 100, 15, 91, 96, 105, 44, 83, 70, 21] chunk 97 optimal weight: 30.0000 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 91 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 chunk 105 optimal weight: 40.0000 chunk 44 optimal weight: 0.7980 chunk 83 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS E 55 GLN E 108 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.027933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.021186 restraints weight = 230633.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.021826 restraints weight = 111413.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.022208 restraints weight = 68567.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.022530 restraints weight = 49836.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.022740 restraints weight = 39108.764| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14846 Z= 0.244 Angle : 0.750 8.254 21563 Z= 0.428 Chirality : 0.049 0.288 2456 Planarity : 0.005 0.046 1498 Dihedral : 33.940 176.556 4789 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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 are not related in a simple way. whole: 1.84 (0.28), residues: 825 helix: 1.94 (0.21), residues: 570 sheet: -1.50 (1.87), residues: 10 loop : -0.33 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 23 TYR 0.017 0.002 TYR E 99 PHE 0.012 0.002 PHE A 67 HIS 0.006 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.24 (14846) covalent geometry : angle 0.75021 / 0.43 (21563) hydrogen bonds : bond 0.08755 / 5.87 ( 882) hydrogen bonds : angle 3.70133 / 2.66 ( 2177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9628 (mmp) cc_final: 0.9276 (mmm) REVERT: A 93 GLN cc_start: 0.9537 (tp40) cc_final: 0.9181 (tm-30) REVERT: A 97 GLU cc_start: 0.9399 (pp20) cc_final: 0.9021 (pp20) REVERT: A 120 MET cc_start: 0.8558 (mtm) cc_final: 0.7909 (mpp) REVERT: D 82 HIS cc_start: 0.9614 (t-90) cc_final: 0.9313 (t-90) REVERT: D 105 GLU cc_start: 0.9425 (pp20) cc_final: 0.9207 (pp20) REVERT: D 108 LYS cc_start: 0.9699 (mtmm) cc_final: 0.9478 (ptpp) REVERT: E 105 GLU cc_start: 0.9599 (mm-30) cc_final: 0.9142 (mm-30) REVERT: E 120 MET cc_start: 0.9286 (tpp) cc_final: 0.8898 (mmm) REVERT: F 62 LEU cc_start: 0.9848 (mt) cc_final: 0.9625 (pp) REVERT: F 74 GLU cc_start: 0.9639 (tm-30) cc_final: 0.9377 (tm-30) REVERT: G 24 GLN cc_start: 0.9218 (mp10) cc_final: 0.9010 (mp10) REVERT: G 41 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8444 (tm-30) REVERT: H 62 MET cc_start: 0.9463 (mmp) cc_final: 0.9253 (mmp) REVERT: H 105 GLU cc_start: 0.9509 (pm20) cc_final: 0.9289 (pm20) REVERT: H 106 LEU cc_start: 0.9858 (mt) cc_final: 0.9477 (mt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1245 time to fit residues: 15.3525 Evaluate side-chains 60 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [38, 93, 105, 70, 7, 100, 103, 27, 67, 42, 44] chunk 38 optimal weight: 8.9990 chunk 93 optimal weight: 30.0000 chunk 105 optimal weight: 40.0000 chunk 70 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 27 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.028100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.021320 restraints weight = 228617.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.021967 restraints weight = 110088.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.022373 restraints weight = 67578.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.022693 restraints weight = 48825.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.022854 restraints weight = 38154.756| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14846 Z= 0.203 Angle : 0.723 8.186 21563 Z= 0.413 Chirality : 0.048 0.283 2456 Planarity : 0.005 0.043 1498 Dihedral : 33.862 175.377 4789 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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 are not related in a simple way. whole: 1.75 (0.28), residues: 825 helix: 1.80 (0.21), residues: 582 sheet: -1.59 (1.83), residues: 10 loop : -0.29 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 83 TYR 0.011 0.002 TYR G 39 PHE 0.031 0.003 PHE G 25 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.20 (14846) covalent geometry : angle 0.72279 / 0.41 (21563) hydrogen bonds : bond 0.08051 / 5.35 ( 882) hydrogen bonds : angle 3.69926 / 2.67 ( 2177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9639 (mmp) cc_final: 0.9188 (mmm) REVERT: A 93 GLN cc_start: 0.9537 (tp40) cc_final: 0.9149 (tm-30) REVERT: A 94 GLU cc_start: 0.9498 (mp0) cc_final: 0.8791 (mp0) REVERT: A 97 GLU cc_start: 0.9365 (pp20) cc_final: 0.9001 (pp20) REVERT: A 104 PHE cc_start: 0.9314 (m-10) cc_final: 0.8842 (m-80) REVERT: A 105 GLU cc_start: 0.9372 (mp0) cc_final: 0.9160 (mp0) REVERT: A 120 MET cc_start: 0.8543 (mtm) cc_final: 0.8007 (mtt) REVERT: B 63 GLU cc_start: 0.9455 (mt-10) cc_final: 0.9234 (pt0) REVERT: D 59 MET cc_start: 0.8713 (tpt) cc_final: 0.8477 (tpt) REVERT: D 82 HIS cc_start: 0.9598 (t-90) cc_final: 0.9285 (t-90) REVERT: D 105 GLU cc_start: 0.9408 (pp20) cc_final: 0.9151 (pp20) REVERT: D 108 LYS cc_start: 0.9701 (mtmm) cc_final: 0.9475 (ptpp) REVERT: E 105 GLU cc_start: 0.9591 (mm-30) cc_final: 0.9165 (mm-30) REVERT: E 120 MET cc_start: 0.9281 (tpp) cc_final: 0.8989 (tpp) REVERT: F 62 LEU cc_start: 0.9848 (mt) cc_final: 0.9616 (pp) REVERT: F 74 GLU cc_start: 0.9644 (tm-30) cc_final: 0.9382 (tm-30) REVERT: G 24 GLN cc_start: 0.9182 (mp10) cc_final: 0.8934 (mp10) REVERT: G 41 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8442 (tm-30) REVERT: H 62 MET cc_start: 0.9469 (mmp) cc_final: 0.9262 (mmp) REVERT: H 105 GLU cc_start: 0.9479 (pm20) cc_final: 0.9233 (pm20) REVERT: H 106 LEU cc_start: 0.9860 (mt) cc_final: 0.9552 (mt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1295 time to fit residues: 15.5389 Evaluate side-chains 64 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [96, 48, 68, 18, 29, 36, 75, 59, 38, 106, 46] chunk 96 optimal weight: 30.0000 chunk 48 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN E 108 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.027304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.020605 restraints weight = 235757.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.021253 restraints weight = 115259.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.021633 restraints weight = 70639.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.021962 restraints weight = 51201.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.022159 restraints weight = 39870.479| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14846 Z= 0.255 Angle : 0.773 8.489 21563 Z= 0.435 Chirality : 0.049 0.293 2456 Planarity : 0.005 0.054 1498 Dihedral : 33.917 178.671 4789 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.14 % Allowed : 3.03 % Favored : 96.83 % 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 are not related in a simple way. whole: 1.50 (0.28), residues: 825 helix: 1.62 (0.21), residues: 582 sheet: -1.67 (1.85), residues: 10 loop : -0.39 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 23 TYR 0.013 0.002 TYR G 39 PHE 0.015 0.002 PHE G 25 HIS 0.008 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.26 (14846) covalent geometry : angle 0.77270 / 0.44 (21563) hydrogen bonds : bond 0.10505 / 7.00 ( 882) hydrogen bonds : angle 3.83666 / 2.76 ( 2177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9612 (mmp) cc_final: 0.9178 (mmm) REVERT: A 93 GLN cc_start: 0.9549 (tp40) cc_final: 0.9296 (tm-30) REVERT: A 94 GLU cc_start: 0.9424 (mp0) cc_final: 0.8708 (mp0) REVERT: A 120 MET cc_start: 0.8596 (mtm) cc_final: 0.8025 (mtt) REVERT: B 63 GLU cc_start: 0.9455 (mt-10) cc_final: 0.9211 (mt-10) REVERT: D 82 HIS cc_start: 0.9601 (t-90) cc_final: 0.9299 (t-90) REVERT: E 120 MET cc_start: 0.9248 (tpp) cc_final: 0.8968 (tpp) REVERT: F 74 GLU cc_start: 0.9661 (tm-30) cc_final: 0.9405 (tm-30) REVERT: G 24 GLN cc_start: 0.9189 (mp10) cc_final: 0.8874 (mp10) REVERT: H 62 MET cc_start: 0.9486 (mmp) cc_final: 0.9280 (mmp) REVERT: H 106 LEU cc_start: 0.9851 (mt) cc_final: 0.9465 (mt) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1081 time to fit residues: 12.1209 Evaluate side-chains 55 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [111, 50, 94, 25, 88, 87, 49, 81, 100, 1, 48] chunk 111 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 40.0000 chunk 87 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.027846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.021125 restraints weight = 229204.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.021774 restraints weight = 110921.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.022165 restraints weight = 67785.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.022469 restraints weight = 49021.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.022651 restraints weight = 38743.828| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14846 Z= 0.195 Angle : 0.727 7.974 21563 Z= 0.414 Chirality : 0.048 0.285 2456 Planarity : 0.004 0.044 1498 Dihedral : 33.907 177.043 4789 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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 are not related in a simple way. whole: 1.70 (0.29), residues: 825 helix: 1.85 (0.21), residues: 570 sheet: -1.61 (1.86), residues: 10 loop : -0.43 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 11 TYR 0.010 0.002 TYR G 39 PHE 0.011 0.002 PHE G 25 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.20 (14846) covalent geometry : angle 0.72685 / 0.41 (21563) hydrogen bonds : bond 0.07742 / 5.11 ( 882) hydrogen bonds : angle 3.81915 / 2.74 ( 2177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9652 (mmp) cc_final: 0.9382 (mmm) REVERT: A 93 GLN cc_start: 0.9537 (tp40) cc_final: 0.9098 (tp-100) REVERT: A 94 GLU cc_start: 0.9498 (mp0) cc_final: 0.9011 (mp0) REVERT: A 97 GLU cc_start: 0.9350 (pp20) cc_final: 0.8928 (pp20) REVERT: A 104 PHE cc_start: 0.9328 (m-10) cc_final: 0.8838 (m-80) REVERT: A 120 MET cc_start: 0.8517 (mtm) cc_final: 0.7925 (mtt) REVERT: B 63 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9191 (mt-10) REVERT: D 82 HIS cc_start: 0.9595 (t-90) cc_final: 0.9292 (t-90) REVERT: D 105 GLU cc_start: 0.9399 (pp20) cc_final: 0.9098 (pp20) REVERT: D 108 LYS cc_start: 0.9690 (mtmm) cc_final: 0.9462 (ptpp) REVERT: E 120 MET cc_start: 0.9222 (tpp) cc_final: 0.8993 (tpp) REVERT: F 74 GLU cc_start: 0.9638 (tm-30) cc_final: 0.9375 (tm-30) REVERT: G 24 GLN cc_start: 0.9216 (mp10) cc_final: 0.8913 (mp10) REVERT: H 62 MET cc_start: 0.9456 (mmp) cc_final: 0.9247 (mmp) REVERT: H 105 GLU cc_start: 0.9489 (pm20) cc_final: 0.9251 (pm20) REVERT: H 106 LEU cc_start: 0.9858 (mt) cc_final: 0.9540 (mt) REVERT: H 121 TYR cc_start: 0.9328 (t80) cc_final: 0.9108 (t80) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1071 time to fit residues: 12.7026 Evaluate side-chains 59 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [62, 17, 73, 74, 51, 85, 47, 55, 37, 63, 32] chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 40.0000 chunk 74 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.027803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.021127 restraints weight = 229379.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.021750 restraints weight = 110640.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.022148 restraints weight = 67941.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.022465 restraints weight = 49048.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.022680 restraints weight = 38804.497| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14846 Z= 0.202 Angle : 0.731 8.449 21563 Z= 0.415 Chirality : 0.047 0.282 2456 Planarity : 0.004 0.046 1498 Dihedral : 33.825 176.328 4789 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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 are not related in a simple way. whole: 1.69 (0.29), residues: 825 helix: 1.85 (0.21), residues: 570 sheet: -1.59 (1.87), residues: 10 loop : -0.45 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 23 TYR 0.014 0.002 TYR D 42 PHE 0.010 0.002 PHE B 100 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.20 (14846) covalent geometry : angle 0.73115 / 0.41 (21563) hydrogen bonds : bond 0.07903 / 5.23 ( 882) hydrogen bonds : angle 3.84006 / 2.77 ( 2177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9637 (mmp) cc_final: 0.9339 (mmm) REVERT: A 93 GLN cc_start: 0.9528 (tp40) cc_final: 0.9033 (tm-30) REVERT: A 94 GLU cc_start: 0.9494 (mp0) cc_final: 0.8875 (mp0) REVERT: A 97 GLU cc_start: 0.9365 (pp20) cc_final: 0.8784 (pp20) REVERT: A 104 PHE cc_start: 0.9317 (m-10) cc_final: 0.9018 (m-10) REVERT: A 120 MET cc_start: 0.8486 (mtm) cc_final: 0.7866 (mtt) REVERT: B 63 GLU cc_start: 0.9443 (mt-10) cc_final: 0.9184 (pt0) REVERT: D 82 HIS cc_start: 0.9605 (t-90) cc_final: 0.9306 (t-90) REVERT: D 108 LYS cc_start: 0.9681 (mtmm) cc_final: 0.9440 (ptpp) REVERT: E 120 MET cc_start: 0.9221 (tpp) cc_final: 0.8984 (tpp) REVERT: F 74 GLU cc_start: 0.9637 (tm-30) cc_final: 0.9373 (tm-30) REVERT: G 24 GLN cc_start: 0.9207 (mp10) cc_final: 0.8910 (mp10) REVERT: H 62 MET cc_start: 0.9454 (mmp) cc_final: 0.9238 (mmp) REVERT: H 105 GLU cc_start: 0.9488 (pm20) cc_final: 0.9204 (pm20) REVERT: H 106 LEU cc_start: 0.9856 (mt) cc_final: 0.9492 (mt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1142 time to fit residues: 13.4922 Evaluate side-chains 59 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [51, 55, 5, 90, 103, 62, 8, 23, 41, 98, 76] chunk 51 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 90 optimal weight: 50.0000 chunk 103 optimal weight: 30.0000 chunk 62 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 30.0000 chunk 76 optimal weight: 30.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.028171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.021434 restraints weight = 226644.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.022083 restraints weight = 108543.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.022536 restraints weight = 65958.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.022810 restraints weight = 46971.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.023005 restraints weight = 36948.129| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14846 Z= 0.167 Angle : 0.700 7.574 21563 Z= 0.400 Chirality : 0.047 0.278 2456 Planarity : 0.004 0.045 1498 Dihedral : 33.733 176.418 4789 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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 are not related in a simple way. whole: 1.90 (0.29), residues: 825 helix: 2.03 (0.21), residues: 566 sheet: -1.59 (1.87), residues: 10 loop : -0.40 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 23 TYR 0.010 0.002 TYR C 57 PHE 0.021 0.002 PHE G 25 HIS 0.013 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.17 (14846) covalent geometry : angle 0.70005 / 0.40 (21563) hydrogen bonds : bond 0.06378 / 4.20 ( 882) hydrogen bonds : angle 3.70984 / 2.68 ( 2177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9618 (mmp) cc_final: 0.9285 (mmm) REVERT: A 93 GLN cc_start: 0.9525 (tp40) cc_final: 0.9053 (tm-30) REVERT: A 94 GLU cc_start: 0.9469 (mp0) cc_final: 0.8897 (mp0) REVERT: A 97 GLU cc_start: 0.9364 (pp20) cc_final: 0.8775 (pp20) REVERT: A 104 PHE cc_start: 0.9294 (m-10) cc_final: 0.8985 (m-10) REVERT: A 120 MET cc_start: 0.8456 (mtm) cc_final: 0.7837 (mtt) REVERT: B 63 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9166 (pt0) REVERT: D 82 HIS cc_start: 0.9588 (t-90) cc_final: 0.9282 (t-90) REVERT: D 108 LYS cc_start: 0.9709 (mtmm) cc_final: 0.9458 (ptpp) REVERT: D 109 HIS cc_start: 0.9764 (m170) cc_final: 0.9434 (m-70) REVERT: E 120 MET cc_start: 0.9221 (tpp) cc_final: 0.8980 (tpp) REVERT: F 74 GLU cc_start: 0.9642 (tm-30) cc_final: 0.9368 (tm-30) REVERT: G 24 GLN cc_start: 0.9176 (mp10) cc_final: 0.8892 (mp10) REVERT: H 62 MET cc_start: 0.9470 (mmp) cc_final: 0.9236 (mmp) REVERT: H 105 GLU cc_start: 0.9499 (pm20) cc_final: 0.9219 (pm20) REVERT: H 106 LEU cc_start: 0.9863 (mt) cc_final: 0.9485 (mt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1295 time to fit residues: 15.9680 Evaluate side-chains 61 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [82, 111, 48, 107, 25, 38, 11, 29, 98, 7, 72] chunk 82 optimal weight: 30.0000 chunk 111 optimal weight: 0.0010 chunk 48 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 98 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 72 optimal weight: 50.0000 overall best weight: 4.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.027770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.021114 restraints weight = 228644.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.021776 restraints weight = 110123.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.022202 restraints weight = 67016.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.022470 restraints weight = 48058.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.022634 restraints weight = 38053.978| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14846 Z= 0.200 Angle : 0.723 8.229 21563 Z= 0.410 Chirality : 0.047 0.279 2456 Planarity : 0.005 0.049 1498 Dihedral : 33.670 176.388 4789 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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 are not related in a simple way. whole: 1.74 (0.29), residues: 825 helix: 1.89 (0.21), residues: 566 sheet: -1.65 (1.84), residues: 10 loop : -0.39 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 23 TYR 0.013 0.002 TYR H 37 PHE 0.025 0.002 PHE G 25 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.20 (14846) covalent geometry : angle 0.72260 / 0.41 (21563) hydrogen bonds : bond 0.07713 / 5.11 ( 882) hydrogen bonds : angle 3.79395 / 2.74 ( 2177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9615 (mmp) cc_final: 0.9293 (mmm) REVERT: A 93 GLN cc_start: 0.9525 (tp40) cc_final: 0.9072 (tm-30) REVERT: A 94 GLU cc_start: 0.9470 (mp0) cc_final: 0.8921 (mp0) REVERT: A 97 GLU cc_start: 0.9373 (pp20) cc_final: 0.8790 (pp20) REVERT: A 104 PHE cc_start: 0.9308 (m-10) cc_final: 0.8981 (m-10) REVERT: A 120 MET cc_start: 0.8441 (mtm) cc_final: 0.7817 (mtt) REVERT: B 63 GLU cc_start: 0.9440 (mt-10) cc_final: 0.9182 (pt0) REVERT: D 82 HIS cc_start: 0.9596 (t-90) cc_final: 0.9291 (t-90) REVERT: D 109 HIS cc_start: 0.9786 (m170) cc_final: 0.9549 (m90) REVERT: E 120 MET cc_start: 0.9198 (tpp) cc_final: 0.8969 (tpp) REVERT: F 74 GLU cc_start: 0.9640 (tm-30) cc_final: 0.9370 (tm-30) REVERT: H 62 MET cc_start: 0.9442 (mmp) cc_final: 0.9209 (mmp) REVERT: H 105 GLU cc_start: 0.9506 (pm20) cc_final: 0.9279 (pm20) REVERT: H 106 LEU cc_start: 0.9860 (mt) cc_final: 0.9430 (mt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1218 time to fit residues: 13.7859 Evaluate side-chains 57 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [66, 106, 81, 103, 48, 22, 100, 89, 94, 46, 79] chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 48 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 89 optimal weight: 50.0000 chunk 94 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 27 GLN F 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.026967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.020334 restraints weight = 236571.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.021020 restraints weight = 115915.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.021459 restraints weight = 70942.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.021689 restraints weight = 49899.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.021893 restraints weight = 40041.763| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14846 Z= 0.262 Angle : 0.772 7.678 21563 Z= 0.435 Chirality : 0.048 0.285 2456 Planarity : 0.005 0.049 1498 Dihedral : 33.800 177.576 4789 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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 are not related in a simple way. whole: 1.35 (0.28), residues: 825 helix: 1.59 (0.21), residues: 568 sheet: -1.68 (1.82), residues: 10 loop : -0.57 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 23 TYR 0.013 0.002 TYR H 37 PHE 0.029 0.002 PHE G 25 HIS 0.008 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.26 (14846) covalent geometry : angle 0.77197 / 0.44 (21563) hydrogen bonds : bond 0.10199 / 6.78 ( 882) hydrogen bonds : angle 4.01937 / 2.91 ( 2177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1898.81 seconds wall clock time: 33 minutes 44.41 seconds (2024.41 seconds total)