Starting phenix.real_space_refine on Wed Mar 4 18:16:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pfv_13381/03_2026/7pfv_13381.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pfv_13381/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7pfv_13381/03_2026/7pfv_13381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pfv_13381/03_2026/7pfv_13381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pfv_13381/03_2026/7pfv_13381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pfv_13381/03_2026/7pfv_13381.map" } 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-dev-5986/lib/python3.9/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: 1.12 Conformation dependent library (CDL) restraints added in 388.0 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: 2.38 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: 3.09 Time building geometry restraints manager: 1.53 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=" CD GLU A 97 " pdb=" OE1 GLU A 97 " ideal model delta sigma weight residual 1.249 1.211 0.038 1.90e-02 2.77e+03 4.01e+00 bond pdb=" CG GLU A 105 " pdb=" CD GLU A 105 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.94e+00 bond pdb=" CG GLU A 97 " pdb=" CD GLU A 97 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.81e+00 bond pdb=" C3' DG I 158 " pdb=" O3' DG I 158 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.69e+00 bond pdb=" CD GLU B 74 " pdb=" OE1 GLU B 74 " ideal model delta sigma weight residual 1.249 1.214 0.035 1.90e-02 2.77e+03 3.36e+00 ... (remaining 14841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 20887 2.16 - 4.31: 609 4.31 - 6.47: 44 6.47 - 8.62: 20 8.62 - 10.78: 3 Bond angle restraints: 21563 Sorted by residual: 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 angle pdb=" N GLU A 97 " pdb=" CA GLU A 97 " pdb=" CB GLU A 97 " ideal model delta sigma weight residual 110.39 118.91 -8.52 1.66e+00 3.63e-01 2.63e+01 angle pdb=" N GLU A 105 " pdb=" CA GLU A 105 " pdb=" CB GLU A 105 " ideal model delta sigma weight residual 110.28 117.86 -7.58 1.55e+00 4.16e-01 2.39e+01 angle pdb=" N GLU B 74 " pdb=" CA GLU B 74 " pdb=" CB GLU B 74 " ideal model delta sigma weight residual 110.28 117.50 -7.22 1.55e+00 4.16e-01 2.17e+01 angle pdb=" N GLU A 94 " pdb=" CA GLU A 94 " pdb=" CB GLU A 94 " ideal model delta sigma weight residual 110.22 117.34 -7.12 1.54e+00 4.22e-01 2.14e+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 - 0.046: 1798 0.046 - 0.092: 526 0.092 - 0.137: 115 0.137 - 0.183: 14 0.183 - 0.229: 3 Chirality restraints: 2456 Sorted by residual: 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 chirality pdb=" CA GLU A 97 " pdb=" N GLU A 97 " pdb=" C GLU A 97 " pdb=" CB GLU A 97 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+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: 2.320 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.960 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 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 : 0.006 0.058 14846 Z= 0.286 Angle : 0.865 10.776 21563 Z= 0.502 Chirality : 0.045 0.229 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 covalent geometry : bond 0.00620 (14846) covalent geometry : angle 0.86463 (21563) hydrogen bonds : bond 0.11251 ( 882) hydrogen bonds : angle 4.69223 ( 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 : 0.326 Fit side-chains revert: symmetry clash 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: 0.8590 (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: 0.9301 (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: 0.1251 time to fit residues: 18.0586 Evaluate side-chains 70 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2899 r_free = 0.2899 target = 0.029112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.022149 restraints weight = 219598.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.022843 restraints weight = 105571.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.023311 restraints weight = 64201.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.023584 restraints weight = 45113.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.023768 restraints weight = 35899.646| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14846 Z= 0.222 Angle : 0.625 5.722 21563 Z= 0.377 Chirality : 0.035 0.161 2456 Planarity : 0.005 0.044 1498 Dihedral : 33.411 179.595 4789 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.14 % Allowed : 3.46 % Favored : 96.39 % 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: 1.72 (0.28), residues: 825 helix: 1.80 (0.21), residues: 582 sheet: -2.11 (1.60), residues: 10 loop : -0.33 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 29 TYR 0.015 0.002 TYR G 39 PHE 0.016 0.002 PHE A 104 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00476 (14846) covalent geometry : angle 0.62471 (21563) hydrogen bonds : bond 0.06024 ( 882) hydrogen bonds : angle 3.42975 ( 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 95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9725 (tmtt) cc_final: 0.9490 (ptpp) REVERT: A 90 MET cc_start: 0.9647 (mmp) cc_final: 0.8991 (mmp) REVERT: A 94 GLU cc_start: 0.9475 (mp0) cc_final: 0.8979 (mp0) REVERT: A 120 MET cc_start: 0.8588 (mtm) cc_final: 0.7918 (mpp) REVERT: B 54 THR cc_start: 0.9849 (p) cc_final: 0.9421 (p) REVERT: D 59 MET cc_start: 0.9040 (tpt) cc_final: 0.8682 (tpt) REVERT: D 82 HIS cc_start: 0.9578 (t-90) cc_final: 0.9247 (t-90) REVERT: D 105 GLU cc_start: 0.9434 (pp20) cc_final: 0.9156 (pp20) REVERT: D 108 LYS cc_start: 0.9669 (mtmm) cc_final: 0.9438 (ptpp) REVERT: D 109 HIS cc_start: 0.9728 (m-70) cc_final: 0.9358 (m90) REVERT: F 62 LEU cc_start: 0.9838 (mt) cc_final: 0.9625 (pp) REVERT: F 74 GLU cc_start: 0.9600 (tm-30) cc_final: 0.9334 (tm-30) REVERT: H 62 MET cc_start: 0.9442 (mmp) cc_final: 0.9190 (mmm) REVERT: H 105 GLU cc_start: 0.9519 (pm20) cc_final: 0.9254 (pm20) REVERT: H 106 LEU cc_start: 0.9872 (mt) cc_final: 0.9473 (mt) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1247 time to fit residues: 16.7078 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 : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 93 GLN G 68 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.027087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.020402 restraints weight = 237506.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.021045 restraints weight = 115816.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.021422 restraints weight = 70843.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.021724 restraints weight = 51302.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.021878 restraints weight = 40082.461| |-----------------------------------------------------------------------------| r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 14846 Z= 0.331 Angle : 0.698 5.780 21563 Z= 0.416 Chirality : 0.038 0.165 2456 Planarity : 0.005 0.046 1498 Dihedral : 33.676 179.627 4789 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % 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: 1.81 (0.21), residues: 578 sheet: -1.83 (1.80), residues: 10 loop : -0.37 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 23 TYR 0.018 0.002 TYR G 39 PHE 0.016 0.002 PHE D 65 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00704 (14846) covalent geometry : angle 0.69830 (21563) hydrogen bonds : bond 0.09097 ( 882) hydrogen bonds : angle 3.86571 ( 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 83 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.309 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: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8680 (mtm) cc_final: 0.8116 (mtt) REVERT: B 63 GLU cc_start: 0.9458 (mt-10) cc_final: 0.9227 (mt-10) REVERT: D 62 MET cc_start: 0.9336 (mmp) cc_final: 0.9128 (mmp) REVERT: D 82 HIS cc_start: 0.9593 (t-90) cc_final: 0.9284 (t-90) REVERT: D 108 LYS cc_start: 0.9680 (mtmm) cc_final: 0.9437 (ptpp) REVERT: E 120 MET cc_start: 0.9170 (tpp) cc_final: 0.8909 (tpp) REVERT: F 74 GLU cc_start: 0.9637 (tm-30) cc_final: 0.9398 (tm-30) REVERT: H 62 MET cc_start: 0.9499 (mmp) cc_final: 0.9297 (mmm) REVERT: H 105 GLU cc_start: 0.9504 (pm20) cc_final: 0.9246 (pm20) REVERT: H 106 LEU cc_start: 0.9857 (mt) cc_final: 0.9536 (mt) REVERT: H 121 TYR cc_start: 0.9526 (t80) cc_final: 0.9261 (t80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1173 time to fit residues: 14.0806 Evaluate side-chains 56 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.028393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.021603 restraints weight = 226246.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.022288 restraints weight = 107685.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.022707 restraints weight = 65300.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.023021 restraints weight = 46949.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.023209 restraints weight = 36802.537| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14846 Z= 0.202 Angle : 0.609 6.128 21563 Z= 0.365 Chirality : 0.035 0.148 2456 Planarity : 0.004 0.047 1498 Dihedral : 33.322 177.104 4789 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 2.21 (0.28), residues: 825 helix: 2.18 (0.21), residues: 578 sheet: -1.68 (1.78), residues: 10 loop : -0.14 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 69 TYR 0.011 0.001 TYR F 72 PHE 0.018 0.002 PHE G 25 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00429 (14846) covalent geometry : angle 0.60939 (21563) hydrogen bonds : bond 0.05473 ( 882) hydrogen bonds : angle 3.38120 ( 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 89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.295 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: symmetry clash REVERT: A 90 MET cc_start: 0.9475 (mmp) cc_final: 0.9206 (mmp) REVERT: A 94 GLU cc_start: 0.9362 (mp0) cc_final: 0.8910 (mp0) REVERT: A 104 PHE cc_start: 0.9333 (m-10) cc_final: 0.8844 (m-80) REVERT: A 105 GLU cc_start: 0.9296 (mp0) cc_final: 0.9093 (mp0) REVERT: A 120 MET cc_start: 0.8429 (mtm) cc_final: 0.7875 (mtt) REVERT: B 20 LYS cc_start: 0.7946 (mmpt) cc_final: 0.7361 (tptt) REVERT: B 63 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9124 (pt0) REVERT: D 82 HIS cc_start: 0.9575 (t-90) cc_final: 0.9249 (t-90) REVERT: D 105 GLU cc_start: 0.9467 (pp20) cc_final: 0.9196 (pp20) REVERT: D 108 LYS cc_start: 0.9655 (mtmm) cc_final: 0.9389 (ptpp) REVERT: E 106 ASP cc_start: 0.9445 (m-30) cc_final: 0.9197 (m-30) REVERT: E 120 MET cc_start: 0.9183 (tpp) cc_final: 0.8909 (tpp) REVERT: F 62 LEU cc_start: 0.9846 (mt) cc_final: 0.9614 (pp) REVERT: F 74 GLU cc_start: 0.9618 (tm-30) cc_final: 0.9351 (tm-30) REVERT: H 62 MET cc_start: 0.9456 (mmp) cc_final: 0.9227 (mmp) REVERT: H 105 GLU cc_start: 0.9540 (pm20) cc_final: 0.9292 (pm20) REVERT: H 106 LEU cc_start: 0.9864 (mt) cc_final: 0.9436 (mt) REVERT: H 121 TYR cc_start: 0.9540 (t80) cc_final: 0.9251 (t80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1184 time to fit residues: 15.0358 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 : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.028267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.021511 restraints weight = 225959.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.022201 restraints weight = 107872.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.022639 restraints weight = 65159.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.022892 restraints weight = 45805.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.023127 restraints weight = 36515.486| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14846 Z= 0.200 Angle : 0.602 5.757 21563 Z= 0.362 Chirality : 0.034 0.146 2456 Planarity : 0.004 0.047 1498 Dihedral : 33.151 178.590 4789 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: 2.29 (0.29), residues: 825 helix: 2.22 (0.21), residues: 578 sheet: -1.69 (1.69), residues: 10 loop : -0.08 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.016 0.002 TYR E 99 PHE 0.020 0.002 PHE D 65 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00427 (14846) covalent geometry : angle 0.60159 (21563) hydrogen bonds : bond 0.05588 ( 882) hydrogen bonds : angle 3.37002 ( 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 92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.349 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9090 (t80) cc_final: 0.8582 (t80) REVERT: A 94 GLU cc_start: 0.9358 (mp0) cc_final: 0.9045 (mp0) REVERT: A 104 PHE cc_start: 0.9380 (m-10) cc_final: 0.8859 (m-80) REVERT: A 105 GLU cc_start: 0.9294 (mp0) cc_final: 0.9090 (mp0) REVERT: A 120 MET cc_start: 0.8375 (mtm) cc_final: 0.7794 (mtt) REVERT: B 20 LYS cc_start: 0.7875 (mmpt) cc_final: 0.7297 (tptt) REVERT: B 63 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9096 (pt0) REVERT: D 62 MET cc_start: 0.9204 (mmp) cc_final: 0.9001 (mmp) REVERT: D 82 HIS cc_start: 0.9568 (t-90) cc_final: 0.9256 (t-90) REVERT: D 105 GLU cc_start: 0.9461 (pp20) cc_final: 0.9171 (pp20) REVERT: D 108 LYS cc_start: 0.9685 (mtmm) cc_final: 0.9415 (ptpp) REVERT: E 106 ASP cc_start: 0.9409 (m-30) cc_final: 0.9141 (m-30) REVERT: E 120 MET cc_start: 0.9205 (tpp) cc_final: 0.8939 (tpp) REVERT: F 62 LEU cc_start: 0.9857 (mt) cc_final: 0.9638 (pp) REVERT: F 74 GLU cc_start: 0.9622 (tm-30) cc_final: 0.9348 (tm-30) REVERT: H 105 GLU cc_start: 0.9546 (pm20) cc_final: 0.9234 (pm20) REVERT: H 106 LEU cc_start: 0.9858 (mt) cc_final: 0.9460 (mt) REVERT: H 121 TYR cc_start: 0.9520 (t80) cc_final: 0.9189 (t80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1232 time to fit residues: 16.1588 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 : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.028353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.021650 restraints weight = 224944.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.022326 restraints weight = 106430.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.022782 restraints weight = 64121.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.023030 restraints weight = 45225.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.023265 restraints weight = 36012.069| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14846 Z= 0.198 Angle : 0.598 5.961 21563 Z= 0.359 Chirality : 0.034 0.144 2456 Planarity : 0.004 0.047 1498 Dihedral : 33.077 178.607 4789 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.14 % Allowed : 1.88 % Favored : 97.98 % 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: 2.34 (0.29), residues: 825 helix: 2.24 (0.21), residues: 578 sheet: -1.57 (1.72), residues: 10 loop : 0.00 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.012 0.002 TYR E 99 PHE 0.007 0.001 PHE A 104 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00422 (14846) covalent geometry : angle 0.59836 (21563) hydrogen bonds : bond 0.05410 ( 882) hydrogen bonds : angle 3.32141 ( 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 91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.466 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9516 (mmp) cc_final: 0.9230 (mmp) REVERT: A 93 GLN cc_start: 0.9187 (mp10) cc_final: 0.8970 (mp10) REVERT: A 94 GLU cc_start: 0.9454 (mp0) cc_final: 0.9027 (mp0) REVERT: A 104 PHE cc_start: 0.9356 (m-10) cc_final: 0.8986 (m-10) REVERT: A 120 MET cc_start: 0.8280 (mtm) cc_final: 0.7719 (mtt) REVERT: B 20 LYS cc_start: 0.7696 (mmpt) cc_final: 0.7122 (tptt) REVERT: D 59 MET cc_start: 0.8636 (tpt) cc_final: 0.8135 (tpt) REVERT: D 62 MET cc_start: 0.9196 (mmp) cc_final: 0.8909 (mmp) REVERT: D 82 HIS cc_start: 0.9571 (t-90) cc_final: 0.9268 (t-90) REVERT: D 105 GLU cc_start: 0.9468 (pp20) cc_final: 0.9189 (pp20) REVERT: D 108 LYS cc_start: 0.9680 (mtmm) cc_final: 0.9411 (ptpp) REVERT: E 106 ASP cc_start: 0.9433 (m-30) cc_final: 0.9173 (m-30) REVERT: E 120 MET cc_start: 0.9169 (tpp) cc_final: 0.8914 (tpp) REVERT: F 62 LEU cc_start: 0.9849 (mt) cc_final: 0.9598 (pp) REVERT: F 63 GLU cc_start: 0.9732 (pt0) cc_final: 0.9495 (pt0) REVERT: F 74 GLU cc_start: 0.9614 (tm-30) cc_final: 0.9336 (tm-30) REVERT: H 59 MET cc_start: 0.8332 (tpt) cc_final: 0.8064 (tpt) REVERT: H 62 MET cc_start: 0.9454 (mmp) cc_final: 0.9238 (mmp) REVERT: H 105 GLU cc_start: 0.9537 (pm20) cc_final: 0.9229 (pm20) REVERT: H 106 LEU cc_start: 0.9854 (mt) cc_final: 0.9455 (mt) REVERT: H 121 TYR cc_start: 0.9528 (t80) cc_final: 0.9191 (t80) outliers start: 1 outliers final: 1 residues processed: 90 average time/residue: 0.1248 time to fit residues: 16.2119 Evaluate side-chains 67 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 110 ASN C 112 GLN F 93 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.026307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.019849 restraints weight = 241164.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.020452 restraints weight = 116494.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.020855 restraints weight = 71419.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.021091 restraints weight = 50650.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.021276 restraints weight = 40784.798| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 14846 Z= 0.354 Angle : 0.711 6.292 21563 Z= 0.420 Chirality : 0.038 0.152 2456 Planarity : 0.005 0.045 1498 Dihedral : 33.567 179.537 4789 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: 1.68 (0.28), residues: 825 helix: 1.69 (0.21), residues: 582 sheet: -1.32 (1.88), residues: 10 loop : -0.15 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 83 TYR 0.016 0.002 TYR G 39 PHE 0.025 0.003 PHE D 65 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00755 (14846) covalent geometry : angle 0.71095 (21563) hydrogen bonds : bond 0.10015 ( 882) hydrogen bonds : angle 4.00012 ( 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 79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.345 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: symmetry clash REVERT: A 67 PHE cc_start: 0.9262 (t80) cc_final: 0.8597 (t80) REVERT: A 104 PHE cc_start: 0.9366 (m-10) cc_final: 0.8873 (m-80) REVERT: A 120 MET cc_start: 0.8463 (mtm) cc_final: 0.7840 (mtt) REVERT: B 20 LYS cc_start: 0.7729 (mmpt) cc_final: 0.7111 (tptt) REVERT: D 59 MET cc_start: 0.8539 (tpt) cc_final: 0.8138 (tpt) REVERT: D 62 MET cc_start: 0.9290 (mmp) cc_final: 0.9010 (mmp) REVERT: D 82 HIS cc_start: 0.9580 (t-90) cc_final: 0.9304 (t-90) REVERT: D 105 GLU cc_start: 0.9446 (pp20) cc_final: 0.9153 (pp20) REVERT: D 108 LYS cc_start: 0.9662 (mtmm) cc_final: 0.9390 (ptpp) REVERT: E 106 ASP cc_start: 0.9431 (m-30) cc_final: 0.9158 (m-30) REVERT: E 120 MET cc_start: 0.9194 (tpp) cc_final: 0.8941 (tpp) REVERT: F 74 GLU cc_start: 0.9660 (tm-30) cc_final: 0.9410 (tm-30) REVERT: H 105 GLU cc_start: 0.9536 (pm20) cc_final: 0.9235 (pm20) REVERT: H 106 LEU cc_start: 0.9856 (mt) cc_final: 0.9483 (mt) REVERT: H 121 TYR cc_start: 0.9488 (t80) cc_final: 0.9090 (t80) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1227 time to fit residues: 13.9930 Evaluate side-chains 58 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.027757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.021156 restraints weight = 226027.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.021816 restraints weight = 108749.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.022217 restraints weight = 66081.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.022539 restraints weight = 47542.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.022707 restraints weight = 36904.397| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14846 Z= 0.210 Angle : 0.623 6.326 21563 Z= 0.372 Chirality : 0.035 0.137 2456 Planarity : 0.005 0.083 1498 Dihedral : 33.236 175.807 4789 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 2.10 (0.29), residues: 825 helix: 2.16 (0.21), residues: 568 sheet: -1.26 (1.85), residues: 10 loop : -0.28 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 69 TYR 0.009 0.002 TYR U 70 PHE 0.017 0.002 PHE G 25 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00449 (14846) covalent geometry : angle 0.62283 (21563) hydrogen bonds : bond 0.05854 ( 882) hydrogen bonds : angle 3.55420 ( 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 90 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.327 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9254 (t80) cc_final: 0.8546 (t80) REVERT: A 104 PHE cc_start: 0.9282 (m-10) cc_final: 0.8724 (m-80) REVERT: A 120 MET cc_start: 0.8285 (mtm) cc_final: 0.7692 (mtt) REVERT: B 20 LYS cc_start: 0.7703 (mmpt) cc_final: 0.6999 (tptt) REVERT: D 59 MET cc_start: 0.8478 (tpt) cc_final: 0.8135 (tpt) REVERT: D 62 MET cc_start: 0.9215 (mmp) cc_final: 0.8904 (mmp) REVERT: D 82 HIS cc_start: 0.9565 (t-90) cc_final: 0.9274 (t-90) REVERT: D 105 GLU cc_start: 0.9396 (pp20) cc_final: 0.9128 (pp20) REVERT: D 108 LYS cc_start: 0.9640 (mtmm) cc_final: 0.9366 (ptpp) REVERT: E 106 ASP cc_start: 0.9486 (m-30) cc_final: 0.9192 (m-30) REVERT: E 120 MET cc_start: 0.9185 (tpp) cc_final: 0.8956 (tpp) REVERT: F 62 LEU cc_start: 0.9842 (mt) cc_final: 0.9549 (pp) REVERT: F 63 GLU cc_start: 0.9663 (mt-10) cc_final: 0.9345 (mp0) REVERT: F 74 GLU cc_start: 0.9629 (tm-30) cc_final: 0.9358 (tm-30) REVERT: H 62 MET cc_start: 0.9438 (mmp) cc_final: 0.9226 (mmp) REVERT: H 99 ARG cc_start: 0.9223 (mpp80) cc_final: 0.8737 (mpp80) REVERT: H 105 GLU cc_start: 0.9546 (pm20) cc_final: 0.9209 (pm20) REVERT: H 106 LEU cc_start: 0.9855 (mt) cc_final: 0.9453 (mt) REVERT: H 121 TYR cc_start: 0.9500 (t80) cc_final: 0.9136 (t80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1247 time to fit residues: 16.0779 Evaluate side-chains 66 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.028524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.021849 restraints weight = 221784.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.022561 restraints weight = 105945.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.022982 restraints weight = 63685.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.023312 restraints weight = 45817.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.023517 restraints weight = 35350.338| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14846 Z= 0.179 Angle : 0.597 6.369 21563 Z= 0.357 Chirality : 0.034 0.169 2456 Planarity : 0.004 0.045 1498 Dihedral : 32.832 177.585 4789 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 2.32 (0.29), residues: 825 helix: 2.25 (0.21), residues: 578 sheet: -1.38 (1.82), residues: 10 loop : -0.10 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 23 TYR 0.009 0.001 TYR B 98 PHE 0.028 0.002 PHE D 65 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00379 (14846) covalent geometry : angle 0.59652 (21563) hydrogen bonds : bond 0.04724 ( 882) hydrogen bonds : angle 3.35007 ( 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 91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.312 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9260 (t80) cc_final: 0.8641 (t80) REVERT: A 90 MET cc_start: 0.9572 (mmp) cc_final: 0.9348 (mmm) REVERT: A 94 GLU cc_start: 0.9338 (mp0) cc_final: 0.8807 (mp0) REVERT: A 104 PHE cc_start: 0.9221 (m-10) cc_final: 0.8664 (m-80) REVERT: A 105 GLU cc_start: 0.9335 (mp0) cc_final: 0.9119 (mp0) REVERT: A 120 MET cc_start: 0.8043 (mtm) cc_final: 0.7503 (mpp) REVERT: B 85 ASP cc_start: 0.8740 (m-30) cc_final: 0.8530 (m-30) REVERT: D 59 MET cc_start: 0.8443 (tpt) cc_final: 0.8165 (tpt) REVERT: D 62 MET cc_start: 0.9212 (mmp) cc_final: 0.8892 (mmp) REVERT: D 82 HIS cc_start: 0.9566 (t-90) cc_final: 0.9274 (t-90) REVERT: D 105 GLU cc_start: 0.9357 (pp20) cc_final: 0.9072 (pp20) REVERT: D 108 LYS cc_start: 0.9641 (mtmm) cc_final: 0.9375 (ptpp) REVERT: E 106 ASP cc_start: 0.9485 (m-30) cc_final: 0.9148 (m-30) REVERT: E 120 MET cc_start: 0.9167 (tpp) cc_final: 0.8941 (tpp) REVERT: F 62 LEU cc_start: 0.9839 (mt) cc_final: 0.9527 (pp) REVERT: F 63 GLU cc_start: 0.9668 (mt-10) cc_final: 0.9253 (mp0) REVERT: F 74 GLU cc_start: 0.9624 (tm-30) cc_final: 0.9332 (tm-30) REVERT: H 62 MET cc_start: 0.9406 (mmp) cc_final: 0.9174 (mmp) REVERT: H 94 ILE cc_start: 0.9780 (mm) cc_final: 0.9550 (tt) REVERT: H 105 GLU cc_start: 0.9501 (pm20) cc_final: 0.9227 (pm20) REVERT: H 106 LEU cc_start: 0.9840 (mt) cc_final: 0.9424 (mt) REVERT: H 121 TYR cc_start: 0.9483 (t80) cc_final: 0.9107 (t80) REVERT: U 86 LEU cc_start: 0.9118 (tp) cc_final: 0.8597 (pp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1203 time to fit residues: 15.7714 Evaluate side-chains 67 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.025863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.019583 restraints weight = 246097.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.020203 restraints weight = 118919.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.020577 restraints weight = 72963.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.020826 restraints weight = 52087.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.020988 restraints weight = 41285.276| |-----------------------------------------------------------------------------| r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 14846 Z= 0.379 Angle : 0.738 6.703 21563 Z= 0.435 Chirality : 0.040 0.169 2456 Planarity : 0.006 0.052 1498 Dihedral : 33.700 179.914 4789 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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: 1.56 (0.28), residues: 825 helix: 1.69 (0.21), residues: 570 sheet: -1.34 (1.91), residues: 10 loop : -0.33 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 83 TYR 0.016 0.002 TYR H 40 PHE 0.016 0.002 PHE E 78 HIS 0.015 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00806 (14846) covalent geometry : angle 0.73754 (21563) hydrogen bonds : bond 0.09936 ( 882) hydrogen bonds : angle 4.14140 ( 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 : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9302 (t80) cc_final: 0.8691 (t80) REVERT: A 90 MET cc_start: 0.9600 (mmp) cc_final: 0.9384 (mmm) REVERT: A 94 GLU cc_start: 0.9420 (mp0) cc_final: 0.8975 (mp0) REVERT: A 104 PHE cc_start: 0.9296 (m-10) cc_final: 0.8780 (m-80) REVERT: A 120 MET cc_start: 0.8442 (mtm) cc_final: 0.7883 (mtt) REVERT: D 59 MET cc_start: 0.8585 (tpt) cc_final: 0.8248 (tpt) REVERT: D 62 MET cc_start: 0.9338 (mmp) cc_final: 0.9042 (mmp) REVERT: D 82 HIS cc_start: 0.9569 (t-90) cc_final: 0.9312 (t-90) REVERT: D 105 GLU cc_start: 0.9390 (pp20) cc_final: 0.9139 (pp20) REVERT: D 108 LYS cc_start: 0.9634 (mtmm) cc_final: 0.9354 (ptpp) REVERT: E 120 MET cc_start: 0.9255 (tpp) cc_final: 0.9012 (tpp) REVERT: F 74 GLU cc_start: 0.9667 (tm-30) cc_final: 0.9419 (tm-30) REVERT: H 105 GLU cc_start: 0.9520 (pm20) cc_final: 0.9224 (pm20) REVERT: H 106 LEU cc_start: 0.9855 (mt) cc_final: 0.9468 (mt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1119 time to fit residues: 12.6347 Evaluate side-chains 56 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 94 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.026669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.020271 restraints weight = 237397.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.020906 restraints weight = 112649.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.021296 restraints weight = 68115.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.021597 restraints weight = 48991.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.021791 restraints weight = 38348.796| |-----------------------------------------------------------------------------| r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14846 Z= 0.267 Angle : 0.668 6.445 21563 Z= 0.397 Chirality : 0.037 0.150 2456 Planarity : 0.005 0.085 1498 Dihedral : 33.578 177.467 4789 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: 1.70 (0.29), residues: 825 helix: 1.83 (0.21), residues: 570 sheet: -1.30 (1.87), residues: 10 loop : -0.37 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 23 TYR 0.011 0.002 TYR H 37 PHE 0.014 0.002 PHE G 25 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00571 (14846) covalent geometry : angle 0.66791 (21563) hydrogen bonds : bond 0.07542 ( 882) hydrogen bonds : angle 3.87025 ( 2177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.73 seconds wall clock time: 32 minutes 42.53 seconds (1962.53 seconds total)