Starting phenix.real_space_refine on Fri Jul 3 18:03:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pfv_13381/07_2026/7pfv_13381.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pfv_13381/07_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_13381/07_2026/7pfv_13381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pfv_13381/07_2026/7pfv_13381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pfv_13381/07_2026/7pfv_13381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pfv_13381/07_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-6108/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: 2.19, per 1000 atoms: 0.16 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: 0.87 Conformation dependent library (CDL) restraints added in 384.8 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: 1.92 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: 2.47 Time building geometry restraints manager: 1.19 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: 20432 2.16 - 4.31: 1053 4.31 - 6.47: 54 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: 1.580 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.330 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.230 ------------------------------------------------------------------------------- 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= 0.648 Angle : 0.998 10.776 21563 Z= 0.812 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 0.99769 / 0.81 (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 : 0.410 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: 0.1030 time to fit residues: 15.1206 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 : 0.242 ------------------------------------------------------------------------------- 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: 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: 7.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN D 109 HIS E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.029168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.022168 restraints weight = 219616.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.022849 restraints weight = 105708.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.023264 restraints weight = 64428.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.023650 restraints weight = 46533.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.023873 restraints weight = 35834.883| |-----------------------------------------------------------------------------| r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14846 Z= 0.194 Angle : 0.732 7.720 21563 Z= 0.427 Chirality : 0.049 0.287 2456 Planarity : 0.005 0.044 1498 Dihedral : 34.095 172.174 4789 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % 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: 1.46 (0.27), residues: 825 helix: 1.65 (0.21), residues: 576 sheet: -2.36 (1.51), residues: 10 loop : -0.51 (0.34), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.015 0.002 TYR G 39 PHE 0.032 0.002 PHE G 25 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.19 (14846) covalent geometry : angle 0.73186 / 0.43 (21563) hydrogen bonds : bond 0.07473 / 5.08 ( 882) hydrogen bonds : angle 3.70399 / 2.64 ( 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 93 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.9411 (tptp) cc_final: 0.9128 (tptp) REVERT: A 90 MET cc_start: 0.9662 (mmp) cc_final: 0.9448 (mmp) REVERT: A 93 GLN cc_start: 0.9197 (tp40) cc_final: 0.8879 (tp-100) REVERT: A 120 MET cc_start: 0.8557 (mtm) cc_final: 0.7935 (mpp) REVERT: D 59 MET cc_start: 0.9062 (tpt) cc_final: 0.8656 (tpt) REVERT: D 82 HIS cc_start: 0.9599 (t-90) cc_final: 0.9288 (t-90) REVERT: D 109 HIS cc_start: 0.9681 (m170) cc_final: 0.9437 (m170) REVERT: F 62 LEU cc_start: 0.9838 (mt) cc_final: 0.9619 (pp) REVERT: F 74 GLU cc_start: 0.9613 (tm-30) cc_final: 0.9353 (tm-30) REVERT: H 62 MET cc_start: 0.9449 (mmp) cc_final: 0.9208 (mmm) REVERT: H 68 ASP cc_start: 0.9542 (t0) cc_final: 0.9300 (t0) REVERT: H 105 GLU cc_start: 0.9516 (pm20) cc_final: 0.9266 (pm20) REVERT: H 106 LEU cc_start: 0.9877 (mt) cc_final: 0.9508 (mt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1129 time to fit residues: 15.2327 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 : 0.292 ------------------------------------------------------------------------------- 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: 1.9990 chunk 97 optimal weight: 30.0000 chunk 60 optimal weight: 6.9990 chunk 104 optimal weight: 30.0000 chunk 65 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.028194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.021406 restraints weight = 228703.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.022055 restraints weight = 110460.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.022512 restraints weight = 67860.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.022780 restraints weight = 48442.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.023009 restraints weight = 38432.318| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1569 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= 0.253 Angle : 0.744 8.445 21563 Z= 0.432 Chirality : 0.049 0.271 2456 Planarity : 0.005 0.045 1498 Dihedral : 34.055 173.737 4789 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.14 % Allowed : 2.89 % 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: 1.76 (0.28), residues: 825 helix: 1.89 (0.21), residues: 570 sheet: -1.73 (1.80), residues: 10 loop : -0.39 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 11 TYR 0.016 0.002 TYR G 39 PHE 0.017 0.002 PHE D 65 HIS 0.008 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.25 (14846) covalent geometry : angle 0.74365 / 0.43 (21563) hydrogen bonds : bond 0.10040 / 6.76 ( 882) hydrogen bonds : angle 3.72684 / 2.69 ( 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 82 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.389 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: 0.9658 (mmp) cc_final: 0.9365 (mmm) REVERT: A 93 GLN cc_start: 0.9382 (tp40) cc_final: 0.9059 (tp-100) REVERT: A 94 GLU cc_start: 0.9432 (mp0) cc_final: 0.9079 (mp0) REVERT: A 120 MET cc_start: 0.8557 (mtm) cc_final: 0.7939 (mpp) REVERT: D 59 MET cc_start: 0.8829 (tpt) cc_final: 0.8395 (tpt) REVERT: D 62 MET cc_start: 0.9236 (mmp) cc_final: 0.9033 (mmp) REVERT: D 82 HIS cc_start: 0.9611 (t-90) cc_final: 0.9298 (t-90) REVERT: E 120 MET cc_start: 0.9331 (tpp) cc_final: 0.9022 (tpp) REVERT: F 74 GLU cc_start: 0.9624 (tm-30) cc_final: 0.9376 (tm-30) REVERT: G 41 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8458 (tm-30) REVERT: H 62 MET cc_start: 0.9459 (mmp) cc_final: 0.9210 (mmm) REVERT: H 105 GLU cc_start: 0.9490 (pm20) cc_final: 0.9223 (pm20) REVERT: H 106 LEU cc_start: 0.9868 (mt) cc_final: 0.9518 (mt) outliers start: 1 outliers final: 1 residues processed: 82 average time/residue: 0.1355 time to fit residues: 16.0333 Evaluate side-chains 61 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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: 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: 30.0000 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 30.0000 chunk 70 optimal weight: 0.1980 chunk 21 optimal weight: 10.0000 overall best weight: 5.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.028083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.021280 restraints weight = 229563.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.021973 restraints weight = 111583.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.022383 restraints weight = 69095.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.022640 restraints weight = 48867.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.022876 restraints weight = 38991.108| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14846 Z= 0.232 Angle : 0.718 8.333 21563 Z= 0.416 Chirality : 0.048 0.266 2456 Planarity : 0.005 0.044 1498 Dihedral : 34.018 175.378 4789 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 1.93 (0.28), residues: 825 helix: 2.01 (0.21), residues: 570 sheet: -1.57 (1.85), residues: 10 loop : -0.31 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.014 0.002 TYR E 99 PHE 0.012 0.002 PHE A 104 HIS 0.006 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.23 (14846) covalent geometry : angle 0.71789 / 0.42 (21563) hydrogen bonds : bond 0.08512 / 5.70 ( 882) hydrogen bonds : angle 3.67395 / 2.64 ( 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 85 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9629 (mmp) cc_final: 0.9279 (mmm) REVERT: A 93 GLN cc_start: 0.9535 (tp40) cc_final: 0.9205 (tm-30) REVERT: A 97 GLU cc_start: 0.9414 (pp20) cc_final: 0.9024 (pp20) REVERT: A 105 GLU cc_start: 0.9356 (mp0) cc_final: 0.9140 (mp0) REVERT: A 120 MET cc_start: 0.8556 (mtm) cc_final: 0.7904 (mpp) REVERT: B 63 GLU cc_start: 0.9477 (mt-10) cc_final: 0.9123 (mp0) REVERT: D 82 HIS cc_start: 0.9609 (t-90) cc_final: 0.9305 (t-90) REVERT: D 105 GLU cc_start: 0.9424 (pp20) cc_final: 0.9202 (pp20) REVERT: D 108 LYS cc_start: 0.9700 (mtmm) cc_final: 0.9485 (ptpp) REVERT: E 120 MET cc_start: 0.9327 (tpp) cc_final: 0.8966 (mmm) REVERT: F 62 LEU cc_start: 0.9846 (mt) cc_final: 0.9622 (pp) REVERT: F 74 GLU cc_start: 0.9636 (tm-30) cc_final: 0.9371 (tm-30) REVERT: G 24 GLN cc_start: 0.9210 (mp10) cc_final: 0.9006 (mp10) REVERT: G 41 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8484 (tm-30) REVERT: H 62 MET cc_start: 0.9471 (mmp) cc_final: 0.9210 (mmm) REVERT: H 106 LEU cc_start: 0.9862 (mt) cc_final: 0.9487 (mt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1306 time to fit residues: 16.2312 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 : 0.373 ------------------------------------------------------------------------------- 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: 8.9990 chunk 93 optimal weight: 20.0000 chunk 105 optimal weight: 30.0000 chunk 70 optimal weight: 0.0980 chunk 7 optimal weight: 6.9990 chunk 100 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 27 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.028709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.021838 restraints weight = 223792.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.022499 restraints weight = 107808.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.022904 restraints weight = 65581.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.023210 restraints weight = 47239.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.023445 restraints weight = 37691.885| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2125 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 : 0.680 8.025 21563 Z= 0.397 Chirality : 0.047 0.260 2456 Planarity : 0.004 0.043 1498 Dihedral : 33.874 174.279 4789 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 1.87 (0.28), residues: 825 helix: 1.90 (0.21), residues: 582 sheet: -1.65 (1.82), residues: 10 loop : -0.28 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 11 TYR 0.014 0.002 TYR E 99 PHE 0.033 0.003 PHE G 25 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.17 (14846) covalent geometry : angle 0.68043 / 0.40 (21563) hydrogen bonds : bond 0.06347 / 4.21 ( 882) hydrogen bonds : angle 3.58970 / 2.58 ( 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 91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.301 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 90 MET cc_start: 0.9651 (mmp) cc_final: 0.9201 (mmm) REVERT: A 93 GLN cc_start: 0.9531 (tp40) cc_final: 0.9138 (tm-30) REVERT: A 94 GLU cc_start: 0.9504 (mp0) cc_final: 0.8777 (mp0) REVERT: A 97 GLU cc_start: 0.9401 (pp20) cc_final: 0.9048 (pp20) REVERT: A 104 PHE cc_start: 0.9314 (m-10) cc_final: 0.8821 (m-80) REVERT: A 120 MET cc_start: 0.8519 (mtm) cc_final: 0.7999 (mtt) REVERT: B 63 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9163 (pt0) REVERT: D 82 HIS cc_start: 0.9585 (t-90) cc_final: 0.9268 (t-90) REVERT: D 105 GLU cc_start: 0.9415 (pp20) cc_final: 0.9162 (pp20) REVERT: D 108 LYS cc_start: 0.9699 (mtmm) cc_final: 0.9477 (ptpp) REVERT: E 120 MET cc_start: 0.9268 (tpp) cc_final: 0.8965 (tpp) REVERT: F 62 LEU cc_start: 0.9844 (mt) cc_final: 0.9626 (pp) REVERT: F 74 GLU cc_start: 0.9641 (tm-30) cc_final: 0.9375 (tm-30) REVERT: G 24 GLN cc_start: 0.9169 (mp10) cc_final: 0.8901 (mp10) REVERT: G 41 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8495 (tm-30) REVERT: H 62 MET cc_start: 0.9469 (mmp) cc_final: 0.9237 (mmp) REVERT: H 105 GLU cc_start: 0.9495 (pm20) cc_final: 0.9257 (pm20) REVERT: H 106 LEU cc_start: 0.9808 (mt) cc_final: 0.9560 (mt) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1380 time to fit residues: 18.0024 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 : 0.369 ------------------------------------------------------------------------------- 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: 30.0000 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN E 55 GLN E 108 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2846 r_free = 0.2846 target = 0.027408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.020735 restraints weight = 236901.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.021358 restraints weight = 117095.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.021743 restraints weight = 72274.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.022064 restraints weight = 52351.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.022290 restraints weight = 41057.848| |-----------------------------------------------------------------------------| r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 14846 Z= 0.276 Angle : 0.763 8.638 21563 Z= 0.437 Chirality : 0.048 0.269 2456 Planarity : 0.005 0.049 1498 Dihedral : 33.966 177.115 4789 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 1.51 (0.28), residues: 825 helix: 1.61 (0.21), residues: 582 sheet: -1.69 (1.81), residues: 10 loop : -0.32 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 23 TYR 0.012 0.002 TYR D 121 PHE 0.015 0.002 PHE G 25 HIS 0.009 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.28 (14846) covalent geometry : angle 0.76346 / 0.44 (21563) hydrogen bonds : bond 0.11081 / 7.40 ( 882) hydrogen bonds : angle 3.90617 / 2.81 ( 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 73 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9624 (mmp) cc_final: 0.9179 (mmm) REVERT: A 93 GLN cc_start: 0.9543 (tp40) cc_final: 0.9174 (tm-30) REVERT: A 94 GLU cc_start: 0.9448 (mp0) cc_final: 0.8798 (mp0) REVERT: A 97 GLU cc_start: 0.9379 (pp20) cc_final: 0.8986 (pp20) REVERT: A 104 PHE cc_start: 0.9370 (m-10) cc_final: 0.8961 (m-80) REVERT: A 120 MET cc_start: 0.8593 (mtm) cc_final: 0.7995 (mtt) REVERT: B 63 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9217 (mt-10) REVERT: D 82 HIS cc_start: 0.9608 (t-90) cc_final: 0.9302 (t-90) REVERT: E 120 MET cc_start: 0.9273 (tpp) cc_final: 0.9020 (tpp) REVERT: F 74 GLU cc_start: 0.9656 (tm-30) cc_final: 0.9401 (tm-30) REVERT: G 24 GLN cc_start: 0.9197 (mp10) cc_final: 0.8902 (mp10) REVERT: H 62 MET cc_start: 0.9488 (mmp) cc_final: 0.9251 (mmp) REVERT: H 106 LEU cc_start: 0.9831 (mt) cc_final: 0.9472 (mt) outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.1286 time to fit residues: 13.7243 Evaluate side-chains 54 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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: 2.9990 chunk 50 optimal weight: 0.9990 chunk 94 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.028248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.021430 restraints weight = 227334.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.022104 restraints weight = 111098.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.022519 restraints weight = 67924.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.022822 restraints weight = 48997.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.022987 restraints weight = 38284.417| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14846 Z= 0.177 Angle : 0.701 7.851 21563 Z= 0.408 Chirality : 0.047 0.261 2456 Planarity : 0.004 0.042 1498 Dihedral : 33.941 176.408 4789 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: 1.71 (0.28), residues: 825 helix: 1.84 (0.21), residues: 570 sheet: -1.61 (1.84), residues: 10 loop : -0.36 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.014 0.002 TYR E 99 PHE 0.016 0.002 PHE G 25 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.18 (14846) covalent geometry : angle 0.70122 / 0.41 (21563) hydrogen bonds : bond 0.06719 / 4.43 ( 882) hydrogen bonds : angle 3.77898 / 2.71 ( 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 83 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.389 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: 0.9650 (mmp) cc_final: 0.9374 (mmm) REVERT: A 93 GLN cc_start: 0.9527 (tp40) cc_final: 0.9062 (tp-100) REVERT: A 94 GLU cc_start: 0.9526 (mp0) cc_final: 0.9022 (mp0) REVERT: A 97 GLU cc_start: 0.9353 (pp20) cc_final: 0.8934 (pp20) REVERT: A 104 PHE cc_start: 0.9332 (m-10) cc_final: 0.8870 (m-80) REVERT: A 120 MET cc_start: 0.8530 (mtm) cc_final: 0.7974 (mtt) REVERT: B 63 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9166 (pt0) REVERT: D 76 GLU cc_start: 0.9604 (mp0) cc_final: 0.9358 (pm20) REVERT: D 82 HIS cc_start: 0.9572 (t-90) cc_final: 0.9259 (t-90) REVERT: D 105 GLU cc_start: 0.9388 (pp20) cc_final: 0.9085 (pp20) REVERT: D 108 LYS cc_start: 0.9684 (mtmm) cc_final: 0.9453 (ptpp) REVERT: E 120 MET cc_start: 0.9258 (tpp) cc_final: 0.8978 (tpp) REVERT: F 74 GLU cc_start: 0.9639 (tm-30) cc_final: 0.9372 (tm-30) REVERT: G 24 GLN cc_start: 0.9235 (mp10) cc_final: 0.8960 (mp10) REVERT: H 62 MET cc_start: 0.9467 (mmp) cc_final: 0.9229 (mmp) REVERT: H 105 GLU cc_start: 0.9491 (pm20) cc_final: 0.9249 (pm20) REVERT: H 106 LEU cc_start: 0.9829 (mt) cc_final: 0.9520 (mt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1222 time to fit residues: 14.8347 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 : 0.358 ------------------------------------------------------------------------------- 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: 0.9980 chunk 17 optimal weight: 9.9990 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: 4.9990 chunk 37 optimal weight: 4.9990 chunk 63 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 = 0.2882 r_free = 0.2882 target = 0.028546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.021656 restraints weight = 224286.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.022357 restraints weight = 109818.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.022778 restraints weight = 67051.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.023100 restraints weight = 48151.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.023274 restraints weight = 37561.187| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14846 Z= 0.165 Angle : 0.683 7.793 21563 Z= 0.397 Chirality : 0.046 0.255 2456 Planarity : 0.004 0.043 1498 Dihedral : 33.745 174.853 4789 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 1.91 (0.29), residues: 825 helix: 2.00 (0.21), residues: 570 sheet: -1.54 (1.85), residues: 10 loop : -0.33 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 42 TYR 0.015 0.002 TYR D 42 PHE 0.014 0.002 PHE G 25 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.17 (14846) covalent geometry : angle 0.68282 / 0.40 (21563) hydrogen bonds : bond 0.06137 / 4.05 ( 882) hydrogen bonds : angle 3.72248 / 2.68 ( 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 88 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9634 (mmp) cc_final: 0.9365 (mmm) REVERT: A 93 GLN cc_start: 0.9537 (tp40) cc_final: 0.9105 (tp-100) REVERT: A 94 GLU cc_start: 0.9464 (mp0) cc_final: 0.8951 (mp0) REVERT: A 97 GLU cc_start: 0.9376 (pp20) cc_final: 0.8946 (pp20) REVERT: A 104 PHE cc_start: 0.9319 (m-10) cc_final: 0.8797 (m-80) REVERT: A 120 MET cc_start: 0.8444 (mtm) cc_final: 0.7869 (mtt) REVERT: B 63 GLU cc_start: 0.9443 (mt-10) cc_final: 0.9167 (pt0) REVERT: D 76 GLU cc_start: 0.9575 (mp0) cc_final: 0.9353 (mp0) REVERT: D 82 HIS cc_start: 0.9579 (t-90) cc_final: 0.9273 (t-90) REVERT: D 105 GLU cc_start: 0.9404 (pp20) cc_final: 0.9137 (pp20) REVERT: D 108 LYS cc_start: 0.9680 (mtmm) cc_final: 0.9450 (ptpp) REVERT: E 90 MET cc_start: 0.9488 (mmp) cc_final: 0.9281 (mmp) REVERT: E 120 MET cc_start: 0.9209 (tpp) cc_final: 0.8950 (tpp) REVERT: F 74 GLU cc_start: 0.9642 (tm-30) cc_final: 0.9362 (tm-30) REVERT: G 24 GLN cc_start: 0.9275 (mp10) cc_final: 0.9048 (mp10) REVERT: H 62 MET cc_start: 0.9466 (mmp) cc_final: 0.9231 (mmp) REVERT: H 102 LEU cc_start: 0.9058 (mm) cc_final: 0.8554 (tp) REVERT: H 106 LEU cc_start: 0.9830 (mt) cc_final: 0.9379 (mt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1083 time to fit residues: 13.8802 Evaluate side-chains 63 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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: 6.9990 chunk 90 optimal weight: 40.0000 chunk 103 optimal weight: 30.0000 chunk 62 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 30.0000 chunk 76 optimal weight: 30.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.028140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.021397 restraints weight = 227739.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.022073 restraints weight = 109907.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.022495 restraints weight = 66826.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.022739 restraints weight = 47364.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.022957 restraints weight = 38191.568| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14846 Z= 0.191 Angle : 0.694 7.668 21563 Z= 0.403 Chirality : 0.046 0.257 2456 Planarity : 0.004 0.048 1498 Dihedral : 33.706 175.690 4789 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % 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: 1.77 (0.29), residues: 825 helix: 1.90 (0.21), residues: 568 sheet: -1.51 (1.85), residues: 10 loop : -0.40 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 23 TYR 0.013 0.002 TYR H 37 PHE 0.030 0.002 PHE G 25 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.19 (14846) covalent geometry : angle 0.69441 / 0.40 (21563) hydrogen bonds : bond 0.07165 / 4.77 ( 882) hydrogen bonds : angle 3.79230 / 2.73 ( 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 80 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.314 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: 0.9617 (mmp) cc_final: 0.9284 (mmm) REVERT: A 93 GLN cc_start: 0.9532 (tp40) cc_final: 0.9068 (tm-30) REVERT: A 94 GLU cc_start: 0.9453 (mp0) cc_final: 0.8922 (mp0) REVERT: A 97 GLU cc_start: 0.9375 (pp20) cc_final: 0.8833 (pp20) REVERT: A 104 PHE cc_start: 0.9311 (m-10) cc_final: 0.8795 (m-80) REVERT: A 120 MET cc_start: 0.8384 (mtm) cc_final: 0.7833 (mtt) REVERT: D 82 HIS cc_start: 0.9592 (t-90) cc_final: 0.9287 (t-90) REVERT: D 105 GLU cc_start: 0.9397 (pp20) cc_final: 0.9127 (pp20) REVERT: D 108 LYS cc_start: 0.9673 (mtmm) cc_final: 0.9424 (ptpp) REVERT: E 120 MET cc_start: 0.9228 (tpp) cc_final: 0.8986 (tpp) REVERT: F 74 GLU cc_start: 0.9645 (tm-30) cc_final: 0.9377 (tm-30) REVERT: G 24 GLN cc_start: 0.9180 (mp10) cc_final: 0.8923 (mp10) REVERT: H 62 MET cc_start: 0.9446 (mmp) cc_final: 0.9226 (mmp) REVERT: H 105 GLU cc_start: 0.9492 (pm20) cc_final: 0.9237 (pm20) REVERT: H 106 LEU cc_start: 0.9845 (mt) cc_final: 0.9544 (mt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1217 time to fit residues: 13.7365 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 : 0.237 ------------------------------------------------------------------------------- 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: 30.0000 chunk 111 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 107 optimal weight: 0.0040 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 98 optimal weight: 30.0000 chunk 7 optimal weight: 8.9990 chunk 72 optimal weight: 40.0000 overall best weight: 3.7998 ------------------------------------------------------------------------------- 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 ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.028188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.021418 restraints weight = 226140.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.022075 restraints weight = 109552.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.022469 restraints weight = 67148.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.022775 restraints weight = 48709.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.022976 restraints weight = 39125.091| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14846 Z= 0.184 Angle : 0.691 8.969 21563 Z= 0.401 Chirality : 0.046 0.257 2456 Planarity : 0.005 0.060 1498 Dihedral : 33.669 175.998 4789 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 1.73 (0.29), residues: 825 helix: 1.88 (0.21), residues: 568 sheet: -1.49 (1.86), residues: 10 loop : -0.44 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 23 TYR 0.019 0.002 TYR D 40 PHE 0.031 0.002 PHE G 25 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.18 (14846) covalent geometry : angle 0.69104 / 0.40 (21563) hydrogen bonds : bond 0.06785 / 4.49 ( 882) hydrogen bonds : angle 3.77421 / 2.71 ( 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 79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.262 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: 0.9617 (mmp) cc_final: 0.9278 (mmm) REVERT: A 93 GLN cc_start: 0.9534 (tp40) cc_final: 0.9062 (tm-30) REVERT: A 94 GLU cc_start: 0.9465 (mp0) cc_final: 0.8903 (mp0) REVERT: A 97 GLU cc_start: 0.9389 (pp20) cc_final: 0.8867 (pp20) REVERT: A 104 PHE cc_start: 0.9323 (m-10) cc_final: 0.8821 (m-80) REVERT: A 120 MET cc_start: 0.8423 (mtm) cc_final: 0.7852 (mtt) REVERT: D 82 HIS cc_start: 0.9586 (t-90) cc_final: 0.9270 (t-90) REVERT: D 105 GLU cc_start: 0.9401 (pp20) cc_final: 0.9138 (pp20) REVERT: D 108 LYS cc_start: 0.9682 (mtmm) cc_final: 0.9438 (ptpp) REVERT: E 90 MET cc_start: 0.9490 (mmp) cc_final: 0.9277 (mmp) REVERT: E 120 MET cc_start: 0.9218 (tpp) cc_final: 0.8985 (tpp) REVERT: F 74 GLU cc_start: 0.9640 (tm-30) cc_final: 0.9369 (tm-30) REVERT: H 105 GLU cc_start: 0.9501 (pm20) cc_final: 0.9227 (pm20) REVERT: H 106 LEU cc_start: 0.9847 (mt) cc_final: 0.9529 (mt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1264 time to fit residues: 14.3412 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 : 0.308 ------------------------------------------------------------------------------- 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: 30.0000 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: 3.9990 chunk 79 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 27 GLN F 64 ASN ** 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 = 0.2817 r_free = 0.2817 target = 0.026624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.020110 restraints weight = 240759.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.020733 restraints weight = 118406.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.021125 restraints weight = 72944.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.021352 restraints weight = 52332.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.021559 restraints weight = 42084.772| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14846 Z= 0.315 Angle : 0.811 7.737 21563 Z= 0.461 Chirality : 0.049 0.271 2456 Planarity : 0.006 0.052 1498 Dihedral : 33.943 177.412 4789 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 26.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: 1.08 (0.28), residues: 825 helix: 1.32 (0.21), residues: 570 sheet: -1.57 (1.84), residues: 10 loop : -0.48 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 23 TYR 0.017 0.003 TYR H 37 PHE 0.032 0.003 PHE G 25 HIS 0.011 0.003 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.31 (14846) covalent geometry : angle 0.81082 / 0.46 (21563) hydrogen bonds : bond 0.12506 / 8.33 ( 882) hydrogen bonds : angle 4.25076 / 3.06 ( 2177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.12 seconds wall clock time: 33 minutes 24.41 seconds (2004.41 seconds total)