Starting phenix.real_space_refine on Thu Jul 31 20:59:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8b_29845/07_2025/8g8b_29845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8b_29845/07_2025/8g8b_29845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g8b_29845/07_2025/8g8b_29845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8b_29845/07_2025/8g8b_29845.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8b_29845/07_2025/8g8b_29845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8b_29845/07_2025/8g8b_29845.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 336 5.49 5 S 17 5.16 5 C 7819 2.51 5 N 2611 2.21 5 O 3284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 14067 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 863 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3419 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "J" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3469 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "X" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1080 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 1 Time building chain proxies: 8.85, per 1000 atoms: 0.63 Number of scatterers: 14067 At special positions: 0 Unit cell: (80.5, 119.14, 172.27, 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 17 16.00 P 336 15.00 O 3284 8.00 N 2611 7.00 C 7819 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: 3.56 Conformation dependent library (CDL) restraints added in 1.2 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 74.5% alpha, 2.4% beta 161 base pairs and 290 stacking pairs defined. Time for finding SS restraints: 7.22 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.053A 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 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.736A 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 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.233A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.950A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.572A 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 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.363A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'X' and resid 141 through 161 Processing helix chain 'X' and resid 163 through 176 Processing helix chain 'X' and resid 180 through 189 removed outlier: 3.552A pdb=" N ILE X 184 " --> pdb=" O SER X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 211 Proline residue: X 202 - end of helix Processing helix chain 'X' and resid 215 through 220 Processing helix chain 'X' and resid 239 through 249 Processing helix chain 'X' and resid 256 through 268 removed outlier: 3.681A pdb=" N HIS X 262 " --> pdb=" O GLN X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 288 removed outlier: 4.059A pdb=" N SER X 288 " --> pdb=" O LYS X 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.928A 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: 6.705A 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: 7.125A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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: 6.758A 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: 6.760A 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: 6.981A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 78 491 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 389 hydrogen bonds 778 hydrogen bond angles 0 basepair planarities 161 basepair parallelities 290 stacking parallelities Total time for adding SS restraints: 6.95 Time building geometry restraints manager: 4.25 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: 2622 1.33 - 1.45: 4963 1.45 - 1.57: 6717 1.57 - 1.69: 670 1.69 - 1.81: 28 Bond restraints: 15000 Sorted by residual: bond pdb=" N THR E 32 " pdb=" CA THR E 32 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.60e+00 bond pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.32e-02 5.74e+03 6.27e+00 bond pdb=" N TYR E 41 " pdb=" CA TYR E 41 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 5.86e+00 bond pdb=" C1' DC J -96 " pdb=" N1 DC J -96 " ideal model delta sigma weight residual 1.490 1.552 -0.062 3.00e-02 1.11e+03 4.20e+00 bond pdb=" C1' DC I 83 " pdb=" N1 DC I 83 " ideal model delta sigma weight residual 1.490 1.549 -0.059 3.00e-02 1.11e+03 3.88e+00 ... (remaining 14995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 21469 2.36 - 4.72: 201 4.72 - 7.08: 20 7.08 - 9.44: 3 9.44 - 11.79: 1 Bond angle restraints: 21694 Sorted by residual: angle pdb=" O3' DG J -71 " pdb=" C3' DG J -71 " pdb=" C2' DG J -71 " ideal model delta sigma weight residual 111.50 103.17 8.33 1.50e+00 4.44e-01 3.08e+01 angle pdb=" O3' DG J -73 " pdb=" C3' DG J -73 " pdb=" C2' DG J -73 " ideal model delta sigma weight residual 111.50 104.37 7.13 1.50e+00 4.44e-01 2.26e+01 angle pdb=" O3' DA I 78 " pdb=" C3' DA I 78 " pdb=" C2' DA I 78 " ideal model delta sigma weight residual 111.50 104.62 6.88 1.50e+00 4.44e-01 2.10e+01 angle pdb=" CB MET X 197 " pdb=" CG MET X 197 " pdb=" SD MET X 197 " ideal model delta sigma weight residual 112.70 124.49 -11.79 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C4' DC I 75 " pdb=" C3' DC I 75 " pdb=" O3' DC I 75 " ideal model delta sigma weight residual 110.00 104.22 5.78 1.50e+00 4.44e-01 1.48e+01 ... (remaining 21689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6500 35.81 - 71.62: 1745 71.62 - 107.42: 15 107.42 - 143.23: 2 143.23 - 179.04: 1 Dihedral angle restraints: 8263 sinusoidal: 5648 harmonic: 2615 Sorted by residual: dihedral pdb=" C4' DA I 20 " pdb=" C3' DA I 20 " pdb=" O3' DA I 20 " pdb=" P DT I 21 " ideal model delta sinusoidal sigma weight residual -140.00 39.04 -179.04 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA I 82 " pdb=" C3' DA I 82 " pdb=" O3' DA I 82 " pdb=" P DC I 83 " ideal model delta sinusoidal sigma weight residual 220.00 80.83 139.17 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 8260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1952 0.041 - 0.083: 438 0.083 - 0.124: 63 0.124 - 0.165: 10 0.165 - 0.206: 5 Chirality restraints: 2468 Sorted by residual: chirality pdb=" C3' DC I 75 " pdb=" C4' DC I 75 " pdb=" O3' DC I 75 " pdb=" C2' DC I 75 " both_signs ideal model delta sigma weight residual False -2.66 -2.87 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C3' DT J -76 " pdb=" C4' DT J -76 " pdb=" O3' DT J -76 " pdb=" C2' DT J -76 " both_signs ideal model delta sigma weight residual False -2.66 -2.85 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" C3' DG J -71 " pdb=" C4' DG J -71 " pdb=" O3' DG J -71 " pdb=" C2' DG J -71 " both_signs ideal model delta sigma weight residual False -2.66 -2.84 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 2465 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 79 " 0.023 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" N1 DT I 79 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DT I 79 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT I 79 " -0.013 2.00e-02 2.50e+03 pdb=" N3 DT I 79 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 79 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 79 " 0.018 2.00e-02 2.50e+03 pdb=" C5 DT I 79 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DT I 79 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT I 79 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 56 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C GLY F 56 " -0.031 2.00e-02 2.50e+03 pdb=" O GLY F 56 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL F 57 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO G 80 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.025 5.00e-02 4.00e+02 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 146 2.63 - 3.20: 11304 3.20 - 3.76: 26958 3.76 - 4.33: 36243 4.33 - 4.90: 50059 Nonbonded interactions: 124710 Sorted by model distance: nonbonded pdb=" O2 DC I 85 " pdb=" N2 DG J -85 " model vdw 2.061 3.120 nonbonded pdb=" N6 DA I 72 " pdb=" N3 DT J -72 " model vdw 2.065 2.560 nonbonded pdb=" CD PRO E 30 " pdb=" OE1 GLU X 209 " model vdw 2.132 3.440 nonbonded pdb=" N1 DA I 72 " pdb=" O2 DT J -72 " model vdw 2.152 2.496 nonbonded pdb=" O GLN X 155 " pdb=" OG1 THR X 159 " model vdw 2.276 3.040 ... (remaining 124705 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' and resid 38 through 133) selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = (chain 'F' and resid 22 through 101) } 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=0.00 max=1.00 mean=0.96 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.690 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15000 Z= 0.208 Angle : 0.639 11.794 21694 Z= 0.388 Chirality : 0.036 0.206 2468 Planarity : 0.004 0.044 1582 Dihedral : 28.756 179.040 6571 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.81 % Favored : 98.07 % Rotamer: Outliers : 1.98 % Allowed : 17.15 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.27), residues: 882 helix: 1.93 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -0.64 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP X 277 HIS 0.005 0.001 HIS B 75 PHE 0.012 0.002 PHE E 67 TYR 0.013 0.002 TYR H 80 ARG 0.004 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.12470 ( 880) hydrogen bonds : angle 5.37206 ( 2227) covalent geometry : bond 0.00450 (15000) covalent geometry : angle 0.63909 (21694) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 312 time to evaluate : 1.065 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: 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: 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 60 LEU cc_start: 0.9228 (mt) cc_final: 0.8846 (tp) REVERT: A 89 VAL cc_start: 0.9748 (t) cc_final: 0.9395 (m) REVERT: A 90 MET cc_start: 0.9569 (mmp) cc_final: 0.9326 (mmm) REVERT: A 99 TYR cc_start: 0.8162 (t80) cc_final: 0.7841 (t80) REVERT: A 106 ASP cc_start: 0.9386 (m-30) cc_final: 0.8954 (t0) REVERT: A 110 CYS cc_start: 0.9719 (m) cc_final: 0.9434 (m) REVERT: B 53 GLU cc_start: 0.9278 (tp30) cc_final: 0.8811 (tt0) REVERT: B 59 LYS cc_start: 0.9633 (tppp) cc_final: 0.9388 (tppp) REVERT: B 61 PHE cc_start: 0.9349 (t80) cc_final: 0.8959 (t80) REVERT: B 66 ILE cc_start: 0.9625 (mt) cc_final: 0.9422 (tt) REVERT: C 51 LEU cc_start: 0.9717 (tp) cc_final: 0.9504 (tp) REVERT: C 75 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8343 (mmmt) REVERT: C 94 ASN cc_start: 0.9568 (t0) cc_final: 0.9177 (m-40) REVERT: C 101 THR cc_start: 0.9445 (m) cc_final: 0.9047 (t) REVERT: D 34 TYR cc_start: 0.9188 (m-80) cc_final: 0.8727 (m-80) REVERT: D 64 ASN cc_start: 0.9598 (m-40) cc_final: 0.8956 (m110) REVERT: E 65 LEU cc_start: 0.9858 (mt) cc_final: 0.9618 (mt) REVERT: E 94 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8919 (tp30) REVERT: E 109 LEU cc_start: 0.9672 (mt) cc_final: 0.9301 (mt) REVERT: F 26 ILE cc_start: 0.9212 (tp) cc_final: 0.8951 (tp) REVERT: F 46 ILE cc_start: 0.9314 (mt) cc_final: 0.8878 (tp) REVERT: F 51 TYR cc_start: 0.8809 (m-80) cc_final: 0.8470 (m-80) REVERT: F 53 GLU cc_start: 0.9195 (tp30) cc_final: 0.8912 (tt0) REVERT: F 64 ASN cc_start: 0.9661 (m-40) cc_final: 0.9248 (m-40) REVERT: F 74 GLU cc_start: 0.9430 (mt-10) cc_final: 0.9102 (mt-10) REVERT: G 25 PHE cc_start: 0.8966 (m-80) cc_final: 0.8594 (m-10) REVERT: G 51 LEU cc_start: 0.9900 (tp) cc_final: 0.9654 (tp) REVERT: G 56 GLU cc_start: 0.8697 (tt0) cc_final: 0.7532 (tt0) REVERT: G 73 ASN cc_start: 0.9480 (m110) cc_final: 0.9070 (m110) REVERT: G 93 LEU cc_start: 0.9811 (mt) cc_final: 0.9580 (tp) REVERT: G 94 ASN cc_start: 0.9749 (t0) cc_final: 0.9359 (m-40) REVERT: G 101 THR cc_start: 0.9441 (m) cc_final: 0.9144 (p) REVERT: H 34 TYR cc_start: 0.9144 (m-80) cc_final: 0.8306 (m-10) REVERT: H 41 VAL cc_start: 0.9742 (t) cc_final: 0.9493 (p) REVERT: H 58 ILE cc_start: 0.9776 (mt) cc_final: 0.9432 (mt) REVERT: H 59 MET cc_start: 0.9744 (mmm) cc_final: 0.9533 (mmm) REVERT: H 64 ASN cc_start: 0.9453 (m-40) cc_final: 0.9223 (m110) REVERT: H 76 ARG cc_start: 0.9617 (mtm-85) cc_final: 0.9298 (ptp-110) REVERT: H 90 GLU cc_start: 0.9535 (mp0) cc_final: 0.9034 (mp0) REVERT: H 98 LEU cc_start: 0.8787 (mt) cc_final: 0.8338 (mt) REVERT: H 109 SER cc_start: 0.9698 (OUTLIER) cc_final: 0.9445 (p) outliers start: 15 outliers final: 2 residues processed: 323 average time/residue: 0.3332 time to fit residues: 143.4372 Evaluate side-chains 187 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN B 75 HIS B 93 GLN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.059947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.046207 restraints weight = 160047.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.046998 restraints weight = 96494.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.047313 restraints weight = 66675.089| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15000 Z= 0.287 Angle : 0.696 13.099 21694 Z= 0.409 Chirality : 0.038 0.207 2468 Planarity : 0.007 0.150 1582 Dihedral : 31.609 178.169 4762 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.27), residues: 882 helix: 1.68 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.37 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP X 207 HIS 0.009 0.002 HIS F 75 PHE 0.018 0.002 PHE X 278 TYR 0.028 0.003 TYR H 80 ARG 0.013 0.001 ARG X 281 Details of bonding type rmsd hydrogen bonds : bond 0.08307 ( 880) hydrogen bonds : angle 3.73894 ( 2227) covalent geometry : bond 0.00625 (15000) covalent geometry : angle 0.69555 (21694) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.082 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9679 (mp) cc_final: 0.9463 (mt) REVERT: A 106 ASP cc_start: 0.9565 (m-30) cc_final: 0.9199 (t0) REVERT: A 126 LEU cc_start: 0.9448 (mm) cc_final: 0.9170 (tp) REVERT: B 53 GLU cc_start: 0.9400 (tp30) cc_final: 0.8933 (tt0) REVERT: B 97 LEU cc_start: 0.9533 (tp) cc_final: 0.9215 (tp) REVERT: C 25 PHE cc_start: 0.8488 (m-10) cc_final: 0.8066 (m-10) REVERT: C 94 ASN cc_start: 0.9252 (t0) cc_final: 0.8929 (t0) REVERT: C 101 THR cc_start: 0.8761 (m) cc_final: 0.8413 (t) REVERT: D 59 MET cc_start: 0.9751 (mmm) cc_final: 0.9293 (mmm) REVERT: D 64 ASN cc_start: 0.9524 (m-40) cc_final: 0.9316 (m-40) REVERT: D 80 TYR cc_start: 0.9114 (m-10) cc_final: 0.8827 (m-10) REVERT: E 73 GLU cc_start: 0.9093 (tt0) cc_final: 0.8854 (tt0) REVERT: E 74 ILE cc_start: 0.9569 (mt) cc_final: 0.9229 (mt) REVERT: E 94 GLU cc_start: 0.9637 (mm-30) cc_final: 0.9271 (mm-30) REVERT: E 99 TYR cc_start: 0.9612 (t80) cc_final: 0.9305 (t80) REVERT: E 130 ILE cc_start: 0.9396 (mt) cc_final: 0.8496 (mt) REVERT: F 26 ILE cc_start: 0.8903 (tp) cc_final: 0.8642 (tp) REVERT: F 53 GLU cc_start: 0.8998 (tp30) cc_final: 0.8745 (tt0) REVERT: F 57 VAL cc_start: 0.9600 (t) cc_final: 0.9294 (p) REVERT: G 25 PHE cc_start: 0.9397 (m-80) cc_final: 0.8767 (m-10) REVERT: G 64 GLU cc_start: 0.9645 (mt-10) cc_final: 0.9440 (mm-30) REVERT: G 73 ASN cc_start: 0.8783 (m110) cc_final: 0.8528 (m110) REVERT: G 94 ASN cc_start: 0.9382 (t0) cc_final: 0.9072 (t0) REVERT: G 101 THR cc_start: 0.8757 (m) cc_final: 0.8411 (p) REVERT: H 34 TYR cc_start: 0.9509 (m-80) cc_final: 0.9296 (m-80) REVERT: H 73 GLU cc_start: 0.9597 (tp30) cc_final: 0.8698 (tp30) REVERT: H 91 ILE cc_start: 0.9665 (mm) cc_final: 0.9440 (mm) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.3274 time to fit residues: 105.4907 Evaluate side-chains 163 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** H 92 GLN ** 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 = 0.3394 r_free = 0.3394 target = 0.056835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.043826 restraints weight = 167768.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.044412 restraints weight = 101820.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.044832 restraints weight = 70195.461| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15000 Z= 0.263 Angle : 0.663 12.704 21694 Z= 0.389 Chirality : 0.037 0.141 2468 Planarity : 0.005 0.053 1582 Dihedral : 32.183 177.288 4762 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 882 helix: 1.46 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.24 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 207 HIS 0.009 0.002 HIS F 75 PHE 0.017 0.002 PHE A 67 TYR 0.026 0.002 TYR B 88 ARG 0.012 0.001 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.07544 ( 880) hydrogen bonds : angle 3.74401 ( 2227) covalent geometry : bond 0.00568 (15000) covalent geometry : angle 0.66325 (21694) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.106 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: 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 62 ILE cc_start: 0.9322 (mm) cc_final: 0.9081 (mm) REVERT: A 67 PHE cc_start: 0.9452 (t80) cc_final: 0.8986 (t80) REVERT: A 81 ASP cc_start: 0.9443 (m-30) cc_final: 0.9220 (m-30) REVERT: A 99 TYR cc_start: 0.9444 (t80) cc_final: 0.9161 (t80) REVERT: A 126 LEU cc_start: 0.9559 (mm) cc_final: 0.9233 (tp) REVERT: B 53 GLU cc_start: 0.9427 (tp30) cc_final: 0.9075 (tt0) REVERT: B 97 LEU cc_start: 0.9510 (tp) cc_final: 0.9129 (tp) REVERT: C 25 PHE cc_start: 0.8211 (m-10) cc_final: 0.7716 (m-10) REVERT: C 39 TYR cc_start: 0.9129 (m-10) cc_final: 0.8868 (m-80) REVERT: C 83 LEU cc_start: 0.9669 (mp) cc_final: 0.9264 (mp) REVERT: C 94 ASN cc_start: 0.9259 (t0) cc_final: 0.8894 (t0) REVERT: C 101 THR cc_start: 0.8685 (m) cc_final: 0.8282 (t) REVERT: C 112 GLN cc_start: 0.9234 (tp40) cc_final: 0.8885 (tp-100) REVERT: D 65 ASP cc_start: 0.9803 (t0) cc_final: 0.9535 (t0) REVERT: D 73 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8869 (mm-30) REVERT: E 85 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8959 (tp-100) REVERT: E 94 GLU cc_start: 0.9642 (mm-30) cc_final: 0.9328 (mm-30) REVERT: E 99 TYR cc_start: 0.9492 (t80) cc_final: 0.9095 (t80) REVERT: F 53 GLU cc_start: 0.9199 (tp30) cc_final: 0.8977 (tt0) REVERT: F 57 VAL cc_start: 0.9624 (t) cc_final: 0.9173 (p) REVERT: F 97 LEU cc_start: 0.9398 (tp) cc_final: 0.9188 (tp) REVERT: F 100 PHE cc_start: 0.7082 (m-80) cc_final: 0.6421 (m-80) REVERT: G 25 PHE cc_start: 0.9183 (m-10) cc_final: 0.8467 (m-10) REVERT: G 73 ASN cc_start: 0.8574 (m110) cc_final: 0.8288 (m110) REVERT: G 94 ASN cc_start: 0.9344 (t0) cc_final: 0.9053 (t0) REVERT: G 95 LYS cc_start: 0.9641 (mtmm) cc_final: 0.9399 (mttt) REVERT: G 101 THR cc_start: 0.8503 (m) cc_final: 0.8088 (p) REVERT: H 64 ASN cc_start: 0.9326 (m110) cc_final: 0.9109 (m-40) REVERT: H 69 ARG cc_start: 0.9026 (ptm160) cc_final: 0.8820 (ttt180) REVERT: H 76 ARG cc_start: 0.9787 (mpt-90) cc_final: 0.9478 (ptp-110) REVERT: H 91 ILE cc_start: 0.9629 (mm) cc_final: 0.9412 (mm) REVERT: H 110 GLU cc_start: 0.9716 (mm-30) cc_final: 0.9383 (mm-30) REVERT: H 117 LYS cc_start: 0.9725 (ptpp) cc_final: 0.9456 (ptmm) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3027 time to fit residues: 84.2582 Evaluate side-chains 147 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 19 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN D 106 HIS E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.043400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.030267 restraints weight = 137235.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.031285 restraints weight = 71272.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.031961 restraints weight = 45160.969| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 15000 Z= 0.325 Angle : 0.731 15.405 21694 Z= 0.423 Chirality : 0.039 0.192 2468 Planarity : 0.006 0.057 1582 Dihedral : 32.733 177.573 4762 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.27), residues: 882 helix: 0.96 (0.19), residues: 659 sheet: None (None), residues: 0 loop : -0.35 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP X 207 HIS 0.015 0.002 HIS D 106 PHE 0.014 0.002 PHE B 100 TYR 0.037 0.003 TYR B 88 ARG 0.017 0.001 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.10372 ( 880) hydrogen bonds : angle 4.12421 ( 2227) covalent geometry : bond 0.00705 (15000) covalent geometry : angle 0.73090 (21694) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.986 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: 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 99 TYR cc_start: 0.9468 (t80) cc_final: 0.9117 (t80) REVERT: A 126 LEU cc_start: 0.9362 (mm) cc_final: 0.9092 (tp) REVERT: B 53 GLU cc_start: 0.9096 (tp30) cc_final: 0.8717 (tt0) REVERT: B 97 LEU cc_start: 0.9448 (tp) cc_final: 0.9083 (tp) REVERT: C 25 PHE cc_start: 0.7545 (m-10) cc_final: 0.7027 (m-10) REVERT: C 83 LEU cc_start: 0.9440 (mp) cc_final: 0.9086 (mp) REVERT: C 94 ASN cc_start: 0.8837 (t0) cc_final: 0.8541 (t0) REVERT: C 101 THR cc_start: 0.8147 (m) cc_final: 0.7786 (t) REVERT: D 73 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8848 (mm-30) REVERT: D 97 LEU cc_start: 0.8791 (tp) cc_final: 0.8411 (tp) REVERT: D 98 LEU cc_start: 0.7395 (mm) cc_final: 0.5779 (mm) REVERT: E 94 GLU cc_start: 0.9599 (mm-30) cc_final: 0.9282 (mm-30) REVERT: E 99 TYR cc_start: 0.9395 (t80) cc_final: 0.9125 (t80) REVERT: E 119 ILE cc_start: 0.9106 (pt) cc_final: 0.8846 (pt) REVERT: E 124 ILE cc_start: 0.9333 (mt) cc_final: 0.9062 (mt) REVERT: F 97 LEU cc_start: 0.8984 (tp) cc_final: 0.8534 (tp) REVERT: F 100 PHE cc_start: 0.5940 (m-80) cc_final: 0.5648 (m-80) REVERT: G 25 PHE cc_start: 0.8971 (m-10) cc_final: 0.8446 (m-10) REVERT: G 101 THR cc_start: 0.7831 (m) cc_final: 0.7500 (p) REVERT: H 68 GLU cc_start: 0.9583 (tm-30) cc_final: 0.9347 (tp30) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3147 time to fit residues: 76.6609 Evaluate side-chains 132 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 89 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS D 64 ASN E 108 ASN H 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.053222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.040827 restraints weight = 178050.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.041505 restraints weight = 104299.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.041888 restraints weight = 70658.244| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15000 Z= 0.275 Angle : 0.695 18.320 21694 Z= 0.403 Chirality : 0.038 0.159 2468 Planarity : 0.005 0.054 1582 Dihedral : 32.799 176.663 4762 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 882 helix: 0.96 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.43 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP X 207 HIS 0.007 0.001 HIS F 75 PHE 0.022 0.002 PHE X 278 TYR 0.030 0.003 TYR H 80 ARG 0.016 0.001 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.08192 ( 880) hydrogen bonds : angle 3.99351 ( 2227) covalent geometry : bond 0.00590 (15000) covalent geometry : angle 0.69473 (21694) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.054 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: 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 74 ILE cc_start: 0.9661 (mt) cc_final: 0.9266 (tt) REVERT: A 81 ASP cc_start: 0.9448 (m-30) cc_final: 0.9236 (m-30) REVERT: A 126 LEU cc_start: 0.9641 (mm) cc_final: 0.9358 (tt) REVERT: B 59 LYS cc_start: 0.9322 (tptp) cc_final: 0.9118 (tppt) REVERT: B 66 ILE cc_start: 0.9564 (mt) cc_final: 0.9325 (tt) REVERT: B 97 LEU cc_start: 0.9386 (tp) cc_final: 0.9162 (tp) REVERT: B 98 TYR cc_start: 0.8347 (m-10) cc_final: 0.8031 (m-80) REVERT: C 25 PHE cc_start: 0.8055 (m-10) cc_final: 0.7433 (m-10) REVERT: C 83 LEU cc_start: 0.9636 (mp) cc_final: 0.9298 (mp) REVERT: C 94 ASN cc_start: 0.9338 (t0) cc_final: 0.8971 (t0) REVERT: C 101 THR cc_start: 0.8808 (m) cc_final: 0.8543 (p) REVERT: C 112 GLN cc_start: 0.9272 (tp40) cc_final: 0.8908 (tp-100) REVERT: D 59 MET cc_start: 0.9827 (mmp) cc_final: 0.9551 (mmm) REVERT: E 99 TYR cc_start: 0.9590 (t80) cc_final: 0.9279 (t80) REVERT: F 51 TYR cc_start: 0.9225 (m-80) cc_final: 0.8989 (m-80) REVERT: F 72 TYR cc_start: 0.9464 (m-80) cc_final: 0.8939 (m-80) REVERT: G 25 PHE cc_start: 0.9056 (m-10) cc_final: 0.7939 (m-10) REVERT: G 56 GLU cc_start: 0.8402 (tt0) cc_final: 0.6939 (tt0) REVERT: G 94 ASN cc_start: 0.9392 (t0) cc_final: 0.9177 (m-40) REVERT: G 101 THR cc_start: 0.8466 (m) cc_final: 0.8243 (m) REVERT: H 64 ASN cc_start: 0.9314 (m-40) cc_final: 0.9089 (m110) REVERT: H 68 GLU cc_start: 0.9715 (tm-30) cc_final: 0.9423 (tp30) REVERT: H 76 ARG cc_start: 0.9624 (ptp-110) cc_final: 0.9395 (ptt-90) REVERT: H 97 LEU cc_start: 0.9313 (mt) cc_final: 0.8769 (mt) REVERT: H 113 LYS cc_start: 0.9551 (ptpp) cc_final: 0.9120 (pttm) REVERT: H 117 LYS cc_start: 0.9739 (ptpp) cc_final: 0.9402 (ptmm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3177 time to fit residues: 78.4297 Evaluate side-chains 131 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 57 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.043102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.030264 restraints weight = 142275.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.031337 restraints weight = 70525.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.032042 restraints weight = 43270.920| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.7470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15000 Z= 0.259 Angle : 0.683 15.218 21694 Z= 0.397 Chirality : 0.037 0.155 2468 Planarity : 0.005 0.050 1582 Dihedral : 32.695 177.127 4762 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.27), residues: 882 helix: 0.99 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.34 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP X 207 HIS 0.006 0.001 HIS E 113 PHE 0.019 0.002 PHE X 278 TYR 0.030 0.002 TYR B 72 ARG 0.010 0.001 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.08095 ( 880) hydrogen bonds : angle 3.99305 ( 2227) covalent geometry : bond 0.00558 (15000) covalent geometry : angle 0.68339 (21694) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.254 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9261 (mt) cc_final: 0.8673 (tt) REVERT: A 99 TYR cc_start: 0.9626 (t80) cc_final: 0.9392 (t80) REVERT: A 126 LEU cc_start: 0.9337 (mm) cc_final: 0.9085 (tt) REVERT: A 130 ILE cc_start: 0.8206 (tp) cc_final: 0.7905 (tp) REVERT: B 53 GLU cc_start: 0.9067 (tp30) cc_final: 0.8703 (tt0) REVERT: B 66 ILE cc_start: 0.9342 (mt) cc_final: 0.9089 (tt) REVERT: B 72 TYR cc_start: 0.8161 (m-80) cc_final: 0.7453 (m-80) REVERT: B 98 TYR cc_start: 0.8231 (m-10) cc_final: 0.8024 (m-80) REVERT: C 25 PHE cc_start: 0.7186 (m-10) cc_final: 0.6390 (m-10) REVERT: C 83 LEU cc_start: 0.9383 (mp) cc_final: 0.9018 (mp) REVERT: C 94 ASN cc_start: 0.8875 (t0) cc_final: 0.8607 (t0) REVERT: D 98 LEU cc_start: 0.6842 (mm) cc_final: 0.5557 (mm) REVERT: E 99 TYR cc_start: 0.9388 (t80) cc_final: 0.9150 (t80) REVERT: E 119 ILE cc_start: 0.9052 (pt) cc_final: 0.8791 (pt) REVERT: G 25 PHE cc_start: 0.8647 (m-10) cc_final: 0.7794 (m-10) REVERT: G 56 GLU cc_start: 0.7689 (tt0) cc_final: 0.6965 (tt0) REVERT: H 68 GLU cc_start: 0.9550 (tm-30) cc_final: 0.9269 (tp30) REVERT: H 113 LYS cc_start: 0.9657 (ptpp) cc_final: 0.9435 (pttm) REVERT: H 117 LYS cc_start: 0.9563 (ptpp) cc_final: 0.9275 (ptmm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.4078 time to fit residues: 100.2062 Evaluate side-chains 131 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 108 optimal weight: 0.0980 chunk 99 optimal weight: 8.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.053466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.040738 restraints weight = 176973.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.041425 restraints weight = 106088.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.041707 restraints weight = 73748.804| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.7611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15000 Z= 0.207 Angle : 0.667 16.152 21694 Z= 0.385 Chirality : 0.036 0.141 2468 Planarity : 0.005 0.054 1582 Dihedral : 32.481 177.062 4762 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.27), residues: 882 helix: 1.05 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.19 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP X 207 HIS 0.005 0.001 HIS F 75 PHE 0.010 0.002 PHE B 100 TYR 0.027 0.002 TYR B 72 ARG 0.007 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.06259 ( 880) hydrogen bonds : angle 3.89349 ( 2227) covalent geometry : bond 0.00446 (15000) covalent geometry : angle 0.66735 (21694) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.991 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9697 (mt) cc_final: 0.9251 (tt) REVERT: A 81 ASP cc_start: 0.9332 (m-30) cc_final: 0.9034 (m-30) REVERT: A 126 LEU cc_start: 0.9663 (mm) cc_final: 0.9355 (tt) REVERT: B 49 LEU cc_start: 0.9697 (mp) cc_final: 0.9145 (mp) REVERT: B 53 GLU cc_start: 0.9634 (tp30) cc_final: 0.9383 (mp0) REVERT: B 59 LYS cc_start: 0.9334 (tptp) cc_final: 0.9118 (tppt) REVERT: B 66 ILE cc_start: 0.9550 (mt) cc_final: 0.9279 (tt) REVERT: B 97 LEU cc_start: 0.9460 (tp) cc_final: 0.9195 (tp) REVERT: C 25 PHE cc_start: 0.8014 (m-10) cc_final: 0.7343 (m-10) REVERT: C 83 LEU cc_start: 0.9639 (mp) cc_final: 0.9415 (mt) REVERT: C 94 ASN cc_start: 0.9380 (t0) cc_final: 0.9102 (t0) REVERT: D 56 MET cc_start: 0.9620 (tpt) cc_final: 0.9407 (tpt) REVERT: D 59 MET cc_start: 0.9837 (mmp) cc_final: 0.9455 (mmm) REVERT: D 64 ASN cc_start: 0.9399 (m-40) cc_final: 0.9183 (m-40) REVERT: D 79 HIS cc_start: 0.9769 (t-90) cc_final: 0.9556 (t-90) REVERT: E 99 TYR cc_start: 0.9591 (t80) cc_final: 0.9258 (t80) REVERT: F 68 ASP cc_start: 0.9524 (m-30) cc_final: 0.9091 (m-30) REVERT: F 72 TYR cc_start: 0.9376 (m-80) cc_final: 0.9077 (m-80) REVERT: G 25 PHE cc_start: 0.8943 (m-10) cc_final: 0.7934 (m-10) REVERT: G 56 GLU cc_start: 0.8576 (tt0) cc_final: 0.7147 (tt0) REVERT: G 94 ASN cc_start: 0.9398 (t0) cc_final: 0.9106 (m-40) REVERT: G 101 THR cc_start: 0.8936 (m) cc_final: 0.8638 (p) REVERT: H 68 GLU cc_start: 0.9686 (tm-30) cc_final: 0.9394 (tp30) REVERT: H 110 GLU cc_start: 0.9711 (mm-30) cc_final: 0.9424 (mm-30) REVERT: H 113 LYS cc_start: 0.9577 (ptpp) cc_final: 0.9268 (pttp) REVERT: H 117 LYS cc_start: 0.9769 (ptpp) cc_final: 0.9490 (ptmm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3409 time to fit residues: 82.0326 Evaluate side-chains 126 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.053473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.040766 restraints weight = 174383.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.041461 restraints weight = 105737.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.041894 restraints weight = 72749.620| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.7858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15000 Z= 0.207 Angle : 0.659 15.207 21694 Z= 0.381 Chirality : 0.036 0.168 2468 Planarity : 0.004 0.045 1582 Dihedral : 32.339 177.328 4762 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 882 helix: 0.94 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.23 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 207 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE F 61 TYR 0.032 0.002 TYR H 80 ARG 0.006 0.000 ARG X 282 Details of bonding type rmsd hydrogen bonds : bond 0.06399 ( 880) hydrogen bonds : angle 3.86262 ( 2227) covalent geometry : bond 0.00444 (15000) covalent geometry : angle 0.65913 (21694) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.272 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9694 (mt) cc_final: 0.9341 (tt) REVERT: A 81 ASP cc_start: 0.9345 (m-30) cc_final: 0.9033 (m-30) REVERT: A 105 GLU cc_start: 0.9258 (tm-30) cc_final: 0.9051 (tm-30) REVERT: A 109 LEU cc_start: 0.9462 (mt) cc_final: 0.9187 (mt) REVERT: A 126 LEU cc_start: 0.9667 (mm) cc_final: 0.9403 (tt) REVERT: B 59 LYS cc_start: 0.9358 (tptp) cc_final: 0.9144 (tppt) REVERT: B 97 LEU cc_start: 0.9490 (tp) cc_final: 0.9164 (tp) REVERT: B 98 TYR cc_start: 0.8171 (m-10) cc_final: 0.7969 (m-80) REVERT: C 25 PHE cc_start: 0.7956 (m-10) cc_final: 0.7444 (m-10) REVERT: C 83 LEU cc_start: 0.9671 (mp) cc_final: 0.9396 (mp) REVERT: C 90 ASP cc_start: 0.8136 (t0) cc_final: 0.7934 (t0) REVERT: C 94 ASN cc_start: 0.9450 (t0) cc_final: 0.9081 (t0) REVERT: D 56 MET cc_start: 0.9623 (tpt) cc_final: 0.9422 (tpt) REVERT: D 59 MET cc_start: 0.9847 (mmp) cc_final: 0.9439 (mmm) REVERT: D 64 ASN cc_start: 0.9357 (m-40) cc_final: 0.9111 (m-40) REVERT: D 73 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8961 (mm-30) REVERT: D 79 HIS cc_start: 0.9749 (t-90) cc_final: 0.9491 (t-90) REVERT: D 98 LEU cc_start: 0.8631 (mm) cc_final: 0.7903 (mm) REVERT: D 103 LEU cc_start: 0.9702 (mt) cc_final: 0.9495 (mt) REVERT: E 99 TYR cc_start: 0.9576 (t80) cc_final: 0.9248 (t80) REVERT: E 115 LYS cc_start: 0.9362 (mppt) cc_final: 0.9122 (mptt) REVERT: F 61 PHE cc_start: 0.9595 (t80) cc_final: 0.9304 (t80) REVERT: F 68 ASP cc_start: 0.9574 (m-30) cc_final: 0.9167 (m-30) REVERT: F 72 TYR cc_start: 0.9369 (m-80) cc_final: 0.8848 (m-80) REVERT: G 25 PHE cc_start: 0.9066 (m-10) cc_final: 0.8062 (m-10) REVERT: G 56 GLU cc_start: 0.8526 (tt0) cc_final: 0.7010 (tt0) REVERT: G 94 ASN cc_start: 0.9434 (t0) cc_final: 0.9140 (m-40) REVERT: G 101 THR cc_start: 0.8971 (m) cc_final: 0.8665 (p) REVERT: H 59 MET cc_start: 0.9839 (mmp) cc_final: 0.9567 (mmm) REVERT: H 76 ARG cc_start: 0.9694 (ptp-110) cc_final: 0.9211 (mtm110) REVERT: H 110 GLU cc_start: 0.9585 (mm-30) cc_final: 0.9281 (mm-30) REVERT: H 113 LYS cc_start: 0.9566 (ptpp) cc_final: 0.9162 (pttp) REVERT: H 117 LYS cc_start: 0.9779 (ptpp) cc_final: 0.9492 (ptmm) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.4021 time to fit residues: 98.4648 Evaluate side-chains 128 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 109 optimal weight: 50.0000 chunk 53 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 63 optimal weight: 0.0970 chunk 70 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 overall best weight: 4.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** 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 = 0.3348 r_free = 0.3348 target = 0.052278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.040147 restraints weight = 179339.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.040358 restraints weight = 108935.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.040796 restraints weight = 73429.452| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.8231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15000 Z= 0.251 Angle : 0.692 16.789 21694 Z= 0.399 Chirality : 0.037 0.144 2468 Planarity : 0.005 0.047 1582 Dihedral : 32.487 177.399 4762 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.27), residues: 882 helix: 0.87 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.25 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP X 207 HIS 0.006 0.001 HIS F 75 PHE 0.027 0.002 PHE B 61 TYR 0.037 0.003 TYR H 80 ARG 0.007 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.07995 ( 880) hydrogen bonds : angle 3.99854 ( 2227) covalent geometry : bond 0.00543 (15000) covalent geometry : angle 0.69154 (21694) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.236 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9706 (mt) cc_final: 0.9438 (tt) REVERT: A 81 ASP cc_start: 0.9317 (m-30) cc_final: 0.9029 (m-30) REVERT: A 109 LEU cc_start: 0.9451 (mt) cc_final: 0.9213 (mt) REVERT: A 126 LEU cc_start: 0.9672 (mm) cc_final: 0.9416 (tt) REVERT: B 66 ILE cc_start: 0.9535 (mt) cc_final: 0.9276 (tt) REVERT: B 97 LEU cc_start: 0.9493 (tp) cc_final: 0.9245 (tp) REVERT: C 83 LEU cc_start: 0.9587 (mp) cc_final: 0.9268 (mp) REVERT: C 94 ASN cc_start: 0.9341 (t0) cc_final: 0.8988 (t0) REVERT: D 59 MET cc_start: 0.9814 (mmp) cc_final: 0.9442 (mmm) REVERT: D 64 ASN cc_start: 0.9357 (m-40) cc_final: 0.9152 (m-40) REVERT: D 65 ASP cc_start: 0.9780 (t70) cc_final: 0.9571 (t0) REVERT: D 79 HIS cc_start: 0.9728 (t-90) cc_final: 0.9502 (t-90) REVERT: D 103 LEU cc_start: 0.9665 (mt) cc_final: 0.9461 (mt) REVERT: E 99 TYR cc_start: 0.9552 (t80) cc_final: 0.9236 (t80) REVERT: F 61 PHE cc_start: 0.9617 (t80) cc_final: 0.9357 (t80) REVERT: F 68 ASP cc_start: 0.9558 (m-30) cc_final: 0.8760 (m-30) REVERT: G 25 PHE cc_start: 0.8996 (m-10) cc_final: 0.8079 (m-10) REVERT: G 56 GLU cc_start: 0.8490 (tt0) cc_final: 0.7277 (tt0) REVERT: G 94 ASN cc_start: 0.9334 (t0) cc_final: 0.9061 (m-40) REVERT: G 101 THR cc_start: 0.8683 (m) cc_final: 0.8293 (p) REVERT: H 76 ARG cc_start: 0.9605 (ptp-110) cc_final: 0.9155 (mtm110) REVERT: H 110 GLU cc_start: 0.9638 (mm-30) cc_final: 0.9421 (mm-30) REVERT: H 113 LYS cc_start: 0.9587 (ptpp) cc_final: 0.9280 (pttp) REVERT: H 117 LYS cc_start: 0.9777 (ptpp) cc_final: 0.9522 (ptmm) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.4286 time to fit residues: 99.1143 Evaluate side-chains 125 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.053840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.041077 restraints weight = 173673.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.041826 restraints weight = 103199.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.042247 restraints weight = 69933.496| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.8270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15000 Z= 0.185 Angle : 0.672 14.131 21694 Z= 0.384 Chirality : 0.037 0.142 2468 Planarity : 0.004 0.051 1582 Dihedral : 32.186 177.090 4762 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 882 helix: 0.90 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.21 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP X 207 HIS 0.005 0.001 HIS F 75 PHE 0.019 0.002 PHE B 61 TYR 0.040 0.003 TYR F 88 ARG 0.008 0.000 ARG X 282 Details of bonding type rmsd hydrogen bonds : bond 0.05386 ( 880) hydrogen bonds : angle 3.79615 ( 2227) covalent geometry : bond 0.00398 (15000) covalent geometry : angle 0.67158 (21694) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.126 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: 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 60 LEU cc_start: 0.9661 (pp) cc_final: 0.9110 (mp) REVERT: A 74 ILE cc_start: 0.9709 (mt) cc_final: 0.9460 (tt) REVERT: A 81 ASP cc_start: 0.9175 (m-30) cc_final: 0.8887 (m-30) REVERT: A 105 GLU cc_start: 0.9243 (tm-30) cc_final: 0.9036 (tm-30) REVERT: A 109 LEU cc_start: 0.9469 (mt) cc_final: 0.9195 (mt) REVERT: A 126 LEU cc_start: 0.9670 (mm) cc_final: 0.9408 (tt) REVERT: B 66 ILE cc_start: 0.9583 (mt) cc_final: 0.9372 (tt) REVERT: B 97 LEU cc_start: 0.9604 (tp) cc_final: 0.9290 (tp) REVERT: C 25 PHE cc_start: 0.7989 (m-10) cc_final: 0.7432 (m-10) REVERT: C 83 LEU cc_start: 0.9648 (mp) cc_final: 0.9313 (mp) REVERT: C 94 ASN cc_start: 0.9323 (t0) cc_final: 0.8898 (m-40) REVERT: D 59 MET cc_start: 0.9824 (mmp) cc_final: 0.9449 (mmm) REVERT: D 64 ASN cc_start: 0.9389 (m-40) cc_final: 0.9154 (m110) REVERT: D 69 ARG cc_start: 0.9041 (mmm-85) cc_final: 0.8717 (ptp-110) REVERT: D 79 HIS cc_start: 0.9744 (t-90) cc_final: 0.9482 (t-90) REVERT: D 98 LEU cc_start: 0.8759 (mm) cc_final: 0.8447 (mm) REVERT: D 103 LEU cc_start: 0.9660 (mt) cc_final: 0.9444 (mt) REVERT: E 99 TYR cc_start: 0.9577 (t80) cc_final: 0.9230 (t80) REVERT: F 61 PHE cc_start: 0.9633 (t80) cc_final: 0.9417 (t80) REVERT: G 25 PHE cc_start: 0.9128 (m-10) cc_final: 0.8122 (m-10) REVERT: G 56 GLU cc_start: 0.8694 (tt0) cc_final: 0.7216 (tt0) REVERT: G 94 ASN cc_start: 0.9440 (t0) cc_final: 0.9102 (m-40) REVERT: G 101 THR cc_start: 0.8957 (m) cc_final: 0.8610 (p) REVERT: H 59 MET cc_start: 0.9826 (mmp) cc_final: 0.9540 (mmm) REVERT: H 69 ARG cc_start: 0.9565 (ptp-170) cc_final: 0.9105 (ttp80) REVERT: H 76 ARG cc_start: 0.9603 (ptp-110) cc_final: 0.9210 (mtm110) REVERT: H 98 LEU cc_start: 0.9160 (tp) cc_final: 0.8895 (tp) REVERT: H 110 GLU cc_start: 0.9609 (mm-30) cc_final: 0.9395 (mm-30) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3303 time to fit residues: 81.0564 Evaluate side-chains 133 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 63 optimal weight: 0.1980 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.051851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.039794 restraints weight = 180654.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.040291 restraints weight = 105541.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.040703 restraints weight = 72718.237| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.8592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15000 Z= 0.264 Angle : 0.711 15.577 21694 Z= 0.408 Chirality : 0.038 0.156 2468 Planarity : 0.005 0.050 1582 Dihedral : 32.414 177.588 4762 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 882 helix: 0.76 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.30 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP X 207 HIS 0.005 0.001 HIS F 75 PHE 0.023 0.002 PHE B 61 TYR 0.028 0.003 TYR C 50 ARG 0.009 0.001 ARG X 282 Details of bonding type rmsd hydrogen bonds : bond 0.08536 ( 880) hydrogen bonds : angle 4.08577 ( 2227) covalent geometry : bond 0.00570 (15000) covalent geometry : angle 0.71089 (21694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4651.64 seconds wall clock time: 84 minutes 57.71 seconds (5097.71 seconds total)