Starting phenix.real_space_refine on Tue Jul 29 16:14:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j92_36085/07_2025/8j92_36085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j92_36085/07_2025/8j92_36085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j92_36085/07_2025/8j92_36085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j92_36085/07_2025/8j92_36085.map" model { file = "/net/cci-nas-00/data/ceres_data/8j92_36085/07_2025/8j92_36085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j92_36085/07_2025/8j92_36085.cif" } resolution = 2.9 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= 0.004 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 298 5.49 5 S 14 5.16 5 C 6641 2.51 5 N 2226 2.21 5 O 2824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12003 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 794 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 665 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 794 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "E" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 794 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "I" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3037 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3072 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Time building chain proxies: 8.28, per 1000 atoms: 0.69 Number of scatterers: 12003 At special positions: 0 Unit cell: (115.54, 121.9, 117.66, 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 14 16.00 P 298 15.00 O 2824 8.00 N 2226 7.00 C 6641 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: 3.00 Conformation dependent library (CDL) restraints added in 989.3 milliseconds 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1390 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 73.3% alpha, 2.9% beta 129 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 6.65 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.538A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) 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: 3.808A 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 25 through 31 Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 55 through 82 Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 99 through 106 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 80 through 107 removed outlier: 3.537A pdb=" N LEU D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 128 through 149 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 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 25 through 31 Processing helix chain 'G' and resid 35 through 46 Processing helix chain 'G' and resid 55 through 82 Processing helix chain 'G' and resid 88 through 99 Processing helix chain 'G' and resid 99 through 106 Processing helix chain 'H' and resid 62 through 74 Processing helix chain 'H' and resid 80 through 109 removed outlier: 3.815A pdb=" N GLU H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 127 Processing helix chain 'H' and resid 128 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.159A 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: 6.805A pdb=" N THR B 96 " --> pdb=" O THR G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 52 removed outlier: 7.004A pdb=" N ARG C 51 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'C' and resid 110 through 111 removed outlier: 7.105A pdb=" N THR C 110 " --> 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: 7.315A 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 51 through 52 removed outlier: 7.182A pdb=" N ARG G 51 " --> pdb=" O ILE H 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 86 through 87 412 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 332 hydrogen bonds 664 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 3.57 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: 2224 1.33 - 1.45: 4271 1.45 - 1.57: 5714 1.57 - 1.69: 592 1.69 - 1.81: 26 Bond restraints: 12827 Sorted by residual: bond pdb=" O3' DA I -68 " pdb=" P DG I -67 " ideal model delta sigma weight residual 1.607 1.537 0.070 1.50e-02 4.44e+03 2.20e+01 bond pdb=" O3' DG I -73 " pdb=" P DC I -72 " ideal model delta sigma weight residual 1.607 1.546 0.061 1.50e-02 4.44e+03 1.64e+01 bond pdb=" O3' DT I -70 " pdb=" P DG I -69 " ideal model delta sigma weight residual 1.607 1.573 0.034 1.50e-02 4.44e+03 5.21e+00 bond pdb=" O3' DC I -72 " pdb=" P DC I -71 " ideal model delta sigma weight residual 1.607 1.579 0.028 1.50e-02 4.44e+03 3.41e+00 bond pdb=" C2' DA I -68 " pdb=" C1' DA I -68 " ideal model delta sigma weight residual 1.525 1.496 0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 12822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 17979 1.48 - 2.96: 561 2.96 - 4.44: 42 4.44 - 5.93: 9 5.93 - 7.41: 3 Bond angle restraints: 18594 Sorted by residual: angle pdb=" O3' DT I -70 " pdb=" C3' DT I -70 " pdb=" C2' DT I -70 " ideal model delta sigma weight residual 111.50 106.64 4.86 1.50e+00 4.44e-01 1.05e+01 angle pdb=" C4' DG I -69 " pdb=" C3' DG I -69 " pdb=" O3' DG I -69 " ideal model delta sigma weight residual 110.00 105.72 4.28 1.50e+00 4.44e-01 8.15e+00 angle pdb=" C4' DG I -74 " pdb=" O4' DG I -74 " pdb=" C1' DG I -74 " ideal model delta sigma weight residual 109.70 105.70 4.00 1.50e+00 4.44e-01 7.10e+00 angle pdb=" N GLU D 96 " pdb=" CA GLU D 96 " pdb=" CB GLU D 96 " ideal model delta sigma weight residual 110.16 114.05 -3.89 1.48e+00 4.57e-01 6.91e+00 angle pdb=" C3' DG J 20 " pdb=" C2' DG J 20 " pdb=" C1' DG J 20 " ideal model delta sigma weight residual 101.60 97.70 3.90 1.50e+00 4.44e-01 6.75e+00 ... (remaining 18589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.69: 5433 33.69 - 67.39: 1475 67.39 - 101.08: 14 101.08 - 134.77: 2 134.77 - 168.46: 3 Dihedral angle restraints: 6927 sinusoidal: 4772 harmonic: 2155 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 51.54 168.46 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC J -58 " pdb=" C3' DC J -58 " pdb=" O3' DC J -58 " pdb=" P DT J -57 " ideal model delta sinusoidal sigma weight residual 220.00 83.96 136.04 1 3.50e+01 8.16e-04 1.35e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 84.70 135.30 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 6924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1488 0.034 - 0.068: 507 0.068 - 0.101: 94 0.101 - 0.135: 28 0.135 - 0.169: 4 Chirality restraints: 2121 Sorted by residual: chirality pdb=" CB ILE H 79 " pdb=" CA ILE H 79 " pdb=" CG1 ILE H 79 " pdb=" CG2 ILE H 79 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" C3' DG I -74 " pdb=" C4' DG I -74 " pdb=" O3' DG I -74 " pdb=" C2' DG I -74 " both_signs ideal model delta sigma weight residual False -2.66 -2.81 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" C3' DT I -70 " pdb=" C4' DT I -70 " pdb=" O3' DT I -70 " pdb=" C2' DT I -70 " both_signs ideal model delta sigma weight residual False -2.66 -2.81 0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 2118 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -73 " 0.048 2.00e-02 2.50e+03 2.59e-02 2.02e+01 pdb=" N9 DG I -73 " -0.015 2.00e-02 2.50e+03 pdb=" C8 DG I -73 " -0.011 2.00e-02 2.50e+03 pdb=" N7 DG I -73 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -73 " -0.031 2.00e-02 2.50e+03 pdb=" C6 DG I -73 " -0.030 2.00e-02 2.50e+03 pdb=" O6 DG I -73 " 0.056 2.00e-02 2.50e+03 pdb=" N1 DG I -73 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I -73 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I -73 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG I -73 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG I -73 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -69 " -0.025 2.00e-02 2.50e+03 1.57e-02 7.39e+00 pdb=" N9 DG I -69 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG I -69 " 0.014 2.00e-02 2.50e+03 pdb=" N7 DG I -69 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -69 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DG I -69 " -0.027 2.00e-02 2.50e+03 pdb=" O6 DG I -69 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG I -69 " 0.020 2.00e-02 2.50e+03 pdb=" C2 DG I -69 " -0.008 2.00e-02 2.50e+03 pdb=" N2 DG I -69 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I -69 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DG I -69 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -70 " -0.014 2.00e-02 2.50e+03 1.35e-02 4.59e+00 pdb=" N1 DT I -70 " 0.034 2.00e-02 2.50e+03 pdb=" C2 DT I -70 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DT I -70 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT I -70 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I -70 " -0.013 2.00e-02 2.50e+03 pdb=" O4 DT I -70 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT I -70 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT I -70 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT I -70 " -0.009 2.00e-02 2.50e+03 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2219 2.79 - 3.32: 10426 3.32 - 3.84: 23617 3.84 - 4.37: 27847 4.37 - 4.90: 39494 Nonbonded interactions: 103603 Sorted by model distance: nonbonded pdb=" OG SER G 27 " pdb=" O LEU G 32 " model vdw 2.259 3.040 nonbonded pdb=" OG SER C 27 " pdb=" O LEU C 32 " model vdw 2.272 3.040 nonbonded pdb=" ND2 ASN E 108 " pdb=" O GLY F 42 " model vdw 2.276 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.278 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.306 3.120 ... (remaining 103598 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 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.490 Find NCS groups from input model: 0.290 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:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 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 0.070 12827 Z= 0.197 Angle : 0.583 7.407 18594 Z= 0.351 Chirality : 0.036 0.169 2121 Planarity : 0.004 0.044 1312 Dihedral : 28.059 168.462 5537 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.70 (0.30), residues: 733 helix: 2.45 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.24 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 75 PHE 0.011 0.001 PHE D 90 TYR 0.011 0.002 TYR H 65 ARG 0.004 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.07540 ( 744) hydrogen bonds : angle 3.41646 ( 1888) covalent geometry : bond 0.00427 (12827) covalent geometry : angle 0.58321 (18594) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.922 Fit side-chains REVERT: A 50 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8181 (mt-10) REVERT: B 84 MET cc_start: 0.7771 (mmm) cc_final: 0.7461 (tpp) REVERT: C 81 ASP cc_start: 0.7890 (m-30) cc_final: 0.7682 (m-30) REVERT: D 72 GLN cc_start: 0.7555 (tt0) cc_final: 0.7206 (tt0) REVERT: G 84 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8358 (mmmm) REVERT: G 104 LYS cc_start: 0.7996 (tttt) cc_final: 0.7735 (mtpt) REVERT: H 147 THR cc_start: 0.7267 (m) cc_final: 0.7030 (p) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 2.0117 time to fit residues: 367.9430 Evaluate side-chains 100 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.0470 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN D 109 ASN D 120 GLN E 108 ASN F 25 ASN G 33 GLN H 72 GLN H 109 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.175386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125723 restraints weight = 13128.334| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 0.85 r_work: 0.3188 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12827 Z= 0.168 Angle : 0.557 6.252 18594 Z= 0.336 Chirality : 0.034 0.136 2121 Planarity : 0.004 0.039 1312 Dihedral : 31.006 170.116 4065 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.22 % Allowed : 12.86 % Favored : 83.92 % 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: 2.89 (0.31), residues: 733 helix: 2.57 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.11 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 134 PHE 0.010 0.001 PHE H 146 TYR 0.012 0.002 TYR F 51 ARG 0.006 0.001 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 744) hydrogen bonds : angle 2.78921 ( 1888) covalent geometry : bond 0.00370 (12827) covalent geometry : angle 0.55750 (18594) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.881 Fit side-chains REVERT: A 53 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8244 (ttmm) REVERT: A 120 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8062 (mtt) REVERT: C 59 TYR cc_start: 0.9275 (t80) cc_final: 0.9044 (t80) REVERT: C 70 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8061 (tp30) REVERT: D 72 GLN cc_start: 0.7879 (tt0) cc_final: 0.7540 (tt0) REVERT: D 111 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8421 (mmtp) REVERT: D 118 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: G 82 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7481 (t0) REVERT: G 84 LYS cc_start: 0.8785 (mmtm) cc_final: 0.8483 (mmmm) REVERT: H 96 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: H 147 THR cc_start: 0.7116 (m) cc_final: 0.6885 (p) outliers start: 20 outliers final: 5 residues processed: 125 average time/residue: 1.7928 time to fit residues: 236.7031 Evaluate side-chains 120 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 96 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 66 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS F 25 ASN G 33 GLN H 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.168857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118997 restraints weight = 13369.550| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 0.85 r_work: 0.3092 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12827 Z= 0.227 Angle : 0.619 5.985 18594 Z= 0.365 Chirality : 0.037 0.161 2121 Planarity : 0.005 0.043 1312 Dihedral : 31.361 169.011 4065 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 5.14 % Allowed : 14.79 % Favored : 80.06 % 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: 2.36 (0.30), residues: 733 helix: 2.18 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.30 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.015 0.002 PHE A 78 TYR 0.016 0.002 TYR F 51 ARG 0.006 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.05185 ( 744) hydrogen bonds : angle 2.97433 ( 1888) covalent geometry : bond 0.00521 (12827) covalent geometry : angle 0.61923 (18594) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 1.979 Fit side-chains REVERT: A 53 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8350 (ttmm) REVERT: A 129 ARG cc_start: 0.7917 (tpt90) cc_final: 0.7671 (tpt-90) REVERT: B 59 LYS cc_start: 0.8681 (tttm) cc_final: 0.8323 (ttpp) REVERT: D 72 GLN cc_start: 0.7850 (tt0) cc_final: 0.7553 (tt0) REVERT: D 96 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7629 (tp30) REVERT: D 111 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8359 (mmtp) REVERT: D 118 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8281 (mp0) REVERT: E 49 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7910 (mtm110) REVERT: F 88 TYR cc_start: 0.9216 (m-10) cc_final: 0.8978 (m-10) REVERT: F 92 ARG cc_start: 0.8335 (mtp85) cc_final: 0.7861 (mtp85) REVERT: G 82 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7554 (t0) REVERT: G 84 LYS cc_start: 0.8784 (mmtm) cc_final: 0.8576 (mmtp) REVERT: H 96 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: H 147 THR cc_start: 0.7200 (m) cc_final: 0.6926 (p) outliers start: 32 outliers final: 10 residues processed: 137 average time/residue: 1.9465 time to fit residues: 281.5984 Evaluate side-chains 130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 110 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN E 108 ASN G 33 GLN H 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.168719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118066 restraints weight = 13175.355| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 0.86 r_work: 0.3080 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12827 Z= 0.214 Angle : 0.596 5.977 18594 Z= 0.353 Chirality : 0.036 0.153 2121 Planarity : 0.005 0.042 1312 Dihedral : 31.135 166.499 4065 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.86 % Allowed : 18.17 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.32 (0.30), residues: 733 helix: 2.18 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.39 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 39 PHE 0.011 0.002 PHE A 67 TYR 0.014 0.002 TYR F 51 ARG 0.007 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 744) hydrogen bonds : angle 2.93296 ( 1888) covalent geometry : bond 0.00486 (12827) covalent geometry : angle 0.59602 (18594) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.923 Fit side-chains REVERT: A 53 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8289 (ttmm) REVERT: A 115 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8241 (mptp) REVERT: A 129 ARG cc_start: 0.7954 (tpt90) cc_final: 0.7674 (tpt-90) REVERT: D 72 GLN cc_start: 0.7750 (tt0) cc_final: 0.7414 (tt0) REVERT: E 56 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8091 (ttmt) REVERT: G 81 ASP cc_start: 0.7832 (m-30) cc_final: 0.7626 (m-30) REVERT: G 82 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7586 (t0) REVERT: G 84 LYS cc_start: 0.8712 (mmtm) cc_final: 0.8445 (mmtp) REVERT: H 96 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7584 (mp0) outliers start: 24 outliers final: 8 residues processed: 122 average time/residue: 1.9270 time to fit residues: 248.1196 Evaluate side-chains 120 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 96 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN H 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.169007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118449 restraints weight = 13176.180| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 0.84 r_work: 0.3085 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12827 Z= 0.193 Angle : 0.585 7.959 18594 Z= 0.347 Chirality : 0.035 0.138 2121 Planarity : 0.005 0.042 1312 Dihedral : 31.138 166.830 4065 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.50 % Allowed : 18.17 % Favored : 77.33 % 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: 2.39 (0.30), residues: 733 helix: 2.23 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.38 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.011 0.002 PHE A 67 TYR 0.014 0.002 TYR F 51 ARG 0.005 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 744) hydrogen bonds : angle 2.92438 ( 1888) covalent geometry : bond 0.00436 (12827) covalent geometry : angle 0.58468 (18594) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.920 Fit side-chains REVERT: A 40 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7039 (tpt-90) REVERT: A 53 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8259 (ttmm) REVERT: A 76 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7775 (pt0) REVERT: A 115 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8327 (mptp) REVERT: A 129 ARG cc_start: 0.7956 (tpt90) cc_final: 0.7664 (tpt-90) REVERT: D 72 GLN cc_start: 0.7784 (tt0) cc_final: 0.7459 (tt0) REVERT: D 111 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8440 (mmtp) REVERT: D 118 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: G 82 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7572 (t0) REVERT: G 84 LYS cc_start: 0.8710 (mmtm) cc_final: 0.8423 (mmtp) REVERT: H 96 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: H 110 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8221 (mtpp) outliers start: 28 outliers final: 12 residues processed: 124 average time/residue: 1.8756 time to fit residues: 245.2611 Evaluate side-chains 129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN H 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.170442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119933 restraints weight = 13360.100| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 0.85 r_work: 0.3105 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12827 Z= 0.154 Angle : 0.554 7.445 18594 Z= 0.334 Chirality : 0.034 0.131 2121 Planarity : 0.004 0.042 1312 Dihedral : 31.094 167.057 4065 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 4.50 % Allowed : 18.17 % Favored : 77.33 % 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: 2.66 (0.30), residues: 733 helix: 2.45 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.37 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.011 0.001 TYR F 51 ARG 0.003 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 744) hydrogen bonds : angle 2.86594 ( 1888) covalent geometry : bond 0.00329 (12827) covalent geometry : angle 0.55390 (18594) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.875 Fit side-chains REVERT: A 53 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8186 (ttmm) REVERT: A 59 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7235 (pt0) REVERT: A 115 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8193 (mptp) REVERT: A 129 ARG cc_start: 0.7934 (tpt90) cc_final: 0.7655 (tpt-90) REVERT: C 59 TYR cc_start: 0.9288 (t80) cc_final: 0.9006 (t80) REVERT: D 72 GLN cc_start: 0.7747 (tt0) cc_final: 0.7429 (tt0) REVERT: D 111 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8425 (mmtp) REVERT: D 118 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: G 82 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7622 (t0) REVERT: G 84 LYS cc_start: 0.8718 (mmtm) cc_final: 0.8379 (mmtp) REVERT: H 96 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: H 100 SER cc_start: 0.9147 (p) cc_final: 0.8764 (m) REVERT: H 104 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7522 (mtpp) REVERT: H 110 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8191 (mtpp) outliers start: 28 outliers final: 10 residues processed: 131 average time/residue: 1.8603 time to fit residues: 257.3400 Evaluate side-chains 129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 104 LYS Chi-restraints excluded: chain H residue 110 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.171414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120972 restraints weight = 13373.026| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 0.87 r_work: 0.3123 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12827 Z= 0.156 Angle : 0.544 8.081 18594 Z= 0.328 Chirality : 0.033 0.130 2121 Planarity : 0.004 0.042 1312 Dihedral : 30.942 166.643 4065 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.50 % Allowed : 19.61 % Favored : 75.88 % 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: 2.80 (0.30), residues: 733 helix: 2.52 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.24 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.011 0.001 TYR F 51 ARG 0.006 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 744) hydrogen bonds : angle 2.79908 ( 1888) covalent geometry : bond 0.00338 (12827) covalent geometry : angle 0.54421 (18594) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.873 Fit side-chains REVERT: A 53 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8216 (ttmm) REVERT: A 59 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7219 (pt0) REVERT: A 65 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8348 (tp) REVERT: A 115 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8299 (mttm) REVERT: A 129 ARG cc_start: 0.7904 (tpt90) cc_final: 0.7666 (tpt-90) REVERT: D 72 GLN cc_start: 0.7764 (tt0) cc_final: 0.7462 (tt0) REVERT: D 111 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8332 (mmtp) REVERT: D 118 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: E 49 ARG cc_start: 0.8513 (mtm110) cc_final: 0.8186 (mtm-85) REVERT: E 120 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7716 (mtm) REVERT: G 80 ARG cc_start: 0.7359 (ttm110) cc_final: 0.6834 (ttm-80) REVERT: G 84 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8315 (mmtp) REVERT: H 96 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: H 100 SER cc_start: 0.9126 (p) cc_final: 0.8754 (m) REVERT: H 104 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7508 (mtpp) REVERT: H 110 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8256 (mtpp) outliers start: 28 outliers final: 10 residues processed: 128 average time/residue: 1.9023 time to fit residues: 256.7319 Evaluate side-chains 129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 104 LYS Chi-restraints excluded: chain H residue 110 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN H 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.171949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121440 restraints weight = 13342.513| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 0.88 r_work: 0.3132 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12827 Z= 0.155 Angle : 0.530 8.297 18594 Z= 0.319 Chirality : 0.033 0.131 2121 Planarity : 0.004 0.041 1312 Dihedral : 30.792 167.503 4065 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.22 % Allowed : 20.26 % Favored : 76.53 % 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: 2.94 (0.30), residues: 733 helix: 2.62 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.18 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.010 0.001 TYR F 51 ARG 0.004 0.000 ARG H 107 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 744) hydrogen bonds : angle 2.76592 ( 1888) covalent geometry : bond 0.00334 (12827) covalent geometry : angle 0.53040 (18594) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.880 Fit side-chains REVERT: A 53 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8214 (ttmm) REVERT: A 59 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: A 115 LYS cc_start: 0.8587 (mptp) cc_final: 0.8356 (mttm) REVERT: A 129 ARG cc_start: 0.7904 (tpt90) cc_final: 0.7681 (tpt-90) REVERT: C 59 TYR cc_start: 0.9255 (t80) cc_final: 0.9048 (t80) REVERT: D 72 GLN cc_start: 0.7770 (tt0) cc_final: 0.7536 (tt0) REVERT: D 111 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8321 (mmtp) REVERT: D 118 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: E 120 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7747 (mtm) REVERT: G 84 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8358 (mmtp) REVERT: H 96 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: H 100 SER cc_start: 0.9091 (p) cc_final: 0.8747 (m) REVERT: H 104 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7505 (mtpp) outliers start: 20 outliers final: 10 residues processed: 125 average time/residue: 1.8442 time to fit residues: 243.2111 Evaluate side-chains 127 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 104 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN H 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.168432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117802 restraints weight = 13252.638| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 0.86 r_work: 0.3064 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12827 Z= 0.218 Angle : 0.593 7.556 18594 Z= 0.349 Chirality : 0.036 0.171 2121 Planarity : 0.005 0.040 1312 Dihedral : 31.111 167.868 4065 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.54 % Allowed : 20.10 % Favored : 76.37 % 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: 2.43 (0.30), residues: 733 helix: 2.26 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.36 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.011 0.002 PHE A 67 TYR 0.014 0.002 TYR E 54 ARG 0.005 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04892 ( 744) hydrogen bonds : angle 2.93339 ( 1888) covalent geometry : bond 0.00501 (12827) covalent geometry : angle 0.59345 (18594) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.569 Fit side-chains REVERT: A 40 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7186 (tpt-90) REVERT: A 53 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8367 (ttmm) REVERT: A 59 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7317 (pt0) REVERT: A 129 ARG cc_start: 0.7992 (tpt90) cc_final: 0.7645 (tpt-90) REVERT: B 59 LYS cc_start: 0.8677 (tttm) cc_final: 0.8282 (ttpp) REVERT: D 72 GLN cc_start: 0.7804 (tt0) cc_final: 0.7451 (tt0) REVERT: D 111 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8387 (mmtp) REVERT: D 118 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: G 80 ARG cc_start: 0.7384 (ttm110) cc_final: 0.6805 (ttm-80) REVERT: G 84 LYS cc_start: 0.8652 (mmtm) cc_final: 0.8322 (mmtp) REVERT: H 96 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7601 (mp0) outliers start: 22 outliers final: 12 residues processed: 124 average time/residue: 2.7286 time to fit residues: 358.4064 Evaluate side-chains 125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN G 33 GLN H 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.169271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.118590 restraints weight = 13198.056| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 0.84 r_work: 0.3085 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12827 Z= 0.170 Angle : 0.570 10.506 18594 Z= 0.339 Chirality : 0.035 0.182 2121 Planarity : 0.004 0.041 1312 Dihedral : 31.082 167.277 4065 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.73 % Allowed : 20.90 % Favored : 76.37 % 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: 2.50 (0.30), residues: 733 helix: 2.32 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.37 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.013 0.002 TYR F 51 ARG 0.004 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 744) hydrogen bonds : angle 2.92620 ( 1888) covalent geometry : bond 0.00373 (12827) covalent geometry : angle 0.56968 (18594) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.914 Fit side-chains REVERT: A 53 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8257 (ttmm) REVERT: A 59 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: A 129 ARG cc_start: 0.7958 (tpt90) cc_final: 0.7605 (tpt-90) REVERT: D 72 GLN cc_start: 0.7736 (tt0) cc_final: 0.7395 (tt0) REVERT: D 111 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8363 (mmtp) REVERT: D 118 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: G 80 ARG cc_start: 0.7347 (ttm110) cc_final: 0.6780 (ttm-80) REVERT: G 84 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8301 (mmtp) REVERT: H 96 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: H 104 LYS cc_start: 0.7866 (mtmm) cc_final: 0.7485 (mtpp) outliers start: 17 outliers final: 9 residues processed: 120 average time/residue: 3.6999 time to fit residues: 467.2202 Evaluate side-chains 121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 96 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 85 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 0.0470 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN G 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.168848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118552 restraints weight = 13222.819| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 0.88 r_work: 0.3075 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12827 Z= 0.202 Angle : 0.578 7.595 18594 Z= 0.341 Chirality : 0.035 0.196 2121 Planarity : 0.004 0.041 1312 Dihedral : 31.013 168.216 4065 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.05 % Allowed : 20.26 % Favored : 76.69 % 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: 2.45 (0.30), residues: 733 helix: 2.29 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.41 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 39 PHE 0.012 0.002 PHE A 67 TYR 0.013 0.002 TYR F 51 ARG 0.005 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 744) hydrogen bonds : angle 2.89280 ( 1888) covalent geometry : bond 0.00459 (12827) covalent geometry : angle 0.57754 (18594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10021.27 seconds wall clock time: 177 minutes 33.59 seconds (10653.59 seconds total)