Starting phenix.real_space_refine on Sat Nov 16 16:20:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j92_36085/11_2024/8j92_36085.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j92_36085/11_2024/8j92_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j92_36085/11_2024/8j92_36085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j92_36085/11_2024/8j92_36085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j92_36085/11_2024/8j92_36085.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j92_36085/11_2024/8j92_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.56, per 1000 atoms: 0.71 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: 3.11 Conformation dependent library (CDL) restraints added in 901.7 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: 6.52 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: 6.26 Time building geometry restraints manager: 3.60 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: 0.000 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: 0.000 Extract box with map and model: 0.700 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 35.740 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.090 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:14.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.540 ------------------------------------------------------------------------------- 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= 0.247 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 *********************** 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 : 0.913 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: 1.9420 time to fit residues: 355.9569 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 : 0.932 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 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= 0.207 Angle : 0.557 6.253 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 *********************** 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 : 0.908 Fit side-chains REVERT: A 53 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.7781 (ttmm) REVERT: A 120 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7235 (mtt) REVERT: C 59 TYR cc_start: 0.9059 (t80) cc_final: 0.8776 (t80) REVERT: C 70 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: C 81 ASP cc_start: 0.7862 (m-30) cc_final: 0.7657 (m-30) REVERT: D 72 GLN cc_start: 0.7483 (tt0) cc_final: 0.7062 (tt0) REVERT: D 111 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8235 (mmtp) REVERT: D 118 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: D 120 GLN cc_start: 0.8590 (tt0) cc_final: 0.8362 (tt0) REVERT: G 82 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7337 (t0) REVERT: G 84 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8442 (mmmm) REVERT: H 96 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: H 110 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7914 (mtpp) REVERT: H 118 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7109 (mp0) outliers start: 20 outliers final: 5 residues processed: 125 average time/residue: 1.8625 time to fit residues: 245.8338 Evaluate side-chains 123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 118 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 HIS F 25 ASN G 33 GLN H 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12827 Z= 0.348 Angle : 0.651 6.468 18594 Z= 0.381 Chirality : 0.039 0.170 2121 Planarity : 0.005 0.044 1312 Dihedral : 31.493 168.714 4065 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 5.47 % Allowed : 14.79 % Favored : 79.74 % 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: 2.15 (0.30), residues: 733 helix: 2.03 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.36 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 39 PHE 0.016 0.003 PHE A 78 TYR 0.018 0.003 TYR F 51 ARG 0.008 0.001 ARG A 42 *********************** 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 158 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 1.003 Fit side-chains REVERT: A 53 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7948 (ttmm) REVERT: A 120 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7430 (mtt) REVERT: A 129 ARG cc_start: 0.7492 (tpt90) cc_final: 0.7211 (tpt-90) REVERT: B 59 LYS cc_start: 0.8185 (tttm) cc_final: 0.7753 (ttpp) REVERT: B 79 LYS cc_start: 0.8687 (mttm) cc_final: 0.8479 (mmmt) REVERT: C 33 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7453 (mm-40) REVERT: C 80 ARG cc_start: 0.7548 (mtm-85) cc_final: 0.7291 (mtm-85) REVERT: D 72 GLN cc_start: 0.7498 (tt0) cc_final: 0.7076 (tt0) REVERT: D 108 TYR cc_start: 0.6028 (m-10) cc_final: 0.5707 (m-10) REVERT: D 111 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8234 (mmtp) REVERT: D 118 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: D 120 GLN cc_start: 0.8622 (tt0) cc_final: 0.8394 (tt0) REVERT: E 49 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7174 (mtm110) REVERT: E 56 LYS cc_start: 0.8046 (ttmm) cc_final: 0.7610 (ttmt) REVERT: F 88 TYR cc_start: 0.8869 (m-10) cc_final: 0.8566 (m-10) REVERT: F 92 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7624 (mtp85) REVERT: G 28 MET cc_start: 0.6503 (tpp) cc_final: 0.6174 (tpt) REVERT: G 82 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7458 (t0) REVERT: G 84 LYS cc_start: 0.8713 (mmtm) cc_final: 0.8494 (mmtp) REVERT: H 59 VAL cc_start: 0.8497 (p) cc_final: 0.8297 (t) REVERT: H 96 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: H 110 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7945 (mtpp) outliers start: 34 outliers final: 9 residues processed: 141 average time/residue: 1.9852 time to fit residues: 295.0361 Evaluate side-chains 129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 120 MET 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 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 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 88 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** E 108 ASN G 33 GLN H 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2882 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= 0.198 Angle : 0.553 6.274 18594 Z= 0.332 Chirality : 0.033 0.127 2121 Planarity : 0.004 0.043 1312 Dihedral : 30.941 166.898 4065 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.70 % Allowed : 18.81 % Favored : 77.49 % 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: 2.67 (0.30), residues: 733 helix: 2.42 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.24 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.011 0.002 TYR F 51 ARG 0.006 0.000 ARG A 42 *********************** 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 135 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.931 Fit side-chains REVERT: A 53 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7759 (ttmm) REVERT: A 115 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8176 (mttm) REVERT: A 129 ARG cc_start: 0.7427 (tpt90) cc_final: 0.7173 (tpt-90) REVERT: C 80 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7172 (ttm-80) REVERT: D 72 GLN cc_start: 0.7394 (tt0) cc_final: 0.7071 (tt0) REVERT: E 56 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7588 (ttmt) REVERT: F 88 TYR cc_start: 0.8844 (m-10) cc_final: 0.8556 (m-10) REVERT: G 82 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.7420 (t0) REVERT: G 84 LYS cc_start: 0.8670 (mmtm) cc_final: 0.8406 (mmtp) REVERT: H 96 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: H 100 SER cc_start: 0.9013 (p) cc_final: 0.8575 (m) REVERT: H 104 LYS cc_start: 0.7711 (mtmm) cc_final: 0.7265 (mtpp) REVERT: H 107 ARG cc_start: 0.7191 (mtm-85) cc_final: 0.6711 (mtm110) REVERT: H 110 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7871 (mtpp) REVERT: H 118 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7292 (mp0) outliers start: 23 outliers final: 8 residues processed: 124 average time/residue: 1.8492 time to fit residues: 242.5250 Evaluate side-chains 124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 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 118 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** D 120 GLN H 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3036 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= 0.226 Angle : 0.562 7.618 18594 Z= 0.335 Chirality : 0.034 0.131 2121 Planarity : 0.004 0.041 1312 Dihedral : 31.005 167.495 4065 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.38 % Allowed : 19.77 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.63 (0.30), residues: 733 helix: 2.39 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.26 (0.43), residues: 186 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 0.013 0.002 TYR F 51 ARG 0.005 0.000 ARG A 42 *********************** 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 132 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.996 Fit side-chains REVERT: A 53 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7798 (ttmm) REVERT: A 115 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8234 (mptp) REVERT: A 129 ARG cc_start: 0.7514 (tpt90) cc_final: 0.7209 (tpt-90) REVERT: C 80 ARG cc_start: 0.7417 (mtm-85) cc_final: 0.7172 (ttm-80) REVERT: D 72 GLN cc_start: 0.7366 (tt0) cc_final: 0.7018 (tt0) REVERT: D 118 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: G 82 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7517 (t0) REVERT: G 84 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8400 (mmtp) REVERT: H 96 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: H 100 SER cc_start: 0.9004 (p) cc_final: 0.8603 (m) REVERT: H 104 LYS cc_start: 0.7615 (mtmm) cc_final: 0.7195 (mtpp) REVERT: H 107 ARG cc_start: 0.7237 (mtm-85) cc_final: 0.6967 (ttm110) REVERT: H 110 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7862 (mtpp) outliers start: 21 outliers final: 9 residues processed: 120 average time/residue: 1.9255 time to fit residues: 243.9160 Evaluate side-chains 123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 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 81 SER Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 110 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 74 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3267 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= 0.221 Angle : 0.551 6.864 18594 Z= 0.329 Chirality : 0.034 0.128 2121 Planarity : 0.004 0.042 1312 Dihedral : 30.905 166.481 4065 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.86 % Allowed : 19.61 % 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: 2.61 (0.30), residues: 733 helix: 2.39 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.28 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.012 0.002 TYR F 51 ARG 0.007 0.000 ARG A 42 *********************** 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 132 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.881 Fit side-chains REVERT: A 53 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.7789 (ttmm) REVERT: A 59 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6758 (pt0) REVERT: A 129 ARG cc_start: 0.7474 (tpt90) cc_final: 0.7199 (tpt-90) REVERT: B 79 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8374 (mtmm) REVERT: C 45 LYS cc_start: 0.7954 (pttt) cc_final: 0.7748 (pttt) REVERT: C 80 ARG cc_start: 0.7382 (mtm-85) cc_final: 0.7160 (ttm-80) REVERT: D 72 GLN cc_start: 0.7358 (tt0) cc_final: 0.7008 (tt0) REVERT: D 118 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: G 84 LYS cc_start: 0.8692 (mmtm) cc_final: 0.8352 (mmtp) REVERT: H 96 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: H 100 SER cc_start: 0.9004 (p) cc_final: 0.8575 (m) REVERT: H 104 LYS cc_start: 0.7606 (mtmm) cc_final: 0.7242 (mttm) REVERT: H 107 ARG cc_start: 0.7227 (mtm-85) cc_final: 0.6958 (ttm110) REVERT: H 110 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7912 (mtpp) outliers start: 24 outliers final: 10 residues processed: 121 average time/residue: 1.9303 time to fit residues: 246.3700 Evaluate side-chains 121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 B residue 79 LYS 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 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** C 119 ASN D 120 GLN E 113 HIS G 33 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3276 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= 0.179 Angle : 0.542 9.222 18594 Z= 0.325 Chirality : 0.033 0.138 2121 Planarity : 0.004 0.041 1312 Dihedral : 30.904 166.579 4065 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.34 % Allowed : 19.45 % Favored : 76.21 % 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: 2.77 (0.30), residues: 733 helix: 2.51 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.26 (0.43), 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 0.006 0.000 ARG A 42 *********************** 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 133 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.970 Fit side-chains REVERT: A 53 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.7760 (ttmm) REVERT: A 129 ARG cc_start: 0.7468 (tpt90) cc_final: 0.7192 (tpt-90) REVERT: B 79 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8371 (mtmm) REVERT: C 45 LYS cc_start: 0.7940 (pttt) cc_final: 0.7724 (pttt) REVERT: C 80 ARG cc_start: 0.7397 (mtm-85) cc_final: 0.7174 (ttm-80) REVERT: D 72 GLN cc_start: 0.7345 (tt0) cc_final: 0.6998 (tt0) REVERT: D 118 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: G 84 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8341 (mmtp) REVERT: H 96 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: H 100 SER cc_start: 0.8963 (p) cc_final: 0.8524 (m) REVERT: H 104 LYS cc_start: 0.7584 (mtmm) cc_final: 0.7212 (mttm) REVERT: H 107 ARG cc_start: 0.7222 (mtm-85) cc_final: 0.6957 (ttm110) REVERT: H 110 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7889 (mtpp) outliers start: 27 outliers final: 13 residues processed: 121 average time/residue: 1.8878 time to fit residues: 241.4760 Evaluate side-chains 123 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 119 ASN 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 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 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 110 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** C 119 ASN G 33 GLN H 74 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3292 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= 0.171 Angle : 0.532 8.729 18594 Z= 0.320 Chirality : 0.033 0.151 2121 Planarity : 0.004 0.041 1312 Dihedral : 30.862 167.336 4065 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.38 % Allowed : 20.58 % Favored : 76.05 % 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: 2.85 (0.30), residues: 733 helix: 2.56 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.20 (0.43), residues: 184 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 0.010 0.001 TYR F 51 ARG 0.006 0.000 ARG A 42 *********************** 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 129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.911 Fit side-chains REVERT: A 53 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7742 (ttmm) REVERT: A 59 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6747 (pt0) REVERT: A 115 LYS cc_start: 0.8487 (mptp) cc_final: 0.8216 (mttm) REVERT: A 129 ARG cc_start: 0.7466 (tpt90) cc_final: 0.7203 (tpt-90) REVERT: B 79 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8355 (mtmm) REVERT: C 80 ARG cc_start: 0.7421 (mtm-85) cc_final: 0.7193 (ttm-80) REVERT: D 72 GLN cc_start: 0.7351 (tt0) cc_final: 0.7020 (tt0) REVERT: D 118 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: G 84 LYS cc_start: 0.8708 (mmtm) cc_final: 0.8355 (mmtp) REVERT: H 96 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: H 100 SER cc_start: 0.8941 (p) cc_final: 0.8525 (m) REVERT: H 104 LYS cc_start: 0.7579 (mtmm) cc_final: 0.7215 (mttm) REVERT: H 107 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6956 (ttm110) REVERT: H 110 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7899 (mtpp) outliers start: 21 outliers final: 10 residues processed: 119 average time/residue: 1.9111 time to fit residues: 240.3975 Evaluate side-chains 121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 79 LYS 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 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 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 110 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12827 Z= 0.303 Angle : 0.600 9.008 18594 Z= 0.352 Chirality : 0.037 0.160 2121 Planarity : 0.005 0.041 1312 Dihedral : 31.138 168.068 4065 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.22 % Allowed : 20.58 % Favored : 76.21 % 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: 2.40 (0.30), residues: 733 helix: 2.23 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.34 (0.43), 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 0.015 0.002 TYR E 54 ARG 0.006 0.001 ARG A 42 *********************** 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 128 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.927 Fit side-chains REVERT: A 53 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7942 (ttmm) REVERT: A 59 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6776 (pt0) REVERT: A 115 LYS cc_start: 0.8517 (mptp) cc_final: 0.8267 (mttm) REVERT: A 129 ARG cc_start: 0.7534 (tpt90) cc_final: 0.7134 (tpt-90) REVERT: B 59 LYS cc_start: 0.8159 (tttm) cc_final: 0.7690 (ttpp) REVERT: B 79 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8334 (mtmm) REVERT: C 80 ARG cc_start: 0.7420 (mtm-85) cc_final: 0.7176 (ttm-80) REVERT: D 72 GLN cc_start: 0.7412 (tt0) cc_final: 0.7001 (tt0) REVERT: D 118 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: G 84 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8253 (mmtp) REVERT: H 96 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: H 104 LYS cc_start: 0.7602 (mtmm) cc_final: 0.7275 (mttm) REVERT: H 110 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7864 (mtpp) outliers start: 20 outliers final: 11 residues processed: 121 average time/residue: 1.9212 time to fit residues: 245.5674 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 : 0.909 ------------------------------------------------------------------------------- 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 B residue 79 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 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 110 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 83 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3437 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= 0.196 Angle : 0.565 9.035 18594 Z= 0.337 Chirality : 0.034 0.173 2121 Planarity : 0.004 0.041 1312 Dihedral : 31.111 167.270 4065 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.73 % Allowed : 21.38 % 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: 2.53 (0.30), residues: 733 helix: 2.34 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.35 (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 D 108 ARG 0.005 0.000 ARG A 42 ********************** 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 122 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.995 Fit side-chains REVERT: A 53 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7822 (ttmm) REVERT: A 59 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6759 (pt0) REVERT: A 115 LYS cc_start: 0.8521 (mptp) cc_final: 0.8275 (mttm) REVERT: A 129 ARG cc_start: 0.7525 (tpt90) cc_final: 0.7140 (tpt-90) REVERT: B 79 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8318 (mtmm) REVERT: C 80 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7171 (ttm-80) REVERT: D 72 GLN cc_start: 0.7368 (tt0) cc_final: 0.6968 (tt0) REVERT: D 118 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: G 80 ARG cc_start: 0.7216 (ttm110) cc_final: 0.6809 (ttm-80) REVERT: G 84 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8233 (mmtp) REVERT: H 96 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: H 104 LYS cc_start: 0.7587 (mtmm) cc_final: 0.7255 (mttm) REVERT: H 110 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7913 (mtpp) outliers start: 17 outliers final: 9 residues processed: 118 average time/residue: 2.0379 time to fit residues: 253.8115 Evaluate side-chains 121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 79 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 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 81 SER Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 110 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.169447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118590 restraints weight = 13170.416| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 0.85 r_work: 0.3085 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3433 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= 0.210 Angle : 0.561 8.668 18594 Z= 0.333 Chirality : 0.034 0.156 2121 Planarity : 0.004 0.041 1312 Dihedral : 31.024 167.777 4065 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.05 % Allowed : 21.22 % Favored : 75.72 % 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: 2.59 (0.30), residues: 733 helix: 2.39 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.33 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.011 0.001 PHE A 67 TYR 0.013 0.002 TYR D 108 ARG 0.006 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4300.44 seconds wall clock time: 77 minutes 53.84 seconds (4673.84 seconds total)