Starting phenix.real_space_refine on Wed May 14 05:16:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q16_18061/05_2025/8q16_18061.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q16_18061/05_2025/8q16_18061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q16_18061/05_2025/8q16_18061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q16_18061/05_2025/8q16_18061.map" model { file = "/net/cci-nas-00/data/ceres_data/8q16_18061/05_2025/8q16_18061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q16_18061/05_2025/8q16_18061.cif" } resolution = 3.6 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= 0.002 sd= 0.052 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 294 5.49 5 S 13 5.16 5 C 6516 2.51 5 N 2175 2.21 5 O 2775 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-5687/modules/chem_data/mon_lib" Total number of atoms: 11773 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 776 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "B" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "D" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "E" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 776 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 737 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "G" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 628 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "H" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 623 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 7.18, per 1000 atoms: 0.61 Number of scatterers: 11773 At special positions: 0 Unit cell: (74.881, 124.317, 118.501, 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 13 16.00 P 294 15.00 O 2775 8.00 N 2175 7.00 C 6516 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: 2.73 Conformation dependent library (CDL) restraints added in 822.9 milliseconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 75.7% alpha, 2.7% beta 147 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 5.38 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 47 through 75 removed outlier: 4.585A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.575A pdb=" N ASP A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 48 through 75 Processing helix chain 'B' and resid 81 through 92 Processing helix chain 'B' and resid 92 through 99 Processing helix chain 'C' and resid 66 through 78 Processing helix chain 'C' and resid 84 through 113 Processing helix chain 'C' and resid 119 through 131 Processing helix chain 'C' and resid 133 through 152 removed outlier: 3.651A pdb=" N SER C 152 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 Processing helix chain 'D' and resid 84 through 113 Processing helix chain 'D' and resid 119 through 131 Processing helix chain 'D' and resid 133 through 153 Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.647A pdb=" N LEU E 49 " --> pdb=" O GLY E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 80 removed outlier: 4.057A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 46 through 58 Processing helix chain 'F' and resid 64 through 80 removed outlier: 4.016A pdb=" N ASP F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE F 79 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 115 Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'G' and resid 25 through 30 removed outlier: 4.006A pdb=" N GLN G 28 " --> pdb=" O GLY G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 42 Processing helix chain 'G' and resid 50 through 77 removed outlier: 3.804A pdb=" N GLU G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG G 56 " --> pdb=" O TYR G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 94 removed outlier: 3.537A pdb=" N GLN G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 30 removed outlier: 3.719A pdb=" N GLN H 28 " --> pdb=" O GLY H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 42 removed outlier: 3.535A pdb=" N ILE H 35 " --> pdb=" O ALA H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 77 removed outlier: 3.963A pdb=" N GLU H 54 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 removed outlier: 7.316A pdb=" N ARG A 44 " --> pdb=" O ILE D 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 104 removed outlier: 7.187A pdb=" N THR A 103 " --> pdb=" O TYR H 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 44 through 45 removed outlier: 7.250A pdb=" N ARG B 44 " --> pdb=" O ILE C 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 104 removed outlier: 6.942A pdb=" N THR B 103 " --> pdb=" O TYR G 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.777A pdb=" N ARG E 84 " --> pdb=" O VAL H 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'F' and resid 84 through 85 removed outlier: 7.022A pdb=" N ARG F 84 " --> pdb=" O VAL G 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 119 through 120 406 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 4.62 Time building geometry restraints manager: 3.23 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: 1894 1.33 - 1.45: 4330 1.45 - 1.57: 5749 1.57 - 1.68: 586 1.68 - 1.80: 24 Bond restraints: 12583 Sorted by residual: bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" C3' DT J 14 " pdb=" C2' DT J 14 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 9.84e-01 bond pdb=" CB PRO E 44 " pdb=" CG PRO E 44 " ideal model delta sigma weight residual 1.492 1.541 -0.049 5.00e-02 4.00e+02 9.61e-01 bond pdb=" C4' DT J -6 " pdb=" O4' DT J -6 " ideal model delta sigma weight residual 1.450 1.432 0.018 2.00e-02 2.50e+03 8.16e-01 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.449 -0.027 3.00e-02 1.11e+03 7.92e-01 ... (remaining 12578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 17308 1.11 - 2.22: 772 2.22 - 3.33: 157 3.33 - 4.44: 7 4.44 - 5.55: 8 Bond angle restraints: 18252 Sorted by residual: angle pdb=" C ARG E 41 " pdb=" CA ARG E 41 " pdb=" CB ARG E 41 " ideal model delta sigma weight residual 110.42 115.09 -4.67 1.99e+00 2.53e-01 5.50e+00 angle pdb=" C3' DG I 2 " pdb=" C2' DG I 2 " pdb=" C1' DG I 2 " ideal model delta sigma weight residual 101.60 104.66 -3.06 1.50e+00 4.44e-01 4.16e+00 angle pdb=" CA VAL F 118 " pdb=" C VAL F 118 " pdb=" N THR F 119 " ideal model delta sigma weight residual 116.60 119.40 -2.80 1.45e+00 4.76e-01 3.72e+00 angle pdb=" C3' DG I -5 " pdb=" C2' DG I -5 " pdb=" C1' DG I -5 " ideal model delta sigma weight residual 101.60 98.76 2.84 1.50e+00 4.44e-01 3.59e+00 angle pdb=" C3' DC I 1 " pdb=" C2' DC I 1 " pdb=" C1' DC I 1 " ideal model delta sigma weight residual 101.60 104.43 -2.83 1.50e+00 4.44e-01 3.57e+00 ... (remaining 18247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 5560 35.95 - 71.90: 1215 71.90 - 107.85: 8 107.85 - 143.80: 2 143.80 - 179.75: 1 Dihedral angle restraints: 6786 sinusoidal: 4674 harmonic: 2112 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual -140.00 39.75 -179.75 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 81.92 138.08 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 86.16 133.84 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 6783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1312 0.027 - 0.053: 576 0.053 - 0.080: 141 0.080 - 0.107: 38 0.107 - 0.134: 20 Chirality restraints: 2087 Sorted by residual: chirality pdb=" CA ILE C 118 " pdb=" N ILE C 118 " pdb=" C ILE C 118 " pdb=" CB ILE C 118 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA PRO G 33 " pdb=" N PRO G 33 " pdb=" C PRO G 33 " pdb=" CB PRO G 33 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE D 118 " pdb=" N ILE D 118 " pdb=" C ILE D 118 " pdb=" CB ILE D 118 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 2084 not shown) Planarity restraints: 1280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -13 " 0.021 2.00e-02 2.50e+03 9.23e-03 2.34e+00 pdb=" N9 DA I -13 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DA I -13 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I -13 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -13 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -13 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -13 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -13 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -13 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -13 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -13 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " -0.022 2.00e-02 2.50e+03 8.94e-03 2.20e+00 pdb=" N9 DA I 47 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 131 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO D 132 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 132 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 132 " -0.020 5.00e-02 4.00e+02 ... (remaining 1277 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 746 2.72 - 3.27: 10591 3.27 - 3.81: 23042 3.81 - 4.36: 26420 4.36 - 4.90: 38709 Nonbonded interactions: 99508 Sorted by model distance: nonbonded pdb=" N2 DG I -10 " pdb=" O2 DC J 10 " model vdw 2.181 2.496 nonbonded pdb=" OG1 THR E 119 " pdb=" NH1 ARG H 46 " model vdw 2.230 3.120 nonbonded pdb=" OG1 THR G 74 " pdb=" OD2 ASP G 86 " model vdw 2.294 3.040 nonbonded pdb=" O SER A 18 " pdb=" OG SER A 21 " model vdw 2.295 3.040 nonbonded pdb=" NH2 ARG B 34 " pdb=" OE1 GLU C 64 " model vdw 2.307 3.120 ... (remaining 99503 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 18 through 118) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 63 through 152) selection = (chain 'D' and resid 63 through 152) } ncs_group { reference = (chain 'E' and resid 45 through 134) selection = (chain 'F' and resid 45 through 134) } ncs_group { reference = (chain 'G' and resid 25 through 102) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.370 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.350 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 0.049 12583 Z= 0.194 Angle : 0.545 5.553 18252 Z= 0.327 Chirality : 0.033 0.134 2087 Planarity : 0.004 0.037 1280 Dihedral : 26.753 179.755 5424 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.50 % Allowed : 2.50 % Favored : 97.00 % 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 (0.31), residues: 716 helix: 2.56 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.03 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 76 PHE 0.009 0.001 PHE E 42 TYR 0.009 0.001 TYR B 59 ARG 0.003 0.000 ARG F 117 Details of bonding type rmsd hydrogen bonds : bond 0.11397 ( 782) hydrogen bonds : angle 3.74409 ( 1948) covalent geometry : bond 0.00445 (12583) covalent geometry : angle 0.54476 (18252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.891 Fit side-chains REVERT: A 25 LEU cc_start: 0.8403 (mt) cc_final: 0.7918 (mt) REVERT: A 26 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7809 (mm110) REVERT: B 77 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8476 (ttmm) REVERT: B 106 SER cc_start: 0.9147 (m) cc_final: 0.8764 (t) REVERT: B 112 ASN cc_start: 0.8459 (t0) cc_final: 0.7993 (p0) REVERT: D 75 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8543 (mmtm) REVERT: D 88 MET cc_start: 0.8337 (tpp) cc_final: 0.7646 (tpp) REVERT: F 74 GLU cc_start: 0.7919 (tt0) cc_final: 0.7671 (tt0) REVERT: H 98 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8628 (tt) outliers start: 3 outliers final: 0 residues processed: 119 average time/residue: 0.4666 time to fit residues: 67.5034 Evaluate side-chains 81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.0030 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN C 124 GLN D 78 HIS D 124 GLN E 69 GLN ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.156136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103194 restraints weight = 15566.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105505 restraints weight = 10387.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106927 restraints weight = 8264.119| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12583 Z= 0.160 Angle : 0.531 5.972 18252 Z= 0.321 Chirality : 0.033 0.127 2087 Planarity : 0.004 0.032 1280 Dihedral : 30.050 179.949 4011 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.67 % Allowed : 9.67 % Favored : 88.67 % 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: 2.96 (0.31), residues: 716 helix: 2.83 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.92 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 114 PHE 0.009 0.001 PHE E 42 TYR 0.008 0.001 TYR B 59 ARG 0.006 0.000 ARG F 53 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 782) hydrogen bonds : angle 2.77835 ( 1948) covalent geometry : bond 0.00354 (12583) covalent geometry : angle 0.53083 (18252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.800 Fit side-chains REVERT: A 25 LEU cc_start: 0.8248 (mt) cc_final: 0.8036 (mp) REVERT: A 26 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7623 (mm110) REVERT: B 106 SER cc_start: 0.8990 (m) cc_final: 0.8747 (t) REVERT: D 88 MET cc_start: 0.8252 (tpp) cc_final: 0.7543 (tpp) REVERT: E 77 GLN cc_start: 0.7891 (tp40) cc_final: 0.7684 (tp40) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 0.3821 time to fit residues: 43.2754 Evaluate side-chains 82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 83 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 76 HIS 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 = 0.156603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103644 restraints weight = 15807.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106038 restraints weight = 10488.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107561 restraints weight = 8299.182| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12583 Z= 0.155 Angle : 0.521 7.698 18252 Z= 0.314 Chirality : 0.032 0.127 2087 Planarity : 0.004 0.031 1280 Dihedral : 30.030 179.931 4009 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.83 % Allowed : 10.50 % Favored : 87.67 % 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: 3.09 (0.31), residues: 716 helix: 2.95 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -0.96 (0.40), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 114 PHE 0.010 0.001 PHE C 71 TYR 0.009 0.001 TYR B 59 ARG 0.006 0.000 ARG F 53 Details of bonding type rmsd hydrogen bonds : bond 0.04428 ( 782) hydrogen bonds : angle 2.66771 ( 1948) covalent geometry : bond 0.00345 (12583) covalent geometry : angle 0.52053 (18252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.927 Fit side-chains REVERT: A 26 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7649 (mm110) REVERT: B 106 SER cc_start: 0.8928 (m) cc_final: 0.8724 (t) REVERT: D 88 MET cc_start: 0.8232 (tpp) cc_final: 0.7562 (tpp) REVERT: H 94 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7232 (mp10) outliers start: 11 outliers final: 7 residues processed: 88 average time/residue: 0.3676 time to fit residues: 41.9339 Evaluate side-chains 82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 94 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 83 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 0.1980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.155221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102585 restraints weight = 15728.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105307 restraints weight = 11385.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106740 restraints weight = 8257.052| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12583 Z= 0.178 Angle : 0.538 8.557 18252 Z= 0.322 Chirality : 0.033 0.137 2087 Planarity : 0.004 0.030 1280 Dihedral : 30.125 179.897 4009 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.00 % Allowed : 11.50 % Favored : 86.50 % 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: 2.98 (0.31), residues: 716 helix: 2.86 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.00 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 114 PHE 0.009 0.001 PHE E 42 TYR 0.008 0.001 TYR B 59 ARG 0.006 0.000 ARG F 129 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 782) hydrogen bonds : angle 2.73623 ( 1948) covalent geometry : bond 0.00408 (12583) covalent geometry : angle 0.53842 (18252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.816 Fit side-chains REVERT: B 106 SER cc_start: 0.9036 (m) cc_final: 0.8820 (t) REVERT: D 88 MET cc_start: 0.8332 (tpp) cc_final: 0.7549 (tpp) REVERT: H 94 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7232 (mp10) outliers start: 12 outliers final: 10 residues processed: 86 average time/residue: 0.3670 time to fit residues: 40.3733 Evaluate side-chains 85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 94 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 86 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN D 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.154834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101968 restraints weight = 15835.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104227 restraints weight = 10850.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105647 restraints weight = 8657.037| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12583 Z= 0.186 Angle : 0.546 8.868 18252 Z= 0.325 Chirality : 0.033 0.140 2087 Planarity : 0.004 0.030 1280 Dihedral : 30.178 179.894 4009 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.83 % Allowed : 12.83 % Favored : 84.33 % 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: 2.90 (0.31), residues: 716 helix: 2.81 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.06 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 114 PHE 0.009 0.001 PHE E 42 TYR 0.009 0.001 TYR B 59 ARG 0.005 0.000 ARG F 129 Details of bonding type rmsd hydrogen bonds : bond 0.04665 ( 782) hydrogen bonds : angle 2.74321 ( 1948) covalent geometry : bond 0.00427 (12583) covalent geometry : angle 0.54576 (18252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.921 Fit side-chains REVERT: A 75 ASN cc_start: 0.8592 (m-40) cc_final: 0.8001 (t0) REVERT: D 88 MET cc_start: 0.8362 (tpp) cc_final: 0.7617 (tpp) REVERT: F 95 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: H 94 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7193 (mp10) outliers start: 17 outliers final: 11 residues processed: 89 average time/residue: 0.3740 time to fit residues: 43.6184 Evaluate side-chains 87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 94 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 0.1980 chunk 74 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.158116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107589 restraints weight = 15810.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108328 restraints weight = 14017.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108677 restraints weight = 12871.040| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12583 Z= 0.156 Angle : 0.524 9.575 18252 Z= 0.315 Chirality : 0.032 0.131 2087 Planarity : 0.004 0.030 1280 Dihedral : 30.039 179.830 4009 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.83 % Allowed : 14.00 % Favored : 83.17 % 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: 3.13 (0.30), residues: 716 helix: 2.99 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -0.98 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 114 PHE 0.008 0.001 PHE E 42 TYR 0.009 0.001 TYR B 59 ARG 0.008 0.000 ARG F 53 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 782) hydrogen bonds : angle 2.57880 ( 1948) covalent geometry : bond 0.00348 (12583) covalent geometry : angle 0.52361 (18252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 1.555 Fit side-chains REVERT: A 75 ASN cc_start: 0.8521 (m-40) cc_final: 0.8016 (t0) REVERT: H 94 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7237 (mp10) outliers start: 17 outliers final: 12 residues processed: 88 average time/residue: 0.3778 time to fit residues: 43.1779 Evaluate side-chains 88 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 19 optimal weight: 0.0370 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.160581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110854 restraints weight = 15925.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111652 restraints weight = 14088.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.112295 restraints weight = 12564.996| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12583 Z= 0.140 Angle : 0.506 10.280 18252 Z= 0.306 Chirality : 0.031 0.126 2087 Planarity : 0.004 0.031 1280 Dihedral : 29.896 179.510 4009 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.33 % Allowed : 15.83 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.44 (0.30), residues: 716 helix: 3.18 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -0.78 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 114 PHE 0.007 0.001 PHE E 42 TYR 0.010 0.001 TYR B 59 ARG 0.007 0.000 ARG F 53 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 782) hydrogen bonds : angle 2.44075 ( 1948) covalent geometry : bond 0.00302 (12583) covalent geometry : angle 0.50586 (18252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.808 Fit side-chains REVERT: A 75 ASN cc_start: 0.8445 (m-40) cc_final: 0.8075 (t0) REVERT: B 101 THR cc_start: 0.8825 (p) cc_final: 0.8539 (t) REVERT: F 129 ARG cc_start: 0.7830 (mmm-85) cc_final: 0.7591 (mmm160) REVERT: H 94 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7306 (mp10) outliers start: 8 outliers final: 5 residues processed: 84 average time/residue: 0.3637 time to fit residues: 39.2360 Evaluate side-chains 79 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 0.0270 chunk 66 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.155584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104550 restraints weight = 16075.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106527 restraints weight = 10594.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107111 restraints weight = 8321.551| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12583 Z= 0.156 Angle : 0.531 11.192 18252 Z= 0.314 Chirality : 0.032 0.131 2087 Planarity : 0.004 0.030 1280 Dihedral : 29.970 179.565 4009 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.67 % Allowed : 16.17 % Favored : 82.17 % 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: 3.33 (0.30), residues: 716 helix: 3.10 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.81 (0.41), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 114 PHE 0.007 0.001 PHE E 42 TYR 0.009 0.001 TYR B 59 ARG 0.006 0.000 ARG F 53 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 782) hydrogen bonds : angle 2.51621 ( 1948) covalent geometry : bond 0.00351 (12583) covalent geometry : angle 0.53099 (18252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.826 Fit side-chains REVERT: A 75 ASN cc_start: 0.8484 (m-40) cc_final: 0.7885 (t0) REVERT: F 129 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7600 (mmm160) REVERT: H 94 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7314 (mp10) outliers start: 10 outliers final: 9 residues processed: 82 average time/residue: 0.3608 time to fit residues: 38.0791 Evaluate side-chains 84 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.154521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103196 restraints weight = 16015.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.105059 restraints weight = 10590.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105436 restraints weight = 8319.719| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12583 Z= 0.162 Angle : 0.535 12.207 18252 Z= 0.317 Chirality : 0.032 0.135 2087 Planarity : 0.004 0.031 1280 Dihedral : 30.027 179.446 4009 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.50 % Allowed : 16.33 % Favored : 82.17 % 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: 3.22 (0.31), residues: 716 helix: 3.04 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.95 (0.40), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 114 PHE 0.008 0.001 PHE E 42 TYR 0.008 0.001 TYR B 59 ARG 0.008 0.000 ARG F 53 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 782) hydrogen bonds : angle 2.57642 ( 1948) covalent geometry : bond 0.00367 (12583) covalent geometry : angle 0.53538 (18252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.824 Fit side-chains REVERT: A 75 ASN cc_start: 0.8544 (m-40) cc_final: 0.7935 (t0) REVERT: H 94 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7229 (mp10) outliers start: 9 outliers final: 7 residues processed: 79 average time/residue: 0.3773 time to fit residues: 38.0293 Evaluate side-chains 82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.155588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.104649 restraints weight = 15809.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106054 restraints weight = 10391.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106347 restraints weight = 8222.121| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12583 Z= 0.153 Angle : 0.523 7.744 18252 Z= 0.312 Chirality : 0.032 0.132 2087 Planarity : 0.004 0.030 1280 Dihedral : 29.952 179.316 4009 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.83 % Allowed : 16.17 % Favored : 82.00 % 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: 3.28 (0.30), residues: 716 helix: 3.09 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.93 (0.41), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 114 PHE 0.007 0.001 PHE E 42 TYR 0.009 0.001 TYR B 59 ARG 0.007 0.000 ARG F 129 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 782) hydrogen bonds : angle 2.50004 ( 1948) covalent geometry : bond 0.00339 (12583) covalent geometry : angle 0.52342 (18252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.894 Fit side-chains REVERT: A 75 ASN cc_start: 0.8491 (m-40) cc_final: 0.7891 (t0) REVERT: F 129 ARG cc_start: 0.7909 (mmm-85) cc_final: 0.7632 (mmm160) REVERT: H 94 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7288 (mp10) outliers start: 11 outliers final: 9 residues processed: 79 average time/residue: 0.3942 time to fit residues: 39.8482 Evaluate side-chains 82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 84 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.152416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.100633 restraints weight = 15917.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102291 restraints weight = 10726.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102574 restraints weight = 8697.040| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12583 Z= 0.212 Angle : 0.579 12.403 18252 Z= 0.336 Chirality : 0.034 0.147 2087 Planarity : 0.004 0.030 1280 Dihedral : 30.153 179.739 4009 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.33 % Allowed : 15.83 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.88 (0.31), residues: 716 helix: 2.84 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.20 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 76 PHE 0.009 0.001 PHE C 94 TYR 0.009 0.001 TYR C 66 ARG 0.007 0.000 ARG F 129 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 782) hydrogen bonds : angle 2.77018 ( 1948) covalent geometry : bond 0.00498 (12583) covalent geometry : angle 0.57853 (18252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3215.65 seconds wall clock time: 57 minutes 6.93 seconds (3426.93 seconds total)