Starting phenix.real_space_refine on Sat Aug 23 13:38:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4d_45182/08_2025/9c4d_45182.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4d_45182/08_2025/9c4d_45182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c4d_45182/08_2025/9c4d_45182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4d_45182/08_2025/9c4d_45182.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c4d_45182/08_2025/9c4d_45182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4d_45182/08_2025/9c4d_45182.map" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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: 6 Type Number sf(0) Gaussians Mn 16 7.51 5 P 154 5.49 5 S 24 5.16 5 C 7426 2.51 5 N 2149 2.21 5 O 2724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12493 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1563 Classifications: {'DNA': 77} Link IDs: {'rna3p': 76} Chain: "B" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1594 Classifications: {'DNA': 77} Link IDs: {'rna3p': 76} Chain: "C" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: D, E, F, G, H, I, J Time building chain proxies: 2.12, per 1000 atoms: 0.17 Number of scatterers: 12493 At special positions: 0 Unit cell: (94.8537, 91.5255, 269.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 16 24.99 S 24 16.00 P 154 15.00 O 2724 8.00 N 2149 7.00 C 7426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 434.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 84.4% alpha, 2.9% beta 74 base pairs and 133 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'C' and resid 3 through 21 removed outlier: 3.662A pdb=" N GLU C 7 " --> pdb=" O THR C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 35 through 49 Processing helix chain 'C' and resid 63 through 88 removed outlier: 3.567A pdb=" N ILE C 87 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 4.172A pdb=" N TYR C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 122 Processing helix chain 'C' and resid 124 through 139 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'D' and resid 4 through 21 Processing helix chain 'D' and resid 24 through 33 Processing helix chain 'D' and resid 35 through 49 Processing helix chain 'D' and resid 63 through 88 removed outlier: 3.567A pdb=" N ILE D 87 " --> pdb=" O PHE D 83 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.172A pdb=" N TYR D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN D 96 " --> pdb=" O GLU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 122 Processing helix chain 'D' and resid 124 through 139 Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'E' and resid 4 through 21 Processing helix chain 'E' and resid 24 through 33 Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 63 through 88 removed outlier: 3.567A pdb=" N ILE E 87 " --> pdb=" O PHE E 83 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 4.171A pdb=" N TYR E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 122 Processing helix chain 'E' and resid 124 through 139 Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'F' and resid 4 through 21 Processing helix chain 'F' and resid 24 through 33 Processing helix chain 'F' and resid 35 through 49 Processing helix chain 'F' and resid 63 through 88 removed outlier: 3.567A pdb=" N ILE F 87 " --> pdb=" O PHE F 83 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 102 removed outlier: 4.173A pdb=" N TYR F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN F 96 " --> pdb=" O GLU F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 122 Processing helix chain 'F' and resid 124 through 139 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'G' and resid 4 through 21 Processing helix chain 'G' and resid 24 through 33 Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 63 through 88 removed outlier: 3.567A pdb=" N ILE G 87 " --> pdb=" O PHE G 83 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY G 88 " --> pdb=" O LEU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 102 removed outlier: 4.172A pdb=" N TYR G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 122 Processing helix chain 'G' and resid 124 through 139 Processing helix chain 'G' and resid 140 through 142 No H-bonds generated for 'chain 'G' and resid 140 through 142' Processing helix chain 'H' and resid 4 through 21 Processing helix chain 'H' and resid 24 through 33 Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 63 through 88 removed outlier: 3.567A pdb=" N ILE H 87 " --> pdb=" O PHE H 83 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY H 88 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 4.172A pdb=" N TYR H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 122 Processing helix chain 'H' and resid 124 through 139 Processing helix chain 'H' and resid 140 through 142 No H-bonds generated for 'chain 'H' and resid 140 through 142' Processing helix chain 'I' and resid 4 through 21 Processing helix chain 'I' and resid 24 through 33 Processing helix chain 'I' and resid 35 through 49 Processing helix chain 'I' and resid 63 through 88 removed outlier: 3.568A pdb=" N ILE I 87 " --> pdb=" O PHE I 83 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 102 removed outlier: 4.172A pdb=" N TYR I 95 " --> pdb=" O GLU I 91 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 122 Processing helix chain 'I' and resid 124 through 139 Processing helix chain 'I' and resid 140 through 142 No H-bonds generated for 'chain 'I' and resid 140 through 142' Processing helix chain 'J' and resid 4 through 21 Processing helix chain 'J' and resid 24 through 33 Processing helix chain 'J' and resid 35 through 49 Processing helix chain 'J' and resid 63 through 88 removed outlier: 3.566A pdb=" N ILE J 87 " --> pdb=" O PHE J 83 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY J 88 " --> pdb=" O LEU J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 102 removed outlier: 4.172A pdb=" N TYR J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN J 96 " --> pdb=" O GLU J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 122 Processing helix chain 'J' and resid 124 through 139 Processing helix chain 'J' and resid 140 through 142 No H-bonds generated for 'chain 'J' and resid 140 through 142' Processing sheet with id=AA1, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AA3, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AA4, first strand: chain 'F' and resid 52 through 54 Processing sheet with id=AA5, first strand: chain 'G' and resid 52 through 54 Processing sheet with id=AA6, first strand: chain 'H' and resid 52 through 54 Processing sheet with id=AA7, first strand: chain 'I' and resid 52 through 54 Processing sheet with id=AA8, first strand: chain 'J' and resid 52 through 54 680 hydrogen bonds defined for protein. 2040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 172 hydrogen bonds 344 hydrogen bond angles 0 basepair planarities 74 basepair parallelities 133 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2516 1.33 - 1.45: 3529 1.45 - 1.57: 6621 1.57 - 1.69: 306 1.69 - 1.80: 48 Bond restraints: 13020 Sorted by residual: bond pdb=" C3' DA B -44 " pdb=" O3' DA B -44 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" C3' DA B -28 " pdb=" O3' DA B -28 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" C3' DA B -25 " pdb=" O3' DA B -25 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" C3' DC B -66 " pdb=" O3' DC B -66 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" C3' DA B -24 " pdb=" O3' DA B -24 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.47e+00 ... (remaining 13015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 17709 1.30 - 2.59: 412 2.59 - 3.89: 50 3.89 - 5.18: 8 5.18 - 6.48: 8 Bond angle restraints: 18187 Sorted by residual: angle pdb=" C3' DT A 22 " pdb=" C2' DT A 22 " pdb=" C1' DT A 22 " ideal model delta sigma weight residual 101.60 98.17 3.43 1.50e+00 4.44e-01 5.23e+00 angle pdb=" C4' DA A 60 " pdb=" C3' DA A 60 " pdb=" C2' DA A 60 " ideal model delta sigma weight residual 102.40 105.68 -3.28 1.50e+00 4.44e-01 4.78e+00 angle pdb=" C3' DA B -25 " pdb=" O3' DA B -25 " pdb=" P DA B -24 " ideal model delta sigma weight residual 120.20 123.45 -3.25 1.50e+00 4.44e-01 4.70e+00 angle pdb=" C4' DA B -24 " pdb=" C3' DA B -24 " pdb=" C2' DA B -24 " ideal model delta sigma weight residual 102.40 105.60 -3.20 1.50e+00 4.44e-01 4.55e+00 angle pdb=" C3' DA B -44 " pdb=" O3' DA B -44 " pdb=" P DT B -43 " ideal model delta sigma weight residual 120.20 123.36 -3.16 1.50e+00 4.44e-01 4.44e+00 ... (remaining 18182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 6882 35.90 - 71.80: 669 71.80 - 107.70: 0 107.70 - 143.60: 1 143.60 - 179.50: 10 Dihedral angle restraints: 7562 sinusoidal: 4250 harmonic: 3312 Sorted by residual: dihedral pdb=" CA GLU H 55 " pdb=" C GLU H 55 " pdb=" N LYS H 56 " pdb=" CA LYS H 56 " ideal model delta harmonic sigma weight residual -180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA GLU I 55 " pdb=" C GLU I 55 " pdb=" N LYS I 56 " pdb=" CA LYS I 56 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA GLU F 55 " pdb=" C GLU F 55 " pdb=" N LYS F 56 " pdb=" CA LYS F 56 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 7559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1311 0.026 - 0.051: 458 0.051 - 0.077: 158 0.077 - 0.102: 53 0.102 - 0.128: 12 Chirality restraints: 1992 Sorted by residual: chirality pdb=" P DT B -46 " pdb=" OP1 DT B -46 " pdb=" OP2 DT B -46 " pdb=" O5' DT B -46 " both_signs ideal model delta sigma weight residual True 2.35 -2.47 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA PRO G 36 " pdb=" N PRO G 36 " pdb=" C PRO G 36 " pdb=" CB PRO G 36 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.08e-01 chirality pdb=" CA PRO I 36 " pdb=" N PRO I 36 " pdb=" C PRO I 36 " pdb=" CB PRO I 36 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.02e-01 ... (remaining 1989 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT A 24 " 0.023 2.00e-02 2.50e+03 1.13e-02 3.17e+00 pdb=" N1 DT A 24 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DT A 24 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT A 24 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT A 24 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT A 24 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT A 24 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT A 24 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT A 24 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT A 24 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 55 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C GLU C 55 " -0.019 2.00e-02 2.50e+03 pdb=" O GLU C 55 " 0.007 2.00e-02 2.50e+03 pdb=" N LYS C 56 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 55 " 0.005 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" C GLU I 55 " -0.019 2.00e-02 2.50e+03 pdb=" O GLU I 55 " 0.007 2.00e-02 2.50e+03 pdb=" N LYS I 56 " 0.006 2.00e-02 2.50e+03 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 248 2.65 - 3.21: 11050 3.21 - 3.77: 22212 3.77 - 4.34: 27150 4.34 - 4.90: 41222 Nonbonded interactions: 101882 Sorted by model distance: nonbonded pdb=" OP1 DT B -20 " pdb=" OH TYR D 54 " model vdw 2.085 3.040 nonbonded pdb=" OP1 DT A 27 " pdb=" NZ LYS E 56 " model vdw 2.114 3.120 nonbonded pdb=" OE1 GLU H 102 " pdb="MN MN H 201 " model vdw 2.123 2.320 nonbonded pdb=" OE1 GLU E 102 " pdb="MN MN E 201 " model vdw 2.124 2.320 nonbonded pdb=" OE1 GLU J 102 " pdb="MN MN J 201 " model vdw 2.124 2.320 ... (remaining 101877 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 11.760 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.850 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 : 0.002 0.039 13020 Z= 0.118 Angle : 0.480 6.477 18187 Z= 0.281 Chirality : 0.032 0.128 1992 Planarity : 0.002 0.014 1778 Dihedral : 22.140 179.502 5434 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.34 % Allowed : 3.91 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.02 (0.26), residues: 1104 helix: 3.09 (0.18), residues: 880 sheet: None (None), residues: 0 loop : 0.86 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 126 TYR 0.005 0.001 TYR D 75 PHE 0.003 0.001 PHE I 120 TRP 0.004 0.001 TRP F 107 HIS 0.002 0.001 HIS J 139 Details of bonding type rmsd covalent geometry : bond 0.00245 (13020) covalent geometry : angle 0.48033 (18187) hydrogen bonds : bond 0.10482 ( 852) hydrogen bonds : angle 4.13775 ( 2384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 MET cc_start: 0.8849 (tpp) cc_final: 0.7901 (tpp) REVERT: E 112 ARG cc_start: 0.8147 (mmp80) cc_final: 0.7903 (mmp80) REVERT: F 14 TYR cc_start: 0.7095 (t80) cc_final: 0.6876 (t80) REVERT: F 51 TYR cc_start: 0.8041 (m-80) cc_final: 0.7619 (m-80) REVERT: F 80 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8414 (tp) REVERT: F 83 PHE cc_start: 0.8905 (t80) cc_final: 0.8607 (t80) REVERT: H 15 MET cc_start: 0.9108 (ttp) cc_final: 0.8853 (ttm) REVERT: H 42 MET cc_start: 0.8371 (tpp) cc_final: 0.8047 (tpp) REVERT: I 51 TYR cc_start: 0.7619 (m-80) cc_final: 0.7234 (m-10) REVERT: I 107 TRP cc_start: 0.5520 (m100) cc_final: 0.5280 (m100) REVERT: J 107 TRP cc_start: 0.6915 (m100) cc_final: 0.6474 (t-100) outliers start: 24 outliers final: 8 residues processed: 179 average time/residue: 0.1182 time to fit residues: 29.7100 Evaluate side-chains 84 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 HIS ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.086807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066452 restraints weight = 81896.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.066742 restraints weight = 59158.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.066691 restraints weight = 46567.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.066359 restraints weight = 36965.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066569 restraints weight = 35713.740| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13020 Z= 0.252 Angle : 0.657 7.862 18187 Z= 0.374 Chirality : 0.039 0.135 1992 Planarity : 0.004 0.054 1778 Dihedral : 27.939 179.772 2986 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.20 % Allowed : 3.42 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.25), residues: 1104 helix: 2.10 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.41 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 126 TYR 0.024 0.002 TYR E 22 PHE 0.017 0.002 PHE F 120 TRP 0.010 0.002 TRP E 107 HIS 0.007 0.001 HIS E 77 Details of bonding type rmsd covalent geometry : bond 0.00551 (13020) covalent geometry : angle 0.65689 (18187) hydrogen bonds : bond 0.05290 ( 852) hydrogen bonds : angle 4.24286 ( 2384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 MET cc_start: 0.8594 (ppp) cc_final: 0.8354 (ppp) REVERT: C 42 MET cc_start: 0.8763 (mmp) cc_final: 0.8453 (tpt) REVERT: D 42 MET cc_start: 0.8429 (tpp) cc_final: 0.7984 (tpp) REVERT: E 42 MET cc_start: 0.8221 (tpp) cc_final: 0.7676 (tpt) REVERT: E 85 ARG cc_start: 0.8981 (ttm110) cc_final: 0.8615 (ttm110) REVERT: F 42 MET cc_start: 0.8394 (tpt) cc_final: 0.7952 (tpp) REVERT: F 51 TYR cc_start: 0.8366 (m-80) cc_final: 0.7948 (m-80) REVERT: F 71 LYS cc_start: 0.8893 (tttt) cc_final: 0.8576 (pttm) REVERT: F 134 GLN cc_start: 0.8511 (pt0) cc_final: 0.8138 (pt0) REVERT: G 137 THR cc_start: 0.8485 (p) cc_final: 0.7927 (t) REVERT: H 42 MET cc_start: 0.8614 (tpp) cc_final: 0.8234 (tpp) REVERT: I 6 MET cc_start: 0.7583 (mmm) cc_final: 0.7347 (mmm) REVERT: I 51 TYR cc_start: 0.7647 (m-80) cc_final: 0.7235 (m-10) REVERT: J 107 TRP cc_start: 0.7531 (m100) cc_final: 0.6557 (t-100) outliers start: 2 outliers final: 0 residues processed: 95 average time/residue: 0.1154 time to fit residues: 15.7096 Evaluate side-chains 65 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 134 GLN ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 ASN J 77 HIS ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.087585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.065786 restraints weight = 80909.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.064761 restraints weight = 60440.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.065231 restraints weight = 48738.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.065252 restraints weight = 39473.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.065587 restraints weight = 36584.031| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13020 Z= 0.173 Angle : 0.554 8.216 18187 Z= 0.320 Chirality : 0.036 0.253 1992 Planarity : 0.003 0.029 1778 Dihedral : 27.854 179.922 2986 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.26), residues: 1104 helix: 2.22 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.54 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 112 TYR 0.013 0.001 TYR E 14 PHE 0.012 0.001 PHE J 83 TRP 0.008 0.001 TRP F 107 HIS 0.006 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00377 (13020) covalent geometry : angle 0.55429 (18187) hydrogen bonds : bond 0.04213 ( 852) hydrogen bonds : angle 4.00933 ( 2384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 MET cc_start: 0.8562 (ppp) cc_final: 0.8362 (ppp) REVERT: D 42 MET cc_start: 0.8404 (tpp) cc_final: 0.7854 (tpp) REVERT: E 42 MET cc_start: 0.8341 (tpp) cc_final: 0.7667 (tpt) REVERT: F 3 THR cc_start: 0.6006 (m) cc_final: 0.5763 (t) REVERT: F 42 MET cc_start: 0.8419 (tpt) cc_final: 0.8000 (tpp) REVERT: F 51 TYR cc_start: 0.8458 (m-80) cc_final: 0.8005 (m-10) REVERT: F 71 LYS cc_start: 0.8903 (tttt) cc_final: 0.8567 (pttm) REVERT: F 134 GLN cc_start: 0.8655 (pt0) cc_final: 0.8264 (pt0) REVERT: H 15 MET cc_start: 0.9180 (ttp) cc_final: 0.8818 (ttm) REVERT: H 42 MET cc_start: 0.8802 (tpp) cc_final: 0.8313 (tpp) REVERT: H 43 VAL cc_start: 0.9416 (t) cc_final: 0.9154 (p) REVERT: I 42 MET cc_start: 0.8110 (tmm) cc_final: 0.7860 (tmm) REVERT: I 51 TYR cc_start: 0.7763 (m-80) cc_final: 0.7380 (m-10) REVERT: J 42 MET cc_start: 0.4989 (ptm) cc_final: 0.4786 (ptt) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.0895 time to fit residues: 11.1733 Evaluate side-chains 63 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 0.9980 chunk 44 optimal weight: 0.0970 chunk 111 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 56 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN D 134 GLN ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.088047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.066322 restraints weight = 80594.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.065423 restraints weight = 57692.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.065835 restraints weight = 44556.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.065890 restraints weight = 38520.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.065954 restraints weight = 34695.926| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13020 Z= 0.149 Angle : 0.548 8.592 18187 Z= 0.312 Chirality : 0.035 0.280 1992 Planarity : 0.003 0.026 1778 Dihedral : 27.754 179.738 2986 Min Nonbonded Distance : 1.582 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.10 % Allowed : 2.25 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.26), residues: 1104 helix: 2.35 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -0.64 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 72 TYR 0.012 0.001 TYR E 14 PHE 0.012 0.001 PHE J 83 TRP 0.008 0.001 TRP F 107 HIS 0.004 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00326 (13020) covalent geometry : angle 0.54832 (18187) hydrogen bonds : bond 0.03838 ( 852) hydrogen bonds : angle 3.93104 ( 2384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 6 MET cc_start: 0.8158 (mmp) cc_final: 0.7847 (mmt) REVERT: D 42 MET cc_start: 0.8875 (tpp) cc_final: 0.8504 (tpp) REVERT: E 6 MET cc_start: 0.8007 (tmm) cc_final: 0.7783 (tmm) REVERT: E 9 TYR cc_start: 0.7648 (m-80) cc_final: 0.7386 (m-80) REVERT: E 42 MET cc_start: 0.8375 (tpp) cc_final: 0.7763 (tpt) REVERT: E 49 ASP cc_start: 0.8768 (t0) cc_final: 0.8564 (t70) REVERT: F 3 THR cc_start: 0.6132 (m) cc_final: 0.5760 (t) REVERT: F 42 MET cc_start: 0.8328 (tpt) cc_final: 0.7948 (tpp) REVERT: F 51 TYR cc_start: 0.8480 (m-80) cc_final: 0.8003 (m-80) REVERT: F 71 LYS cc_start: 0.8800 (tttt) cc_final: 0.8451 (pttm) REVERT: F 134 GLN cc_start: 0.8596 (pt0) cc_final: 0.8164 (pt0) REVERT: H 15 MET cc_start: 0.9206 (ttp) cc_final: 0.8795 (ttm) REVERT: H 42 MET cc_start: 0.8726 (tpp) cc_final: 0.8232 (tpp) REVERT: H 43 VAL cc_start: 0.9424 (t) cc_final: 0.9190 (p) REVERT: I 42 MET cc_start: 0.8395 (tmm) cc_final: 0.7951 (tmm) REVERT: I 51 TYR cc_start: 0.7863 (m-80) cc_final: 0.7359 (m-10) REVERT: I 136 LYS cc_start: 0.7979 (mptt) cc_final: 0.7659 (mttt) REVERT: J 117 VAL cc_start: 0.3116 (OUTLIER) cc_final: 0.2708 (t) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1110 time to fit residues: 14.4310 Evaluate side-chains 66 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 122 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 GLN ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 HIS J 103 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.087299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.065874 restraints weight = 81395.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.065535 restraints weight = 59079.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.066068 restraints weight = 44579.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.065810 restraints weight = 37782.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.066046 restraints weight = 35934.718| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13020 Z= 0.166 Angle : 0.563 11.321 18187 Z= 0.322 Chirality : 0.036 0.198 1992 Planarity : 0.003 0.036 1778 Dihedral : 27.697 179.845 2986 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.20 % Allowed : 1.86 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.26), residues: 1104 helix: 2.27 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.79 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 85 TYR 0.013 0.001 TYR E 14 PHE 0.007 0.001 PHE F 120 TRP 0.008 0.001 TRP F 107 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00362 (13020) covalent geometry : angle 0.56346 (18187) hydrogen bonds : bond 0.04088 ( 852) hydrogen bonds : angle 4.01569 ( 2384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 MET cc_start: 0.8791 (ppp) cc_final: 0.8573 (ppp) REVERT: D 42 MET cc_start: 0.8716 (tpp) cc_final: 0.8258 (tpp) REVERT: E 42 MET cc_start: 0.8276 (tpp) cc_final: 0.7685 (tpt) REVERT: E 49 ASP cc_start: 0.9009 (t0) cc_final: 0.8632 (t0) REVERT: F 3 THR cc_start: 0.6477 (m) cc_final: 0.5496 (p) REVERT: F 51 TYR cc_start: 0.8357 (m-80) cc_final: 0.7923 (m-80) REVERT: F 71 LYS cc_start: 0.8944 (tttt) cc_final: 0.8611 (pttm) REVERT: F 134 GLN cc_start: 0.8777 (pt0) cc_final: 0.8360 (pt0) REVERT: H 42 MET cc_start: 0.8816 (tpp) cc_final: 0.8206 (tpp) REVERT: H 43 VAL cc_start: 0.9415 (t) cc_final: 0.9189 (p) REVERT: I 51 TYR cc_start: 0.7856 (m-80) cc_final: 0.7348 (m-10) REVERT: I 136 LYS cc_start: 0.7991 (mptt) cc_final: 0.7711 (mtmt) outliers start: 2 outliers final: 1 residues processed: 101 average time/residue: 0.0865 time to fit residues: 13.1272 Evaluate side-chains 74 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.0770 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.087056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065762 restraints weight = 82678.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.065581 restraints weight = 60219.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.065757 restraints weight = 46478.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.065787 restraints weight = 38978.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065839 restraints weight = 37033.589| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13020 Z= 0.157 Angle : 0.547 9.973 18187 Z= 0.311 Chirality : 0.035 0.131 1992 Planarity : 0.003 0.029 1778 Dihedral : 27.658 179.768 2986 Min Nonbonded Distance : 1.450 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.29 % Allowed : 1.66 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.26), residues: 1104 helix: 2.34 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -0.86 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 85 TYR 0.012 0.001 TYR E 14 PHE 0.010 0.001 PHE F 120 TRP 0.007 0.001 TRP J 107 HIS 0.004 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00343 (13020) covalent geometry : angle 0.54686 (18187) hydrogen bonds : bond 0.03854 ( 852) hydrogen bonds : angle 3.92268 ( 2384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 MET cc_start: 0.7568 (tpp) cc_final: 0.7103 (tpp) REVERT: D 42 MET cc_start: 0.8806 (tpp) cc_final: 0.8321 (tpp) REVERT: E 6 MET cc_start: 0.8240 (tmm) cc_final: 0.7884 (tmm) REVERT: E 42 MET cc_start: 0.8065 (tpp) cc_final: 0.7414 (tpt) REVERT: E 49 ASP cc_start: 0.9095 (t0) cc_final: 0.8682 (t0) REVERT: F 71 LYS cc_start: 0.8970 (tttt) cc_final: 0.8595 (pttm) REVERT: F 134 GLN cc_start: 0.8794 (pt0) cc_final: 0.8277 (tt0) REVERT: H 42 MET cc_start: 0.8732 (tpp) cc_final: 0.8277 (tpp) REVERT: H 43 VAL cc_start: 0.9422 (t) cc_final: 0.9208 (p) REVERT: I 51 TYR cc_start: 0.7909 (m-80) cc_final: 0.7403 (m-10) REVERT: I 136 LYS cc_start: 0.7994 (mptt) cc_final: 0.7736 (mttt) REVERT: J 107 TRP cc_start: 0.6433 (t-100) cc_final: 0.6219 (m100) outliers start: 3 outliers final: 0 residues processed: 92 average time/residue: 0.1065 time to fit residues: 14.5591 Evaluate side-chains 67 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 86 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 GLN ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.085949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.065560 restraints weight = 82049.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.065171 restraints weight = 67582.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065790 restraints weight = 49828.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065608 restraints weight = 41239.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.066098 restraints weight = 38813.984| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13020 Z= 0.188 Angle : 0.585 7.526 18187 Z= 0.333 Chirality : 0.036 0.142 1992 Planarity : 0.003 0.033 1778 Dihedral : 27.712 179.973 2986 Min Nonbonded Distance : 1.396 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.10 % Allowed : 1.56 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.26), residues: 1104 helix: 2.17 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.12 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 85 TYR 0.030 0.002 TYR F 9 PHE 0.008 0.001 PHE E 120 TRP 0.007 0.001 TRP F 107 HIS 0.005 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00410 (13020) covalent geometry : angle 0.58459 (18187) hydrogen bonds : bond 0.04402 ( 852) hydrogen bonds : angle 4.06341 ( 2384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.8333 (ptm) cc_final: 0.7551 (ppp) REVERT: C 42 MET cc_start: 0.7386 (tpp) cc_final: 0.6720 (tpp) REVERT: D 42 MET cc_start: 0.8592 (tpp) cc_final: 0.8056 (tpp) REVERT: D 134 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: E 6 MET cc_start: 0.8304 (tmm) cc_final: 0.7847 (tmm) REVERT: E 49 ASP cc_start: 0.9079 (t0) cc_final: 0.8643 (t0) REVERT: F 3 THR cc_start: 0.6936 (m) cc_final: 0.6244 (p) REVERT: F 134 GLN cc_start: 0.8778 (pt0) cc_final: 0.8340 (pt0) REVERT: G 42 MET cc_start: 0.8082 (tpt) cc_final: 0.7672 (tpp) REVERT: H 42 MET cc_start: 0.8658 (tpp) cc_final: 0.8181 (tpp) REVERT: I 51 TYR cc_start: 0.7785 (m-80) cc_final: 0.7246 (m-10) REVERT: J 43 VAL cc_start: 0.7439 (t) cc_final: 0.7216 (t) REVERT: J 124 ASP cc_start: 0.7253 (m-30) cc_final: 0.6188 (t0) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.0890 time to fit residues: 12.2614 Evaluate side-chains 65 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN D 134 GLN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.084763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.064185 restraints weight = 81934.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.064182 restraints weight = 62716.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.064358 restraints weight = 49486.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.064200 restraints weight = 39424.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.064492 restraints weight = 37310.705| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13020 Z= 0.239 Angle : 0.638 7.721 18187 Z= 0.365 Chirality : 0.038 0.148 1992 Planarity : 0.003 0.035 1778 Dihedral : 27.823 179.729 2986 Min Nonbonded Distance : 1.350 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.25), residues: 1104 helix: 1.87 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.33 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 85 TYR 0.037 0.002 TYR F 9 PHE 0.008 0.002 PHE C 120 TRP 0.008 0.002 TRP H 107 HIS 0.012 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00520 (13020) covalent geometry : angle 0.63820 (18187) hydrogen bonds : bond 0.05150 ( 852) hydrogen bonds : angle 4.29764 ( 2384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.8335 (ptm) cc_final: 0.8050 (ptm) REVERT: C 42 MET cc_start: 0.7334 (tpp) cc_final: 0.6553 (tpp) REVERT: D 42 MET cc_start: 0.8591 (tpp) cc_final: 0.8349 (tpp) REVERT: E 6 MET cc_start: 0.8506 (tmm) cc_final: 0.8100 (tmm) REVERT: E 49 ASP cc_start: 0.9178 (t0) cc_final: 0.8793 (t0) REVERT: E 121 GLU cc_start: 0.8892 (pt0) cc_final: 0.8473 (pp20) REVERT: F 134 GLN cc_start: 0.8803 (pt0) cc_final: 0.8377 (pt0) REVERT: H 42 MET cc_start: 0.8727 (tpp) cc_final: 0.8333 (tpp) REVERT: I 51 TYR cc_start: 0.7923 (m-80) cc_final: 0.7386 (m-10) REVERT: J 124 ASP cc_start: 0.7484 (m-30) cc_final: 0.6342 (t0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0905 time to fit residues: 11.8406 Evaluate side-chains 63 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 29 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 92 optimal weight: 0.0170 chunk 124 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.086533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.064943 restraints weight = 80477.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.065184 restraints weight = 56474.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.065320 restraints weight = 41262.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.065251 restraints weight = 36887.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.065952 restraints weight = 33879.958| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13020 Z= 0.144 Angle : 0.557 7.402 18187 Z= 0.317 Chirality : 0.036 0.139 1992 Planarity : 0.003 0.032 1778 Dihedral : 27.780 179.603 2986 Min Nonbonded Distance : 1.398 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.26), residues: 1104 helix: 2.13 (0.18), residues: 896 sheet: None (None), residues: 0 loop : -1.06 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 85 TYR 0.017 0.001 TYR F 9 PHE 0.012 0.001 PHE H 120 TRP 0.009 0.001 TRP F 107 HIS 0.006 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00311 (13020) covalent geometry : angle 0.55657 (18187) hydrogen bonds : bond 0.03759 ( 852) hydrogen bonds : angle 3.96338 ( 2384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.8384 (ptm) cc_final: 0.7712 (ppp) REVERT: C 42 MET cc_start: 0.7776 (tpp) cc_final: 0.7079 (tpp) REVERT: D 42 MET cc_start: 0.8838 (tpp) cc_final: 0.8378 (tpp) REVERT: E 6 MET cc_start: 0.8353 (tmm) cc_final: 0.7990 (tmm) REVERT: E 49 ASP cc_start: 0.9079 (t0) cc_final: 0.8799 (t0) REVERT: E 121 GLU cc_start: 0.8686 (pt0) cc_final: 0.8401 (pp20) REVERT: F 134 GLN cc_start: 0.8716 (pt0) cc_final: 0.8135 (tt0) REVERT: G 142 GLN cc_start: 0.7306 (mt0) cc_final: 0.6889 (mp10) REVERT: H 42 MET cc_start: 0.8795 (tpp) cc_final: 0.8198 (tpp) REVERT: I 51 TYR cc_start: 0.7973 (m-80) cc_final: 0.7446 (m-10) REVERT: J 124 ASP cc_start: 0.7504 (m-30) cc_final: 0.6417 (t0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0900 time to fit residues: 11.5188 Evaluate side-chains 64 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 76 optimal weight: 0.0470 chunk 45 optimal weight: 0.5980 chunk 109 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** 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 = 0.3929 r_free = 0.3929 target = 0.086237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.064905 restraints weight = 80610.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.064413 restraints weight = 54181.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064767 restraints weight = 45273.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.064753 restraints weight = 37466.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.065661 restraints weight = 34054.335| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13020 Z= 0.153 Angle : 0.558 7.316 18187 Z= 0.318 Chirality : 0.036 0.146 1992 Planarity : 0.003 0.033 1778 Dihedral : 27.680 179.907 2986 Min Nonbonded Distance : 1.396 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.26), residues: 1104 helix: 2.18 (0.18), residues: 896 sheet: None (None), residues: 0 loop : -1.07 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 85 TYR 0.021 0.002 TYR F 9 PHE 0.013 0.001 PHE E 120 TRP 0.008 0.001 TRP F 107 HIS 0.007 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00334 (13020) covalent geometry : angle 0.55779 (18187) hydrogen bonds : bond 0.03889 ( 852) hydrogen bonds : angle 3.94960 ( 2384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.8371 (ptm) cc_final: 0.7751 (ppp) REVERT: C 42 MET cc_start: 0.7867 (tpp) cc_final: 0.7139 (tpp) REVERT: D 42 MET cc_start: 0.8809 (tpp) cc_final: 0.8361 (tpp) REVERT: E 6 MET cc_start: 0.8414 (tmm) cc_final: 0.8090 (tmm) REVERT: E 49 ASP cc_start: 0.9067 (t0) cc_final: 0.8809 (t0) REVERT: E 121 GLU cc_start: 0.8637 (pt0) cc_final: 0.8310 (pp20) REVERT: F 130 LEU cc_start: 0.9321 (tt) cc_final: 0.9091 (tt) REVERT: F 134 GLN cc_start: 0.8738 (pt0) cc_final: 0.8391 (pt0) REVERT: G 82 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8748 (tm-30) REVERT: H 42 MET cc_start: 0.8805 (tpp) cc_final: 0.8193 (tpp) REVERT: J 124 ASP cc_start: 0.7533 (m-30) cc_final: 0.6440 (t0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0849 time to fit residues: 10.7283 Evaluate side-chains 65 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.085907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.064015 restraints weight = 80053.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.064552 restraints weight = 57449.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064214 restraints weight = 41935.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.064079 restraints weight = 38710.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.065302 restraints weight = 34260.673| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13020 Z= 0.170 Angle : 0.569 7.357 18187 Z= 0.325 Chirality : 0.036 0.137 1992 Planarity : 0.003 0.031 1778 Dihedral : 27.740 179.924 2986 Min Nonbonded Distance : 1.367 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.26), residues: 1104 helix: 2.07 (0.18), residues: 896 sheet: None (None), residues: 0 loop : -1.13 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 85 TYR 0.025 0.002 TYR F 9 PHE 0.013 0.001 PHE E 120 TRP 0.008 0.001 TRP F 107 HIS 0.005 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00371 (13020) covalent geometry : angle 0.56851 (18187) hydrogen bonds : bond 0.04113 ( 852) hydrogen bonds : angle 4.00966 ( 2384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1912.81 seconds wall clock time: 33 minutes 56.09 seconds (2036.09 seconds total)