Starting phenix.real_space_refine on Wed Jun 11 04:05:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4d_45182/06_2025/9c4d_45182.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4d_45182/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9c4d_45182/06_2025/9c4d_45182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4d_45182/06_2025/9c4d_45182.map" model { file = "/net/cci-nas-00/data/ceres_data/9c4d_45182/06_2025/9c4d_45182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4d_45182/06_2025/9c4d_45182.cif" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.58, per 1000 atoms: 0.61 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: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 5.95 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: 4.64 Time building geometry restraints manager: 3.71 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: 10.490 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.850 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.710 ------------------------------------------------------------------------------- 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 (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: 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 TRP 0.004 0.001 TRP F 107 HIS 0.002 0.001 HIS J 139 PHE 0.003 0.001 PHE I 120 TYR 0.005 0.001 TYR D 75 ARG 0.001 0.000 ARG I 126 Details of bonding type rmsd hydrogen bonds : bond 0.10482 ( 852) hydrogen bonds : angle 4.13775 ( 2384) covalent geometry : bond 0.00245 (13020) covalent geometry : angle 0.48033 (18187) *********************** 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 : 1.278 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: 0.2671 time to fit residues: 66.6033 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 : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.0970 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 0.0270 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- 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 E 139 HIS ** 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.091167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.070895 restraints weight = 82027.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.070583 restraints weight = 57482.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.071049 restraints weight = 45508.941| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2289 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= 0.137 Angle : 0.527 7.167 18187 Z= 0.301 Chirality : 0.034 0.131 1992 Planarity : 0.003 0.043 1778 Dihedral : 27.793 179.468 2986 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.20 % Allowed : 1.66 % Favored : 98.14 % 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: 3.31 (0.26), residues: 1104 helix: 2.66 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.17 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 107 HIS 0.005 0.001 HIS F 77 PHE 0.010 0.001 PHE F 120 TYR 0.012 0.001 TYR I 119 ARG 0.008 0.001 ARG I 76 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 852) hydrogen bonds : angle 3.70987 ( 2384) covalent geometry : bond 0.00299 (13020) covalent geometry : angle 0.52669 (18187) *********************** 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 102 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 MET cc_start: 0.8635 (mmp) cc_final: 0.8303 (tpp) REVERT: D 42 MET cc_start: 0.8491 (tpp) cc_final: 0.8039 (tpp) REVERT: E 121 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8481 (pp20) REVERT: F 42 MET cc_start: 0.8014 (tpt) cc_final: 0.7751 (tpp) REVERT: F 51 TYR cc_start: 0.8233 (m-80) cc_final: 0.7912 (m-80) REVERT: F 112 ARG cc_start: 0.8878 (mmp80) cc_final: 0.8611 (mmp80) REVERT: F 134 GLN cc_start: 0.8435 (pt0) cc_final: 0.7957 (mt0) REVERT: G 137 THR cc_start: 0.8032 (p) cc_final: 0.7574 (t) REVERT: H 15 MET cc_start: 0.8959 (ttp) cc_final: 0.7960 (ttm) REVERT: H 42 MET cc_start: 0.8356 (tpp) cc_final: 0.8075 (tpp) REVERT: I 51 TYR cc_start: 0.7971 (m-80) cc_final: 0.7444 (m-10) REVERT: J 107 TRP cc_start: 0.7399 (m100) cc_final: 0.6486 (t-100) outliers start: 2 outliers final: 0 residues processed: 102 average time/residue: 0.3127 time to fit residues: 44.2158 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 : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 HIS E 134 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 12 GLN ** 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 = 0.3965 r_free = 0.3965 target = 0.088740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.067221 restraints weight = 82371.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.066249 restraints weight = 57122.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066822 restraints weight = 46856.360| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3376 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= 0.169 Angle : 0.552 8.686 18187 Z= 0.318 Chirality : 0.036 0.292 1992 Planarity : 0.003 0.072 1778 Dihedral : 27.691 179.525 2986 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.29 % Allowed : 2.83 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.26), residues: 1104 helix: 2.42 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -0.34 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 107 HIS 0.005 0.001 HIS F 35 PHE 0.017 0.001 PHE J 83 TYR 0.012 0.001 TYR E 22 ARG 0.013 0.001 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 852) hydrogen bonds : angle 3.89646 ( 2384) covalent geometry : bond 0.00368 (13020) covalent geometry : angle 0.55179 (18187) *********************** 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 94 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 MET cc_start: 0.8761 (mmp) cc_final: 0.8389 (tpt) REVERT: D 42 MET cc_start: 0.8628 (tpp) cc_final: 0.8129 (tpp) REVERT: E 6 MET cc_start: 0.8158 (tmm) cc_final: 0.7956 (tmm) REVERT: E 42 MET cc_start: 0.8145 (tpt) cc_final: 0.7936 (tpt) REVERT: E 121 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8635 (pt0) REVERT: F 42 MET cc_start: 0.8288 (tpt) cc_final: 0.7835 (tpp) REVERT: F 51 TYR cc_start: 0.8297 (m-80) cc_final: 0.7964 (m-80) REVERT: F 134 GLN cc_start: 0.8527 (pt0) cc_final: 0.7855 (mt0) REVERT: G 142 GLN cc_start: 0.6893 (mt0) cc_final: 0.6442 (mp10) REVERT: H 42 MET cc_start: 0.8826 (tpp) cc_final: 0.8337 (tpp) REVERT: I 51 TYR cc_start: 0.7832 (m-80) cc_final: 0.7595 (m-10) outliers start: 3 outliers final: 1 residues processed: 93 average time/residue: 0.2572 time to fit residues: 35.4378 Evaluate side-chains 60 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 123 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** F 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** J 12 GLN J 77 HIS ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.088150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.066521 restraints weight = 81963.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.066690 restraints weight = 59308.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.066848 restraints weight = 43103.608| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13020 Z= 0.161 Angle : 0.562 10.894 18187 Z= 0.318 Chirality : 0.035 0.166 1992 Planarity : 0.003 0.038 1778 Dihedral : 27.716 179.838 2986 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: 2.65 (0.26), residues: 1104 helix: 2.29 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.55 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 107 HIS 0.005 0.001 HIS F 35 PHE 0.012 0.001 PHE J 83 TYR 0.012 0.001 TYR E 14 ARG 0.010 0.001 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 852) hydrogen bonds : angle 3.91210 ( 2384) covalent geometry : bond 0.00350 (13020) covalent geometry : angle 0.56177 (18187) *********************** 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 81 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 MET cc_start: 0.8641 (ppp) cc_final: 0.8408 (ppp) REVERT: C 42 MET cc_start: 0.8665 (mmp) cc_final: 0.8335 (tpp) REVERT: D 6 MET cc_start: 0.8263 (mmp) cc_final: 0.7965 (mmt) REVERT: D 42 MET cc_start: 0.8888 (tpp) cc_final: 0.8552 (tpp) REVERT: E 6 MET cc_start: 0.8164 (tmm) cc_final: 0.7956 (tmm) REVERT: E 121 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8650 (pt0) REVERT: F 42 MET cc_start: 0.8300 (tpt) cc_final: 0.7869 (tpp) REVERT: F 134 GLN cc_start: 0.8619 (pt0) cc_final: 0.8341 (pt0) REVERT: G 142 GLN cc_start: 0.7026 (mt0) cc_final: 0.6599 (mp10) REVERT: H 42 MET cc_start: 0.8867 (tpp) cc_final: 0.8285 (tpp) REVERT: H 43 VAL cc_start: 0.9413 (t) cc_final: 0.9167 (p) REVERT: I 51 TYR cc_start: 0.8046 (m-80) cc_final: 0.7684 (m-10) REVERT: I 136 LYS cc_start: 0.7926 (mptt) cc_final: 0.7595 (mttt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2588 time to fit residues: 31.2083 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 : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 120 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS F 12 GLN ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.087729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.066345 restraints weight = 80323.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.065609 restraints weight = 63454.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.065795 restraints weight = 51111.516| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4589 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= 0.156 Angle : 0.548 8.087 18187 Z= 0.314 Chirality : 0.035 0.146 1992 Planarity : 0.003 0.025 1778 Dihedral : 27.702 179.721 2986 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.20 % Allowed : 1.46 % 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 (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: 2.71 (0.26), residues: 1104 helix: 2.35 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -0.61 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 107 HIS 0.005 0.001 HIS F 35 PHE 0.008 0.001 PHE J 83 TYR 0.019 0.001 TYR D 57 ARG 0.010 0.001 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 852) hydrogen bonds : angle 3.93837 ( 2384) covalent geometry : bond 0.00340 (13020) covalent geometry : angle 0.54770 (18187) *********************** 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 83 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.7673 (ptt) cc_final: 0.7379 (ppp) REVERT: C 15 MET cc_start: 0.8649 (ppp) cc_final: 0.8392 (ppp) REVERT: C 42 MET cc_start: 0.8760 (mmp) cc_final: 0.8402 (tpp) REVERT: D 42 MET cc_start: 0.8824 (tpp) cc_final: 0.8359 (tpp) REVERT: E 6 MET cc_start: 0.8375 (tmm) cc_final: 0.8117 (tmm) REVERT: E 121 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8717 (pt0) REVERT: E 140 HIS cc_start: 0.6689 (OUTLIER) cc_final: 0.6190 (p90) REVERT: F 42 MET cc_start: 0.8465 (tpt) cc_final: 0.8039 (tpp) REVERT: F 71 LYS cc_start: 0.8971 (tttt) cc_final: 0.8645 (pttm) REVERT: F 134 GLN cc_start: 0.8489 (pt0) cc_final: 0.8051 (mt0) REVERT: H 42 MET cc_start: 0.8697 (tpp) cc_final: 0.8223 (tpp) REVERT: H 43 VAL cc_start: 0.9411 (t) cc_final: 0.9188 (p) REVERT: I 51 TYR cc_start: 0.7996 (m-80) cc_final: 0.7684 (m-10) REVERT: I 136 LYS cc_start: 0.7966 (mptt) cc_final: 0.7681 (mttt) outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 0.2747 time to fit residues: 33.8499 Evaluate side-chains 63 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN ** F 139 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.087097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.066144 restraints weight = 80748.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.065558 restraints weight = 57415.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065719 restraints weight = 44608.538| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5131 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= 0.165 Angle : 0.551 7.814 18187 Z= 0.317 Chirality : 0.035 0.136 1992 Planarity : 0.003 0.026 1778 Dihedral : 27.715 179.352 2986 Min Nonbonded Distance : 1.308 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.20 % Allowed : 1.56 % Favored : 98.24 % 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: 2.62 (0.26), residues: 1104 helix: 2.32 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.81 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 107 HIS 0.005 0.001 HIS F 35 PHE 0.009 0.001 PHE F 120 TYR 0.015 0.001 TYR E 14 ARG 0.008 0.000 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 852) hydrogen bonds : angle 3.94666 ( 2384) covalent geometry : bond 0.00360 (13020) covalent geometry : angle 0.55122 (18187) *********************** 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 96 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.7768 (ptt) cc_final: 0.7395 (ptm) REVERT: C 15 MET cc_start: 0.8744 (ppp) cc_final: 0.8529 (ppp) REVERT: D 42 MET cc_start: 0.8855 (tpp) cc_final: 0.8300 (tpp) REVERT: E 42 MET cc_start: 0.7977 (tpt) cc_final: 0.7592 (tpt) REVERT: E 121 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8725 (pt0) REVERT: F 71 LYS cc_start: 0.8989 (tttt) cc_final: 0.8636 (pttm) REVERT: F 134 GLN cc_start: 0.8537 (pt0) cc_final: 0.7940 (mt0) REVERT: G 142 GLN cc_start: 0.6943 (mt0) cc_final: 0.6547 (mp10) REVERT: H 42 MET cc_start: 0.8889 (tpp) cc_final: 0.8299 (tpp) REVERT: H 43 VAL cc_start: 0.9460 (t) cc_final: 0.9251 (p) REVERT: I 43 VAL cc_start: 0.9441 (t) cc_final: 0.9157 (t) REVERT: I 51 TYR cc_start: 0.7933 (m-80) cc_final: 0.7436 (m-10) REVERT: I 136 LYS cc_start: 0.7976 (mptt) cc_final: 0.7738 (mttt) REVERT: J 42 MET cc_start: 0.7283 (mmp) cc_final: 0.7074 (tpp) REVERT: J 47 ASP cc_start: 0.6158 (t70) cc_final: 0.5878 (t0) outliers start: 2 outliers final: 0 residues processed: 96 average time/residue: 0.2329 time to fit residues: 33.5933 Evaluate side-chains 70 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 134 GLN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS F 103 HIS ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.086730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.064904 restraints weight = 79977.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.065129 restraints weight = 54736.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.065017 restraints weight = 41911.623| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5500 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 : 0.566 8.811 18187 Z= 0.321 Chirality : 0.036 0.131 1992 Planarity : 0.003 0.027 1778 Dihedral : 27.683 179.589 2986 Min Nonbonded Distance : 1.459 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.10 % Allowed : 1.07 % Favored : 98.83 % 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: 2.63 (0.26), residues: 1104 helix: 2.36 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -0.96 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 107 HIS 0.011 0.001 HIS E 139 PHE 0.013 0.002 PHE F 120 TYR 0.016 0.001 TYR F 9 ARG 0.008 0.000 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 852) hydrogen bonds : angle 3.99919 ( 2384) covalent geometry : bond 0.00362 (13020) covalent geometry : angle 0.56618 (18187) *********************** 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 90 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.8084 (ptt) cc_final: 0.7263 (ptm) REVERT: C 42 MET cc_start: 0.7458 (tpp) cc_final: 0.6809 (tpp) REVERT: D 42 MET cc_start: 0.8765 (tpp) cc_final: 0.8313 (tpp) REVERT: E 42 MET cc_start: 0.7770 (tpt) cc_final: 0.7248 (tpt) REVERT: E 121 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8723 (pt0) REVERT: E 140 HIS cc_start: 0.7034 (OUTLIER) cc_final: 0.6433 (p90) REVERT: F 71 LYS cc_start: 0.9040 (tttt) cc_final: 0.8643 (pttm) REVERT: F 134 GLN cc_start: 0.8448 (pt0) cc_final: 0.7779 (mt0) REVERT: H 42 MET cc_start: 0.8801 (tpp) cc_final: 0.8273 (tpp) REVERT: H 43 VAL cc_start: 0.9420 (t) cc_final: 0.9209 (p) REVERT: I 51 TYR cc_start: 0.7917 (m-80) cc_final: 0.7391 (m-10) REVERT: I 136 LYS cc_start: 0.7994 (mptt) cc_final: 0.7743 (mttt) REVERT: J 47 ASP cc_start: 0.6551 (t70) cc_final: 0.6239 (t0) REVERT: J 107 TRP cc_start: 0.6742 (t-100) cc_final: 0.6350 (m100) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.2690 time to fit residues: 35.6787 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 : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN I 12 GLN J 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.086107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064079 restraints weight = 80568.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.064432 restraints weight = 54884.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.064481 restraints weight = 42263.615| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13020 Z= 0.181 Angle : 0.589 7.883 18187 Z= 0.336 Chirality : 0.036 0.137 1992 Planarity : 0.003 0.023 1778 Dihedral : 27.746 179.440 2986 Min Nonbonded Distance : 1.402 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.10 % Allowed : 1.07 % Favored : 98.83 % 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: 2.38 (0.26), residues: 1104 helix: 2.20 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -1.14 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 107 HIS 0.010 0.001 HIS E 139 PHE 0.007 0.001 PHE J 83 TYR 0.039 0.002 TYR F 9 ARG 0.007 0.001 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 852) hydrogen bonds : angle 4.11467 ( 2384) covalent geometry : bond 0.00394 (13020) covalent geometry : angle 0.58902 (18187) *********************** 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 80 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.8106 (ptt) cc_final: 0.7409 (ptm) REVERT: C 42 MET cc_start: 0.7440 (tpp) cc_final: 0.6784 (tpp) REVERT: D 42 MET cc_start: 0.8719 (tpp) cc_final: 0.8265 (tpp) REVERT: E 85 ARG cc_start: 0.9370 (mtt-85) cc_final: 0.8687 (mtp85) REVERT: F 84 LEU cc_start: 0.8150 (tp) cc_final: 0.7935 (tp) REVERT: F 134 GLN cc_start: 0.8452 (pt0) cc_final: 0.7899 (mt0) REVERT: H 42 MET cc_start: 0.8647 (tpp) cc_final: 0.8176 (tpp) REVERT: I 51 TYR cc_start: 0.8051 (m-80) cc_final: 0.7527 (m-10) REVERT: I 136 LYS cc_start: 0.7994 (mptt) cc_final: 0.7781 (mttt) REVERT: J 47 ASP cc_start: 0.5925 (t70) cc_final: 0.5678 (t0) REVERT: J 107 TRP cc_start: 0.6767 (t-100) cc_final: 0.6458 (m100) REVERT: J 111 ASP cc_start: 0.6020 (m-30) cc_final: 0.5449 (m-30) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.2851 time to fit residues: 36.9502 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 : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 7 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 19 optimal weight: 0.0040 chunk 55 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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** E 104 HIS ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** G 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 = 0.3959 r_free = 0.3959 target = 0.087658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.065014 restraints weight = 79033.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.063359 restraints weight = 60246.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064097 restraints weight = 44362.364| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5859 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= 0.131 Angle : 0.556 9.405 18187 Z= 0.312 Chirality : 0.035 0.136 1992 Planarity : 0.003 0.027 1778 Dihedral : 27.692 178.971 2986 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.20 % Allowed : 0.29 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.26), residues: 1104 helix: 2.34 (0.18), residues: 896 sheet: None (None), residues: 0 loop : -0.86 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 107 HIS 0.009 0.001 HIS E 139 PHE 0.052 0.002 PHE J 83 TYR 0.018 0.001 TYR F 9 ARG 0.006 0.000 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 852) hydrogen bonds : angle 3.92130 ( 2384) covalent geometry : bond 0.00283 (13020) covalent geometry : angle 0.55629 (18187) *********************** 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 79 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.8033 (ptt) cc_final: 0.7388 (ptm) REVERT: C 15 MET cc_start: 0.8707 (ppp) cc_final: 0.8459 (ppp) REVERT: C 42 MET cc_start: 0.7696 (tpp) cc_final: 0.7011 (tpp) REVERT: D 42 MET cc_start: 0.8950 (tpp) cc_final: 0.8426 (tpp) REVERT: E 6 MET cc_start: 0.8371 (tmm) cc_final: 0.8084 (tmm) REVERT: E 140 HIS cc_start: 0.6715 (OUTLIER) cc_final: 0.6241 (p90) REVERT: F 134 GLN cc_start: 0.8410 (pt0) cc_final: 0.7888 (mt0) REVERT: G 42 MET cc_start: 0.8094 (tpt) cc_final: 0.7640 (tpp) REVERT: G 142 GLN cc_start: 0.7305 (mt0) cc_final: 0.6779 (mp10) REVERT: H 42 MET cc_start: 0.8754 (tpp) cc_final: 0.8247 (tpp) REVERT: J 47 ASP cc_start: 0.6275 (t70) cc_final: 0.6014 (t0) REVERT: J 107 TRP cc_start: 0.6709 (t-100) cc_final: 0.6455 (m100) outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 0.2404 time to fit residues: 29.3848 Evaluate side-chains 59 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 6.9990 chunk 99 optimal weight: 0.2980 chunk 59 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 120 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** 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 = 0.3948 r_free = 0.3948 target = 0.087062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.064519 restraints weight = 79088.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.063729 restraints weight = 52644.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.064075 restraints weight = 42005.583| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.6042 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= 0.141 Angle : 0.559 9.158 18187 Z= 0.315 Chirality : 0.035 0.135 1992 Planarity : 0.003 0.024 1778 Dihedral : 27.644 179.422 2986 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.26), residues: 1104 helix: 2.32 (0.18), residues: 896 sheet: None (None), residues: 0 loop : -0.99 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 107 HIS 0.009 0.001 HIS E 139 PHE 0.035 0.002 PHE F 120 TYR 0.024 0.001 TYR F 9 ARG 0.006 0.000 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 852) hydrogen bonds : angle 3.94963 ( 2384) covalent geometry : bond 0.00307 (13020) covalent geometry : angle 0.55945 (18187) ********************** 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 76 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.8082 (ptt) cc_final: 0.7445 (ptm) REVERT: C 15 MET cc_start: 0.8711 (ppp) cc_final: 0.8472 (ppp) REVERT: C 42 MET cc_start: 0.7747 (tpp) cc_final: 0.7093 (tpp) REVERT: D 42 MET cc_start: 0.8889 (tpp) cc_final: 0.8551 (tpp) REVERT: F 134 GLN cc_start: 0.8430 (pt0) cc_final: 0.7912 (mt0) REVERT: G 42 MET cc_start: 0.8127 (tpt) cc_final: 0.7668 (tpp) REVERT: G 142 GLN cc_start: 0.7152 (mt0) cc_final: 0.6589 (mp10) REVERT: H 42 MET cc_start: 0.8721 (tpp) cc_final: 0.8214 (tpp) REVERT: J 47 ASP cc_start: 0.6424 (t70) cc_final: 0.6110 (t0) REVERT: J 111 ASP cc_start: 0.6333 (m-30) cc_final: 0.5772 (m-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2241 time to fit residues: 27.9423 Evaluate side-chains 57 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 0.0070 chunk 84 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 139 HIS ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.087394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065271 restraints weight = 79641.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.065002 restraints weight = 52331.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.065301 restraints weight = 40712.756| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.6149 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= 0.135 Angle : 0.555 8.733 18187 Z= 0.312 Chirality : 0.035 0.135 1992 Planarity : 0.003 0.024 1778 Dihedral : 27.612 179.216 2986 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.26), residues: 1104 helix: 2.33 (0.18), residues: 896 sheet: None (None), residues: 0 loop : -1.05 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 107 HIS 0.009 0.001 HIS E 139 PHE 0.039 0.002 PHE J 83 TYR 0.022 0.001 TYR F 9 ARG 0.005 0.000 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 852) hydrogen bonds : angle 3.91390 ( 2384) covalent geometry : bond 0.00293 (13020) covalent geometry : angle 0.55450 (18187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4291.47 seconds wall clock time: 77 minutes 21.34 seconds (4641.34 seconds total)