Starting phenix.real_space_refine on Sun Nov 17 00:28:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4d_45182/11_2024/9c4d_45182.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4d_45182/11_2024/9c4d_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4d_45182/11_2024/9c4d_45182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4d_45182/11_2024/9c4d_45182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4d_45182/11_2024/9c4d_45182.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4d_45182/11_2024/9c4d_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-5513/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: 7.59, 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: 2.99 Conformation dependent library (CDL) restraints added in 1.2 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: 4.78 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: 4.61 Time building geometry restraints manager: 3.49 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: 0.010 Normalize map: mean=0, sd=1: 6.820 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.480 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.200 ------------------------------------------------------------------------------- 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= 0.130 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 *********************** 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 : 1.230 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: 0.2777 time to fit residues: 69.3181 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 : 1.250 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 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= 0.169 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 *********************** 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 : 1.446 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: 0.8609 (mmp) cc_final: 0.8325 (tpp) REVERT: D 42 MET cc_start: 0.8572 (tpp) cc_final: 0.7945 (tpp) REVERT: F 42 MET cc_start: 0.7937 (tpt) cc_final: 0.7703 (tpp) REVERT: F 51 TYR cc_start: 0.8069 (m-80) cc_final: 0.7845 (m-80) REVERT: F 112 ARG cc_start: 0.8805 (mmp80) cc_final: 0.8541 (mmp80) REVERT: F 134 GLN cc_start: 0.8444 (pt0) cc_final: 0.7928 (mt0) REVERT: G 137 THR cc_start: 0.8017 (p) cc_final: 0.7564 (t) REVERT: H 15 MET cc_start: 0.8999 (ttp) cc_final: 0.7973 (ttm) REVERT: H 42 MET cc_start: 0.8393 (tpp) cc_final: 0.8057 (tpp) REVERT: I 51 TYR cc_start: 0.7818 (m-80) cc_final: 0.7297 (m-10) REVERT: J 107 TRP cc_start: 0.7365 (m100) cc_final: 0.6433 (t-100) outliers start: 2 outliers final: 0 residues processed: 102 average time/residue: 0.3139 time to fit residues: 44.4465 Evaluate side-chains 66 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 114 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13020 Z= 0.198 Angle : 0.543 7.733 18187 Z= 0.313 Chirality : 0.035 0.279 1992 Planarity : 0.003 0.052 1778 Dihedral : 27.672 179.776 2986 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: 2.90 (0.26), residues: 1104 helix: 2.44 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -0.32 (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 0.015 0.001 PHE J 83 TYR 0.011 0.001 TYR E 22 ARG 0.012 0.001 ARG E 126 *********************** 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 : 1.318 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 42 MET cc_start: 0.8710 (mmp) cc_final: 0.8408 (tpt) REVERT: D 42 MET cc_start: 0.8585 (tpp) cc_final: 0.7952 (tpp) REVERT: E 6 MET cc_start: 0.8089 (tmm) cc_final: 0.7688 (tmm) REVERT: E 42 MET cc_start: 0.8157 (tpt) cc_final: 0.7944 (tpt) REVERT: E 85 ARG cc_start: 0.9351 (mtt-85) cc_final: 0.8786 (mtp85) REVERT: F 42 MET cc_start: 0.8154 (tpt) cc_final: 0.7761 (tpp) REVERT: F 51 TYR cc_start: 0.8190 (m-80) cc_final: 0.7863 (m-80) REVERT: F 120 PHE cc_start: 0.7191 (m-80) cc_final: 0.6792 (m-80) REVERT: F 134 GLN cc_start: 0.8524 (pt0) cc_final: 0.7835 (mt0) REVERT: H 42 MET cc_start: 0.8808 (tpp) cc_final: 0.8298 (tpp) REVERT: I 51 TYR cc_start: 0.7544 (m-80) cc_final: 0.7303 (m-10) outliers start: 3 outliers final: 1 residues processed: 93 average time/residue: 0.2545 time to fit residues: 34.7341 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 : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 12 GLN ** F 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS G 134 GLN ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 HIS J 12 GLN J 77 HIS ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4435 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= 0.254 Angle : 0.603 8.585 18187 Z= 0.345 Chirality : 0.037 0.185 1992 Planarity : 0.003 0.038 1778 Dihedral : 27.783 179.769 2986 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.26), residues: 1104 helix: 2.13 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.75 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 107 HIS 0.006 0.001 HIS F 35 PHE 0.058 0.003 PHE J 83 TYR 0.017 0.002 TYR E 14 ARG 0.012 0.001 ARG E 126 *********************** 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: 0 poor density : 90 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 MET cc_start: 0.8660 (ppp) cc_final: 0.8388 (ppp) REVERT: C 42 MET cc_start: 0.8764 (mmp) cc_final: 0.8519 (tpp) REVERT: D 6 MET cc_start: 0.8449 (mmp) cc_final: 0.8054 (mmt) REVERT: D 42 MET cc_start: 0.8774 (tpp) cc_final: 0.8261 (tpp) REVERT: E 42 MET cc_start: 0.8225 (tpt) cc_final: 0.7876 (tpt) REVERT: E 49 ASP cc_start: 0.9089 (t0) cc_final: 0.8688 (t0) REVERT: E 85 ARG cc_start: 0.9349 (mtt-85) cc_final: 0.8702 (mtp85) REVERT: F 42 MET cc_start: 0.8294 (tpt) cc_final: 0.7831 (tpp) REVERT: F 51 TYR cc_start: 0.8277 (m-80) cc_final: 0.7879 (m-80) REVERT: F 71 LYS cc_start: 0.8983 (tttt) cc_final: 0.8650 (pttm) REVERT: F 134 GLN cc_start: 0.8493 (pt0) cc_final: 0.7942 (mt0) REVERT: H 42 MET cc_start: 0.8822 (tpp) cc_final: 0.8262 (tpp) REVERT: I 51 TYR cc_start: 0.7576 (m-80) cc_final: 0.7086 (m-10) REVERT: I 136 LYS cc_start: 0.7946 (mptt) cc_final: 0.7608 (mttt) REVERT: J 47 ASP cc_start: 0.6240 (t70) cc_final: 0.6017 (t0) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2484 time to fit residues: 33.2078 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 : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 140 HIS F 12 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13020 Z= 0.205 Angle : 0.556 8.144 18187 Z= 0.318 Chirality : 0.035 0.142 1992 Planarity : 0.003 0.033 1778 Dihedral : 27.769 179.964 2986 Min Nonbonded Distance : 1.613 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.29 % Allowed : 1.56 % 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: 2.58 (0.26), residues: 1104 helix: 2.28 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.74 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 107 HIS 0.010 0.001 HIS E 139 PHE 0.007 0.001 PHE F 120 TYR 0.020 0.001 TYR D 57 ARG 0.009 0.001 ARG E 126 *********************** 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 91 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.7645 (ptt) cc_final: 0.7414 (ppp) REVERT: C 15 MET cc_start: 0.8718 (ppp) cc_final: 0.8492 (ppp) REVERT: C 42 MET cc_start: 0.8792 (mmp) cc_final: 0.8421 (tpp) REVERT: D 42 MET cc_start: 0.8891 (tpp) cc_final: 0.8271 (tpp) REVERT: E 42 MET cc_start: 0.8092 (tpt) cc_final: 0.7858 (tpt) REVERT: E 85 ARG cc_start: 0.9328 (mtt-85) cc_final: 0.8741 (mtp85) REVERT: E 140 HIS cc_start: 0.7014 (OUTLIER) cc_final: 0.6332 (p90) REVERT: F 42 MET cc_start: 0.8350 (tpt) cc_final: 0.7991 (tpp) REVERT: F 71 LYS cc_start: 0.8942 (tttt) cc_final: 0.8619 (pttm) REVERT: F 134 GLN cc_start: 0.8527 (pt0) cc_final: 0.7966 (mt0) REVERT: H 42 MET cc_start: 0.8932 (tpp) cc_final: 0.8326 (tpp) REVERT: H 43 VAL cc_start: 0.9499 (t) cc_final: 0.9255 (p) REVERT: I 51 TYR cc_start: 0.7716 (m-80) cc_final: 0.7212 (m-10) REVERT: I 136 LYS cc_start: 0.7979 (mptt) cc_final: 0.7676 (mttt) REVERT: J 47 ASP cc_start: 0.5912 (t70) cc_final: 0.5684 (t0) outliers start: 3 outliers final: 0 residues processed: 91 average time/residue: 0.2600 time to fit residues: 34.9102 Evaluate side-chains 67 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 J 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5282 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= 0.202 Angle : 0.553 7.876 18187 Z= 0.316 Chirality : 0.035 0.137 1992 Planarity : 0.003 0.031 1778 Dihedral : 27.709 179.308 2986 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.29 % Allowed : 1.07 % Favored : 98.63 % 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: 2.33 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.86 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 107 HIS 0.007 0.001 HIS E 139 PHE 0.007 0.001 PHE F 120 TYR 0.016 0.001 TYR D 57 ARG 0.009 0.001 ARG E 126 *********************** 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 84 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 1.226 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: 0.7721 (ptt) cc_final: 0.7366 (ptm) REVERT: D 42 MET cc_start: 0.8877 (tpp) cc_final: 0.8267 (tpp) REVERT: E 85 ARG cc_start: 0.9298 (mtt-85) cc_final: 0.8676 (mtp85) REVERT: F 71 LYS cc_start: 0.9027 (tttt) cc_final: 0.8628 (pttm) REVERT: F 134 GLN cc_start: 0.8507 (pt0) cc_final: 0.7982 (mt0) REVERT: H 42 MET cc_start: 0.8846 (tpp) cc_final: 0.8300 (tpp) REVERT: H 43 VAL cc_start: 0.9500 (t) cc_final: 0.9268 (p) REVERT: I 51 TYR cc_start: 0.7778 (m-80) cc_final: 0.7255 (m-10) REVERT: I 136 LYS cc_start: 0.7994 (mptt) cc_final: 0.7727 (mttt) REVERT: J 47 ASP cc_start: 0.6770 (t70) cc_final: 0.6523 (t0) outliers start: 3 outliers final: 0 residues processed: 84 average time/residue: 0.2444 time to fit residues: 30.7038 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 : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 75 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** E 140 HIS ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5465 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= 0.175 Angle : 0.549 9.859 18187 Z= 0.309 Chirality : 0.035 0.191 1992 Planarity : 0.003 0.027 1778 Dihedral : 27.678 179.607 2986 Min Nonbonded Distance : 1.429 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: 2.83 (0.26), residues: 1104 helix: 2.44 (0.18), residues: 896 sheet: None (None), residues: 0 loop : -0.73 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 107 HIS 0.006 0.001 HIS E 139 PHE 0.044 0.002 PHE J 83 TYR 0.014 0.001 TYR D 57 ARG 0.007 0.000 ARG E 126 *********************** 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 88 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.8130 (ptt) cc_final: 0.7332 (ptm) REVERT: C 42 MET cc_start: 0.7388 (tpp) cc_final: 0.6781 (tpp) REVERT: D 42 MET cc_start: 0.8910 (tpp) cc_final: 0.8388 (tpp) REVERT: E 42 MET cc_start: 0.7936 (tpt) cc_final: 0.7092 (tpt) REVERT: E 49 ASP cc_start: 0.9234 (t0) cc_final: 0.8676 (t0) REVERT: E 85 ARG cc_start: 0.9279 (mtt-85) cc_final: 0.8690 (mtp85) REVERT: E 121 GLU cc_start: 0.8263 (pp20) cc_final: 0.8060 (pp20) REVERT: E 140 HIS cc_start: 0.6941 (OUTLIER) cc_final: 0.6296 (p90) REVERT: F 71 LYS cc_start: 0.9043 (tttt) cc_final: 0.8629 (pttm) REVERT: F 134 GLN cc_start: 0.8501 (pt0) cc_final: 0.7923 (mt0) REVERT: G 82 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8627 (tm-30) REVERT: G 142 GLN cc_start: 0.7058 (mt0) cc_final: 0.6533 (mp10) REVERT: H 42 MET cc_start: 0.8726 (tpp) cc_final: 0.8218 (tpp) REVERT: I 51 TYR cc_start: 0.7774 (m-80) cc_final: 0.7255 (m-10) REVERT: I 136 LYS cc_start: 0.7982 (mptt) cc_final: 0.7775 (mttt) REVERT: J 47 ASP cc_start: 0.6700 (t70) cc_final: 0.6457 (t0) REVERT: J 107 TRP cc_start: 0.6679 (t-100) cc_final: 0.6308 (m100) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.2407 time to fit residues: 31.8376 Evaluate side-chains 70 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 0.0370 chunk 110 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5619 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= 0.169 Angle : 0.547 8.764 18187 Z= 0.309 Chirality : 0.035 0.138 1992 Planarity : 0.003 0.027 1778 Dihedral : 27.651 179.728 2986 Min Nonbonded Distance : 1.435 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: 2.79 (0.26), residues: 1104 helix: 2.42 (0.18), residues: 896 sheet: None (None), residues: 0 loop : -0.80 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 107 HIS 0.006 0.001 HIS E 139 PHE 0.007 0.001 PHE F 120 TYR 0.029 0.001 TYR F 9 ARG 0.007 0.000 ARG E 126 *********************** 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 82 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.8085 (ptt) cc_final: 0.7375 (ptm) REVERT: C 42 MET cc_start: 0.7406 (tpp) cc_final: 0.6752 (tpp) REVERT: D 42 MET cc_start: 0.8911 (tpp) cc_final: 0.8386 (tpp) REVERT: E 6 MET cc_start: 0.8104 (tmm) cc_final: 0.7729 (tmm) REVERT: E 49 ASP cc_start: 0.9116 (t0) cc_final: 0.8687 (t0) REVERT: E 85 ARG cc_start: 0.9346 (mtt-85) cc_final: 0.8726 (mtp85) REVERT: F 71 LYS cc_start: 0.9035 (tttt) cc_final: 0.8624 (pttm) REVERT: F 134 GLN cc_start: 0.8495 (pt0) cc_final: 0.7943 (mt0) REVERT: G 142 GLN cc_start: 0.6896 (mt0) cc_final: 0.6378 (mp10) REVERT: H 42 MET cc_start: 0.8754 (tpp) cc_final: 0.8212 (tpp) REVERT: I 136 LYS cc_start: 0.7980 (mptt) cc_final: 0.7765 (mttt) REVERT: J 47 ASP cc_start: 0.6292 (t70) cc_final: 0.6071 (t0) REVERT: J 107 TRP cc_start: 0.6689 (t-100) cc_final: 0.6314 (m100) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2540 time to fit residues: 31.5702 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 : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.0040 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 112 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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** E 140 HIS ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5909 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= 0.195 Angle : 0.564 9.180 18187 Z= 0.319 Chirality : 0.035 0.142 1992 Planarity : 0.003 0.043 1778 Dihedral : 27.687 178.851 2986 Min Nonbonded Distance : 1.397 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % 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: 2.58 (0.26), residues: 1104 helix: 2.29 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -0.96 (0.43), residues: 208 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 0.036 0.002 PHE J 83 TYR 0.020 0.001 TYR F 9 ARG 0.007 0.000 ARG E 126 *********************** 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 82 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.8146 (ptt) cc_final: 0.7453 (ptm) REVERT: C 42 MET cc_start: 0.7559 (tpp) cc_final: 0.6870 (tpp) REVERT: D 42 MET cc_start: 0.8884 (tpp) cc_final: 0.8308 (tpp) REVERT: E 6 MET cc_start: 0.8140 (tmm) cc_final: 0.7716 (tmm) REVERT: E 49 ASP cc_start: 0.9207 (t0) cc_final: 0.8933 (t0) REVERT: E 85 ARG cc_start: 0.9336 (mtt-85) cc_final: 0.8745 (mtp85) REVERT: E 140 HIS cc_start: 0.6798 (OUTLIER) cc_final: 0.6210 (p90) REVERT: F 134 GLN cc_start: 0.8413 (pt0) cc_final: 0.7900 (mt0) REVERT: G 142 GLN cc_start: 0.6967 (mt0) cc_final: 0.6408 (mp10) REVERT: H 42 MET cc_start: 0.8776 (tpp) cc_final: 0.8201 (tpp) REVERT: I 136 LYS cc_start: 0.7987 (mptt) cc_final: 0.7764 (mttt) REVERT: J 47 ASP cc_start: 0.5834 (t70) cc_final: 0.5576 (t0) REVERT: J 111 ASP cc_start: 0.6460 (m-30) cc_final: 0.6029 (m-30) REVERT: J 124 ASP cc_start: 0.6961 (m-30) cc_final: 0.5769 (t0) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.2310 time to fit residues: 29.2633 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 : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** J 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13020 Z= 0.215 Angle : 0.576 8.580 18187 Z= 0.326 Chirality : 0.036 0.150 1992 Planarity : 0.003 0.028 1778 Dihedral : 27.723 179.854 2986 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 2.48 (0.26), residues: 1104 helix: 2.23 (0.18), residues: 896 sheet: None (None), residues: 0 loop : -1.04 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 107 HIS 0.006 0.001 HIS H 140 PHE 0.010 0.001 PHE F 120 TYR 0.020 0.002 TYR F 9 ARG 0.007 0.000 ARG E 126 ********************** 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 75 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 MET cc_start: 0.8078 (ptt) cc_final: 0.7549 (ptm) REVERT: C 42 MET cc_start: 0.7684 (tpp) cc_final: 0.7035 (tpp) REVERT: D 42 MET cc_start: 0.8869 (tpp) cc_final: 0.8298 (tpp) REVERT: E 49 ASP cc_start: 0.9230 (t0) cc_final: 0.8917 (t0) REVERT: E 85 ARG cc_start: 0.9372 (mtt-85) cc_final: 0.9120 (mtp85) REVERT: F 134 GLN cc_start: 0.8416 (pt0) cc_final: 0.7891 (mt0) REVERT: G 142 GLN cc_start: 0.6995 (mt0) cc_final: 0.6436 (mp10) REVERT: H 42 MET cc_start: 0.8788 (tpp) cc_final: 0.8170 (tpp) REVERT: H 142 GLN cc_start: 0.7817 (mp10) cc_final: 0.7477 (mp10) REVERT: I 136 LYS cc_start: 0.7993 (mptt) cc_final: 0.7758 (mttt) REVERT: J 47 ASP cc_start: 0.5919 (t70) cc_final: 0.5662 (t0) REVERT: J 124 ASP cc_start: 0.6995 (m-30) cc_final: 0.5836 (t0) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2348 time to fit residues: 26.9044 Evaluate side-chains 62 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 87 optimal weight: 0.0020 chunk 5 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 E 139 HIS ** G 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 = 0.3937 r_free = 0.3937 target = 0.086671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.064672 restraints weight = 79883.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.064227 restraints weight = 53071.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.064674 restraints weight = 41912.593| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.6290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13020 Z= 0.179 Angle : 0.556 7.921 18187 Z= 0.314 Chirality : 0.035 0.144 1992 Planarity : 0.003 0.025 1778 Dihedral : 27.681 179.617 2986 Min Nonbonded Distance : 1.390 Molprobity Statistics. All-atom Clashscore : 10.74 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 (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: 2.57 (0.26), residues: 1104 helix: 2.30 (0.18), residues: 896 sheet: None (None), residues: 0 loop : -1.03 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 107 HIS 0.006 0.001 HIS E 139 PHE 0.008 0.001 PHE E 120 TYR 0.018 0.001 TYR F 9 ARG 0.006 0.000 ARG E 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2343.11 seconds wall clock time: 47 minutes 46.24 seconds (2866.24 seconds total)