Starting phenix.real_space_refine on Fri Mar 15 14:57:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohc_12900/03_2024/7ohc_12900.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohc_12900/03_2024/7ohc_12900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohc_12900/03_2024/7ohc_12900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohc_12900/03_2024/7ohc_12900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohc_12900/03_2024/7ohc_12900.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohc_12900/03_2024/7ohc_12900.pdb" } resolution = 2.5 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 289 5.49 5 S 12 5.16 5 C 6648 2.51 5 N 2262 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 81": "OD1" <-> "OD2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12019 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 6.68, per 1000 atoms: 0.56 Number of scatterers: 12019 At special positions: 0 Unit cell: (74.55, 119.7, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 289 15.00 O 2808 8.00 N 2262 7.00 C 6648 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 - 3.50 Amino acid : False - 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: 5.90 Conformation dependent library (CDL) restraints added in 1.1 seconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 72.3% alpha, 3.1% beta 144 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 6.11 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.244A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.340A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 23 through 29 removed outlier: 4.030A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.355A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.917A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.461A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.407A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.754A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.182A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 419 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1813 1.33 - 1.45: 4503 1.45 - 1.57: 5904 1.57 - 1.69: 580 1.69 - 1.81: 22 Bond restraints: 12822 Sorted by residual: bond pdb=" CB GLU H 110 " pdb=" CG GLU H 110 " ideal model delta sigma weight residual 1.520 1.407 0.113 3.00e-02 1.11e+03 1.41e+01 bond pdb=" CG GLU H 110 " pdb=" CD GLU H 110 " ideal model delta sigma weight residual 1.516 1.428 0.088 2.50e-02 1.60e+03 1.24e+01 bond pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 1.422 1.494 -0.072 3.00e-02 1.11e+03 5.75e+00 bond pdb=" CB ASN C 73 " pdb=" CG ASN C 73 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.57e+00 bond pdb=" CD GLU H 110 " pdb=" OE2 GLU H 110 " ideal model delta sigma weight residual 1.249 1.209 0.040 1.90e-02 2.77e+03 4.39e+00 ... (remaining 12817 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.07: 1261 105.07 - 111.98: 6853 111.98 - 118.89: 3462 118.89 - 125.79: 6018 125.79 - 132.70: 962 Bond angle restraints: 18556 Sorted by residual: angle pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " pdb=" CG ASN C 73 " ideal model delta sigma weight residual 112.60 118.94 -6.34 1.00e+00 1.00e+00 4.03e+01 angle pdb=" C ASN C 73 " pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " ideal model delta sigma weight residual 110.56 119.26 -8.70 1.69e+00 3.50e-01 2.65e+01 angle pdb=" CA THR A 58 " pdb=" CB THR A 58 " pdb=" CG2 THR A 58 " ideal model delta sigma weight residual 110.50 118.23 -7.73 1.70e+00 3.46e-01 2.07e+01 angle pdb=" N ASN C 73 " pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " ideal model delta sigma weight residual 110.56 104.19 6.37 1.46e+00 4.69e-01 1.90e+01 angle pdb=" CA LYS G 74 " pdb=" CB LYS G 74 " pdb=" CG LYS G 74 " ideal model delta sigma weight residual 114.10 122.71 -8.61 2.00e+00 2.50e-01 1.85e+01 ... (remaining 18551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 4465 21.47 - 42.93: 1384 42.93 - 64.40: 1085 64.40 - 85.87: 47 85.87 - 107.34: 4 Dihedral angle restraints: 6985 sinusoidal: 4767 harmonic: 2218 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -161.86 -18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 6982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1910 0.082 - 0.165: 191 0.165 - 0.247: 9 0.247 - 0.330: 0 0.330 - 0.412: 1 Chirality restraints: 2111 Sorted by residual: chirality pdb=" CB THR D 116 " pdb=" CA THR D 116 " pdb=" OG1 THR D 116 " pdb=" CG2 THR D 116 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CB THR A 58 " pdb=" CA THR A 58 " pdb=" OG1 THR A 58 " pdb=" CG2 THR A 58 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB THR H 112 " pdb=" CA THR H 112 " pdb=" OG1 THR H 112 " pdb=" CG2 THR H 112 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2108 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 73 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C ASN C 73 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN C 73 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 74 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 58 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C THR A 58 " 0.057 2.00e-02 2.50e+03 pdb=" O THR A 58 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 59 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 69 " 0.036 2.00e-02 2.50e+03 2.11e-02 9.97e+00 pdb=" N1 DC I 69 " -0.049 2.00e-02 2.50e+03 pdb=" C2 DC I 69 " 0.010 2.00e-02 2.50e+03 pdb=" O2 DC I 69 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC I 69 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 69 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC I 69 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 69 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 69 " -0.003 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 951 2.73 - 3.28: 10386 3.28 - 3.82: 24870 3.82 - 4.36: 30273 4.36 - 4.90: 41885 Nonbonded interactions: 108365 Sorted by model distance: nonbonded pdb=" O ASN C 73 " pdb=" ND2 ASN C 73 " model vdw 2.193 2.520 nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 30 " model vdw 2.238 2.440 nonbonded pdb=" O2 DC I -23 " pdb=" N2 DG J 23 " model vdw 2.255 2.496 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.275 2.440 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.299 2.440 ... (remaining 108360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 122) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 2.300 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 39.160 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 0.005 0.113 12822 Z= 0.314 Angle : 0.856 10.429 18556 Z= 0.503 Chirality : 0.049 0.412 2111 Planarity : 0.006 0.052 1344 Dihedral : 29.622 107.336 5553 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.16 % Allowed : 15.70 % Favored : 84.14 % 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: 0.04 (0.27), residues: 748 helix: 0.44 (0.20), residues: 537 sheet: None (None), residues: 0 loop : -0.81 (0.35), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.029 0.003 PHE G 25 TYR 0.051 0.003 TYR H 118 ARG 0.014 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.008 Fit side-chains REVERT: A 42 ARG cc_start: 0.7818 (mmm160) cc_final: 0.7580 (mmm-85) REVERT: A 50 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7984 (mt-10) REVERT: C 90 ASP cc_start: 0.8094 (t70) cc_final: 0.7798 (t0) REVERT: D 31 LYS cc_start: 0.8728 (mptt) cc_final: 0.8420 (mmtm) REVERT: D 68 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7362 (tp30) REVERT: D 90 GLU cc_start: 0.8180 (mp0) cc_final: 0.7932 (mp0) REVERT: D 105 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8266 (ttpp) REVERT: E 129 ARG cc_start: 0.8251 (tpt90) cc_final: 0.8010 (tpt90) REVERT: G 74 LYS cc_start: 0.8830 (ptpp) cc_final: 0.8400 (mtmm) REVERT: G 99 ARG cc_start: 0.7960 (mmm160) cc_final: 0.7691 (mmm-85) REVERT: H 65 ASP cc_start: 0.8752 (t70) cc_final: 0.8469 (t0) REVERT: H 76 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7532 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 1.7221 time to fit residues: 373.0910 Evaluate side-chains 184 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 104 GLN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12822 Z= 0.336 Angle : 0.611 6.163 18556 Z= 0.369 Chirality : 0.038 0.161 2111 Planarity : 0.005 0.046 1344 Dihedral : 31.555 108.424 4030 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.98 % Allowed : 17.11 % Favored : 79.91 % 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: 1.66 (0.29), residues: 748 helix: 1.68 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.023 0.002 PHE G 25 TYR 0.018 0.002 TYR H 37 ARG 0.007 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 1.076 Fit side-chains REVERT: A 42 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7625 (mmm-85) REVERT: A 50 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8018 (mt-10) REVERT: B 79 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8443 (mttm) REVERT: C 64 GLU cc_start: 0.7911 (tt0) cc_final: 0.7603 (tp30) REVERT: C 73 ASN cc_start: 0.8995 (t160) cc_final: 0.8502 (t0) REVERT: D 68 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7468 (tp30) REVERT: E 68 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: E 129 ARG cc_start: 0.8297 (tpt90) cc_final: 0.7843 (tpt90) REVERT: F 63 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: G 113 SER cc_start: 0.9004 (m) cc_final: 0.8794 (p) REVERT: H 39 TYR cc_start: 0.7583 (t80) cc_final: 0.7198 (t80) REVERT: H 65 ASP cc_start: 0.8678 (t70) cc_final: 0.8438 (t0) REVERT: H 76 ARG cc_start: 0.7856 (mtp180) cc_final: 0.7440 (mtm-85) outliers start: 19 outliers final: 5 residues processed: 196 average time/residue: 1.7763 time to fit residues: 367.7787 Evaluate side-chains 191 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 12822 Z= 0.423 Angle : 0.636 8.053 18556 Z= 0.381 Chirality : 0.040 0.184 2111 Planarity : 0.004 0.042 1344 Dihedral : 31.496 117.682 4028 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.98 % Allowed : 19.94 % Favored : 77.08 % 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: 1.95 (0.29), residues: 748 helix: 1.89 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.021 0.002 PHE G 25 TYR 0.013 0.002 TYR D 37 ARG 0.007 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8464 (mttm) REVERT: C 64 GLU cc_start: 0.7970 (tt0) cc_final: 0.7627 (tp30) REVERT: C 73 ASN cc_start: 0.8918 (t160) cc_final: 0.8387 (t0) REVERT: D 90 GLU cc_start: 0.8303 (mp0) cc_final: 0.7883 (mp0) REVERT: E 59 GLU cc_start: 0.8665 (pm20) cc_final: 0.8197 (pm20) REVERT: E 68 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: E 115 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8718 (mtpt) REVERT: E 120 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7331 (mpp) REVERT: F 63 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: H 30 ARG cc_start: 0.6784 (mtp-110) cc_final: 0.6496 (mtt180) REVERT: H 39 TYR cc_start: 0.7639 (t80) cc_final: 0.7384 (t80) REVERT: H 65 ASP cc_start: 0.8716 (t70) cc_final: 0.8452 (t0) REVERT: H 73 GLU cc_start: 0.8361 (tp30) cc_final: 0.7186 (tp30) REVERT: H 76 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6765 (mtp180) REVERT: H 110 GLU cc_start: 0.7897 (pt0) cc_final: 0.7620 (pt0) outliers start: 19 outliers final: 9 residues processed: 190 average time/residue: 1.8292 time to fit residues: 367.0160 Evaluate side-chains 195 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12822 Z= 0.207 Angle : 0.586 5.332 18556 Z= 0.359 Chirality : 0.035 0.144 2111 Planarity : 0.004 0.043 1344 Dihedral : 31.518 119.367 4028 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.45 % Allowed : 21.04 % Favored : 75.51 % 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: 2.25 (0.30), residues: 748 helix: 2.11 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.20 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.021 0.002 TYR F 88 ARG 0.005 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 0.868 Fit side-chains REVERT: A 42 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7765 (mmm-85) REVERT: C 64 GLU cc_start: 0.7925 (tt0) cc_final: 0.7592 (tp30) REVERT: C 73 ASN cc_start: 0.8896 (t160) cc_final: 0.8358 (t0) REVERT: D 54 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8406 (mmtp) REVERT: E 59 GLU cc_start: 0.8655 (pm20) cc_final: 0.8164 (pm20) REVERT: E 68 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: E 120 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7297 (mpp) REVERT: F 63 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: H 30 ARG cc_start: 0.6728 (mtp-110) cc_final: 0.6464 (mtt180) REVERT: H 39 TYR cc_start: 0.7561 (t80) cc_final: 0.7076 (t80) REVERT: H 43 LYS cc_start: 0.8260 (mmpt) cc_final: 0.7999 (mmtt) REVERT: H 65 ASP cc_start: 0.8679 (t70) cc_final: 0.8397 (t0) REVERT: H 73 GLU cc_start: 0.8231 (tp30) cc_final: 0.7052 (tp30) REVERT: H 76 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6724 (mtp180) REVERT: H 110 GLU cc_start: 0.7780 (pt0) cc_final: 0.7570 (pt0) outliers start: 22 outliers final: 13 residues processed: 189 average time/residue: 1.7939 time to fit residues: 357.6639 Evaluate side-chains 196 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12822 Z= 0.194 Angle : 0.583 5.475 18556 Z= 0.354 Chirality : 0.034 0.207 2111 Planarity : 0.004 0.043 1344 Dihedral : 31.411 119.978 4028 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.92 % Allowed : 20.57 % Favored : 75.51 % 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: 2.45 (0.30), residues: 748 helix: 2.25 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.10 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE A 67 TYR 0.023 0.002 TYR F 88 ARG 0.004 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 182 time to evaluate : 0.939 Fit side-chains REVERT: A 42 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7799 (mmm-85) REVERT: C 64 GLU cc_start: 0.7987 (tt0) cc_final: 0.7635 (tp30) REVERT: C 73 ASN cc_start: 0.8910 (t160) cc_final: 0.8370 (t0) REVERT: C 90 ASP cc_start: 0.8164 (t70) cc_final: 0.7798 (t70) REVERT: D 54 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8438 (mmtp) REVERT: E 68 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: F 63 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: F 93 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.6908 (mp10) REVERT: H 30 ARG cc_start: 0.6707 (mtp-110) cc_final: 0.6465 (mtt180) REVERT: H 39 TYR cc_start: 0.7548 (t80) cc_final: 0.7087 (t80) REVERT: H 65 ASP cc_start: 0.8667 (t70) cc_final: 0.8399 (t0) REVERT: H 73 GLU cc_start: 0.8272 (tp30) cc_final: 0.7066 (tp30) REVERT: H 76 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6717 (mtp180) REVERT: H 110 GLU cc_start: 0.7806 (pt0) cc_final: 0.7603 (pt0) outliers start: 25 outliers final: 12 residues processed: 187 average time/residue: 1.8542 time to fit residues: 365.3083 Evaluate side-chains 196 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12822 Z= 0.232 Angle : 0.564 5.402 18556 Z= 0.345 Chirality : 0.034 0.158 2111 Planarity : 0.004 0.043 1344 Dihedral : 31.046 122.833 4028 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.61 % Allowed : 21.19 % Favored : 75.20 % 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: 2.68 (0.30), residues: 748 helix: 2.41 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.02 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE G 25 TYR 0.011 0.002 TYR D 37 ARG 0.008 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8888 (t160) cc_final: 0.8407 (t0) REVERT: C 90 ASP cc_start: 0.8074 (t70) cc_final: 0.7821 (t70) REVERT: D 54 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8411 (mmtp) REVERT: E 68 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8505 (tp40) REVERT: F 63 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: F 93 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.6852 (mp10) REVERT: H 30 ARG cc_start: 0.6649 (mtp-110) cc_final: 0.6447 (mtt180) REVERT: H 65 ASP cc_start: 0.8646 (t70) cc_final: 0.8399 (t0) REVERT: H 76 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6750 (mtp180) REVERT: H 90 GLU cc_start: 0.8096 (mp0) cc_final: 0.6999 (mp0) outliers start: 23 outliers final: 11 residues processed: 191 average time/residue: 1.7712 time to fit residues: 357.2195 Evaluate side-chains 195 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 180 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12822 Z= 0.297 Angle : 0.583 5.482 18556 Z= 0.354 Chirality : 0.036 0.146 2111 Planarity : 0.004 0.042 1344 Dihedral : 31.066 127.606 4028 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.83 % Allowed : 22.92 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.30), residues: 748 helix: 2.41 (0.22), residues: 544 sheet: None (None), residues: 0 loop : 0.11 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE G 25 TYR 0.029 0.002 TYR G 57 ARG 0.011 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7718 (tp30) REVERT: C 73 ASN cc_start: 0.8906 (t160) cc_final: 0.8397 (t0) REVERT: C 90 ASP cc_start: 0.8174 (t70) cc_final: 0.7806 (t70) REVERT: D 54 LYS cc_start: 0.8775 (mmmt) cc_final: 0.8418 (mmtp) REVERT: E 68 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: F 63 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: F 93 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.6892 (mp10) REVERT: H 65 ASP cc_start: 0.8671 (t70) cc_final: 0.8394 (t0) REVERT: H 76 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7379 (mtm-85) outliers start: 18 outliers final: 11 residues processed: 187 average time/residue: 1.8648 time to fit residues: 367.4654 Evaluate side-chains 196 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12822 Z= 0.329 Angle : 0.595 5.517 18556 Z= 0.360 Chirality : 0.037 0.137 2111 Planarity : 0.004 0.041 1344 Dihedral : 31.097 137.560 4028 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.83 % Allowed : 23.23 % Favored : 73.94 % 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: 2.64 (0.30), residues: 748 helix: 2.34 (0.22), residues: 544 sheet: None (None), residues: 0 loop : 0.15 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.013 0.002 PHE G 25 TYR 0.017 0.002 TYR G 57 ARG 0.010 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 0.994 Fit side-chains REVERT: C 64 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7735 (tp30) REVERT: C 73 ASN cc_start: 0.8919 (t160) cc_final: 0.8384 (t0) REVERT: C 90 ASP cc_start: 0.8141 (t70) cc_final: 0.7813 (t70) REVERT: C 91 GLU cc_start: 0.7754 (pm20) cc_final: 0.7532 (pm20) REVERT: D 30 ARG cc_start: 0.8633 (mpt-90) cc_final: 0.8421 (mtt90) REVERT: D 54 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8398 (mmtp) REVERT: E 68 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: F 63 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: F 93 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.6902 (mp10) REVERT: H 65 ASP cc_start: 0.8684 (t70) cc_final: 0.8419 (t0) REVERT: H 73 GLU cc_start: 0.8223 (tp30) cc_final: 0.7107 (tp30) REVERT: H 76 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.6798 (mtp180) REVERT: H 110 GLU cc_start: 0.7708 (pt0) cc_final: 0.7490 (pt0) outliers start: 18 outliers final: 12 residues processed: 186 average time/residue: 1.8416 time to fit residues: 361.4349 Evaluate side-chains 194 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12822 Z= 0.267 Angle : 0.593 5.936 18556 Z= 0.359 Chirality : 0.035 0.145 2111 Planarity : 0.004 0.041 1344 Dihedral : 31.109 137.832 4028 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.98 % Allowed : 23.39 % Favored : 73.63 % 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: 2.68 (0.30), residues: 748 helix: 2.38 (0.22), residues: 544 sheet: None (None), residues: 0 loop : 0.17 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.002 PHE G 25 TYR 0.013 0.002 TYR F 88 ARG 0.009 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 0.972 Fit side-chains REVERT: C 64 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7713 (tp30) REVERT: C 73 ASN cc_start: 0.8913 (t160) cc_final: 0.8376 (t0) REVERT: C 90 ASP cc_start: 0.8134 (t70) cc_final: 0.7830 (t70) REVERT: C 91 GLU cc_start: 0.7764 (pm20) cc_final: 0.7544 (pm20) REVERT: D 30 ARG cc_start: 0.8634 (mpt-90) cc_final: 0.8429 (mtt90) REVERT: D 54 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8395 (mmtp) REVERT: E 68 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: F 63 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: F 93 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.6887 (mp10) REVERT: G 64 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: H 65 ASP cc_start: 0.8680 (t70) cc_final: 0.8412 (t0) REVERT: H 73 GLU cc_start: 0.8236 (tp30) cc_final: 0.7118 (tp30) REVERT: H 76 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6762 (mtp180) outliers start: 19 outliers final: 12 residues processed: 183 average time/residue: 1.7974 time to fit residues: 347.1734 Evaluate side-chains 196 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 24 optimal weight: 0.0570 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12822 Z= 0.252 Angle : 0.589 6.907 18556 Z= 0.358 Chirality : 0.035 0.136 2111 Planarity : 0.004 0.041 1344 Dihedral : 31.101 138.184 4028 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.83 % Allowed : 23.70 % Favored : 73.47 % 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: 2.66 (0.30), residues: 748 helix: 2.34 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.19 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.021 0.002 TYR G 57 ARG 0.009 0.000 ARG D 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 1.046 Fit side-chains REVERT: C 64 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7722 (tp30) REVERT: C 73 ASN cc_start: 0.8911 (t160) cc_final: 0.8374 (t0) REVERT: C 90 ASP cc_start: 0.8130 (t70) cc_final: 0.7848 (t70) REVERT: C 91 GLU cc_start: 0.7768 (pm20) cc_final: 0.7547 (pm20) REVERT: D 54 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8400 (mmtp) REVERT: E 68 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: E 90 MET cc_start: 0.8627 (mmp) cc_final: 0.8397 (mmm) REVERT: F 63 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: F 93 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.6876 (mp10) REVERT: G 64 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: G 74 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8484 (mtmm) REVERT: H 65 ASP cc_start: 0.8674 (t70) cc_final: 0.8409 (t0) REVERT: H 73 GLU cc_start: 0.8233 (tp30) cc_final: 0.7117 (tp30) REVERT: H 76 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6761 (mtp180) outliers start: 18 outliers final: 11 residues processed: 183 average time/residue: 1.8242 time to fit residues: 351.7512 Evaluate side-chains 195 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 178 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.103005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.081816 restraints weight = 20400.559| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.31 r_work: 0.3112 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 12822 Z= 0.252 Angle : 0.588 6.012 18556 Z= 0.357 Chirality : 0.035 0.137 2111 Planarity : 0.004 0.042 1344 Dihedral : 31.081 138.438 4028 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.98 % Allowed : 23.55 % Favored : 73.47 % 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: 2.66 (0.30), residues: 748 helix: 2.33 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.21 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.039 0.002 TYR F 88 ARG 0.010 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5388.78 seconds wall clock time: 94 minutes 50.98 seconds (5690.98 seconds total)