Starting phenix.real_space_refine on Fri Dec 8 00:13:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tea_41179/12_2023/8tea_41179.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tea_41179/12_2023/8tea_41179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tea_41179/12_2023/8tea_41179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tea_41179/12_2023/8tea_41179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tea_41179/12_2023/8tea_41179.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tea_41179/12_2023/8tea_41179.pdb" } resolution = 3.4 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= 0.003 sd= 1.135 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 3798 2.51 5 N 1058 2.21 5 O 1164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6054 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 827 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 847 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "E" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 918 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "G" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 799 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "H" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 919 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "F" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 822 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Time building chain proxies: 3.95, per 1000 atoms: 0.65 Number of scatterers: 6054 At special positions: 0 Unit cell: (72.38, 103.4, 112.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1164 8.00 N 1058 7.00 C 3798 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 49 " distance=2.03 Simple disulfide: pdb=" SG CYS C 31 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 111 " distance=2.04 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 207 " distance=2.02 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS E 40 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 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: 2.08 Conformation dependent library (CDL) restraints added in 1.2 seconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 16 sheets defined 16.7% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 79 through 84 removed outlier: 5.669A pdb=" N HIS C 82 " --> pdb=" O THR C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.568A pdb=" N LEU C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 removed outlier: 3.705A pdb=" N ASN C 97 " --> pdb=" O THR C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 97' Processing helix chain 'D' and resid 119 through 130 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 21 through 26 removed outlier: 4.457A pdb=" N GLU E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 40 removed outlier: 3.521A pdb=" N ALA E 39 " --> pdb=" O HIS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 70 removed outlier: 3.837A pdb=" N LYS E 51 " --> pdb=" O GLN E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.791A pdb=" N VAL E 76 " --> pdb=" O ASN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 95 removed outlier: 4.594A pdb=" N ARG E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN E 95 " --> pdb=" O ASP E 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.844A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.722A pdb=" N GLU I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48 Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AA3, first strand: chain 'C' and resid 130 through 132 removed outlier: 3.845A pdb=" N VAL E 124 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR E 106 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE E 107 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.511A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AA6, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.148A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR H 50 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.148A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N HIS H 108 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 97 through 98 Processing sheet with id=AB2, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.811A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'I' and resid 9 through 11 removed outlier: 3.509A pdb=" N VAL I 11 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 9 through 11 removed outlier: 3.509A pdb=" N VAL I 11 " --> pdb=" O MET I 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 19 through 24 256 hydrogen bonds defined for protein. 618 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1966 1.34 - 1.46: 1381 1.46 - 1.58: 2802 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 6197 Sorted by residual: bond pdb=" CA PHE C 46 " pdb=" CB PHE C 46 " ideal model delta sigma weight residual 1.535 1.569 -0.034 2.09e-02 2.29e+03 2.65e+00 bond pdb=" C TYR C 98 " pdb=" N ASN C 99 " ideal model delta sigma weight residual 1.331 1.290 0.041 2.83e-02 1.25e+03 2.05e+00 bond pdb=" C MET D 125 " pdb=" N PRO D 126 " ideal model delta sigma weight residual 1.335 1.350 -0.016 1.28e-02 6.10e+03 1.53e+00 bond pdb=" C GLN G 53 " pdb=" N ARG G 54 " ideal model delta sigma weight residual 1.331 1.356 -0.025 2.07e-02 2.33e+03 1.49e+00 bond pdb=" N TYR F 100B" pdb=" CA TYR F 100B" ideal model delta sigma weight residual 1.462 1.480 -0.018 1.46e-02 4.69e+03 1.46e+00 ... (remaining 6192 not shown) Histogram of bond angle deviations from ideal: 97.26 - 104.63: 104 104.63 - 111.99: 2938 111.99 - 119.36: 2098 119.36 - 126.72: 3179 126.72 - 134.09: 98 Bond angle restraints: 8417 Sorted by residual: angle pdb=" CA TYR H 33 " pdb=" CB TYR H 33 " pdb=" CG TYR H 33 " ideal model delta sigma weight residual 113.90 120.73 -6.83 1.80e+00 3.09e-01 1.44e+01 angle pdb=" C ASP F 72 " pdb=" N GLU F 73 " pdb=" CA GLU F 73 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" N ASN I 52 " pdb=" CA ASN I 52 " pdb=" C ASN I 52 " ideal model delta sigma weight residual 114.64 109.90 4.74 1.52e+00 4.33e-01 9.74e+00 angle pdb=" C PHE H 27 " pdb=" CA PHE H 27 " pdb=" CB PHE H 27 " ideal model delta sigma weight residual 109.89 114.93 -5.04 1.69e+00 3.50e-01 8.90e+00 angle pdb=" N TYR F 100A" pdb=" CA TYR F 100A" pdb=" C TYR F 100A" ideal model delta sigma weight residual 113.61 118.03 -4.42 1.50e+00 4.44e-01 8.69e+00 ... (remaining 8412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 3365 17.57 - 35.14: 249 35.14 - 52.72: 49 52.72 - 70.29: 9 70.29 - 87.86: 7 Dihedral angle restraints: 3679 sinusoidal: 1432 harmonic: 2247 Sorted by residual: dihedral pdb=" CB CYS C 96 " pdb=" SG CYS C 96 " pdb=" SG CYS C 111 " pdb=" CB CYS C 111 " ideal model delta sinusoidal sigma weight residual 93.00 168.03 -75.03 1 1.00e+01 1.00e-02 7.12e+01 dihedral pdb=" CB CYS C 30 " pdb=" SG CYS C 30 " pdb=" SG CYS C 49 " pdb=" CB CYS C 49 " ideal model delta sinusoidal sigma weight residual -86.00 -33.98 -52.02 1 1.00e+01 1.00e-02 3.69e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 50.11 42.89 1 1.00e+01 1.00e-02 2.57e+01 ... (remaining 3676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 663 0.049 - 0.098: 175 0.098 - 0.147: 72 0.147 - 0.196: 8 0.196 - 0.245: 2 Chirality restraints: 920 Sorted by residual: chirality pdb=" CB THR H 87 " pdb=" CA THR H 87 " pdb=" OG1 THR H 87 " pdb=" CG2 THR H 87 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU F 82 " pdb=" CB LEU F 82 " pdb=" CD1 LEU F 82 " pdb=" CD2 LEU F 82 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL F 18 " pdb=" CA VAL F 18 " pdb=" CG1 VAL F 18 " pdb=" CG2 VAL F 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 917 not shown) Planarity restraints: 1087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 114 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO E 115 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO E 115 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO E 115 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 36 " 0.025 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP F 36 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP F 36 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP F 36 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 36 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP F 36 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP F 36 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 36 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP F 36 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 46 " 0.017 2.00e-02 2.50e+03 2.03e-02 7.23e+00 pdb=" CG PHE C 46 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE C 46 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 46 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE C 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 46 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 46 " 0.002 2.00e-02 2.50e+03 ... (remaining 1084 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1310 2.78 - 3.31: 5057 3.31 - 3.84: 9976 3.84 - 4.37: 11414 4.37 - 4.90: 20226 Nonbonded interactions: 47983 Sorted by model distance: nonbonded pdb=" O ARG C 74 " pdb=" OG1 THR C 78 " model vdw 2.256 2.440 nonbonded pdb=" OE1 GLN H 39 " pdb=" OH TYR H 91 " model vdw 2.280 2.440 nonbonded pdb=" N PHE H 29 " pdb=" OH TYR H 32 " model vdw 2.304 2.520 nonbonded pdb=" O GLY I 25 " pdb=" OG1 THR I 69 " model vdw 2.312 2.440 nonbonded pdb=" OH TYR D 169 " pdb=" O TYR F 100 " model vdw 2.332 2.440 ... (remaining 47978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 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: 3.220 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: 0.000 Extract box with map and model: 12.660 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.980 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6197 Z= 0.278 Angle : 0.740 9.227 8417 Z= 0.409 Chirality : 0.052 0.245 920 Planarity : 0.008 0.117 1087 Dihedral : 13.184 87.862 2222 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.30 % Allowed : 0.15 % Favored : 99.55 % 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: -0.71 (0.29), residues: 766 helix: -1.08 (0.53), residues: 80 sheet: 0.56 (0.32), residues: 229 loop : -0.91 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP F 36 HIS 0.007 0.001 HIS H 108 PHE 0.047 0.002 PHE C 46 TYR 0.022 0.002 TYR G 49 ARG 0.005 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.716 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 98 average time/residue: 0.1954 time to fit residues: 24.9393 Evaluate side-chains 96 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.630 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.0270 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95AASN F 6 GLN F 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 6197 Z= 0.398 Angle : 0.646 9.368 8417 Z= 0.353 Chirality : 0.047 0.167 920 Planarity : 0.006 0.075 1087 Dihedral : 5.641 23.844 865 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.36 % Allowed : 9.34 % Favored : 89.31 % 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: -0.93 (0.29), residues: 766 helix: -0.81 (0.53), residues: 88 sheet: 0.19 (0.31), residues: 234 loop : -1.02 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 36 HIS 0.005 0.001 HIS C 82 PHE 0.025 0.002 PHE E 122 TYR 0.019 0.002 TYR H 33 ARG 0.007 0.001 ARG G 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.680 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 98 average time/residue: 0.1906 time to fit residues: 24.3856 Evaluate side-chains 96 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0572 time to fit residues: 1.2581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95AASN F 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6197 Z= 0.330 Angle : 0.635 18.341 8417 Z= 0.339 Chirality : 0.046 0.186 920 Planarity : 0.005 0.059 1087 Dihedral : 5.507 27.575 865 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.81 % Allowed : 11.45 % Favored : 86.75 % 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: -0.85 (0.29), residues: 766 helix: -0.72 (0.52), residues: 94 sheet: 0.29 (0.31), residues: 233 loop : -1.00 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 36 HIS 0.004 0.001 HIS H 108 PHE 0.024 0.002 PHE E 122 TYR 0.022 0.002 TYR G 49 ARG 0.004 0.000 ARG G 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.703 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 98 average time/residue: 0.2113 time to fit residues: 26.9867 Evaluate side-chains 97 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1126 time to fit residues: 2.0076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 35 optimal weight: 0.1980 chunk 7 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 19 optimal weight: 0.0020 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 GLN G 95AASN F 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6197 Z= 0.227 Angle : 0.596 17.008 8417 Z= 0.316 Chirality : 0.045 0.327 920 Planarity : 0.005 0.053 1087 Dihedral : 5.154 29.196 865 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.96 % Allowed : 13.55 % Favored : 84.49 % 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: -0.65 (0.30), residues: 766 helix: -0.36 (0.54), residues: 94 sheet: 0.31 (0.31), residues: 240 loop : -0.86 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 36 HIS 0.004 0.001 HIS H 108 PHE 0.021 0.001 PHE E 122 TYR 0.024 0.002 TYR G 49 ARG 0.003 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.662 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 97 average time/residue: 0.2040 time to fit residues: 25.5913 Evaluate side-chains 97 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0647 time to fit residues: 1.6213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95AASN F 39 GLN I 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6197 Z= 0.275 Angle : 0.613 11.528 8417 Z= 0.325 Chirality : 0.046 0.322 920 Planarity : 0.005 0.048 1087 Dihedral : 5.170 27.457 865 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.11 % Allowed : 15.21 % Favored : 82.68 % 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: -0.63 (0.29), residues: 766 helix: -0.10 (0.55), residues: 88 sheet: 0.32 (0.31), residues: 235 loop : -0.89 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 36 HIS 0.004 0.001 HIS H 108 PHE 0.022 0.002 PHE E 122 TYR 0.021 0.002 TYR G 49 ARG 0.003 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.682 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 103 average time/residue: 0.1866 time to fit residues: 25.5154 Evaluate side-chains 101 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0727 time to fit residues: 1.9349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95AASN F 39 GLN I 37 GLN I 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 6197 Z= 0.434 Angle : 0.698 19.822 8417 Z= 0.373 Chirality : 0.050 0.393 920 Planarity : 0.005 0.046 1087 Dihedral : 5.710 40.468 865 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.56 % Allowed : 16.42 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.06 (0.29), residues: 766 helix: -0.56 (0.53), residues: 93 sheet: 0.08 (0.30), residues: 252 loop : -1.23 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP F 36 HIS 0.005 0.001 HIS H 108 PHE 0.026 0.002 PHE E 122 TYR 0.023 0.002 TYR H 50 ARG 0.006 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.692 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 105 average time/residue: 0.1887 time to fit residues: 25.9113 Evaluate side-chains 101 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1245 time to fit residues: 2.3735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 44 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95AASN F 39 GLN I 37 GLN I 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6197 Z= 0.329 Angle : 0.665 18.862 8417 Z= 0.352 Chirality : 0.047 0.369 920 Planarity : 0.005 0.045 1087 Dihedral : 5.557 39.268 865 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.90 % Allowed : 17.32 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.03 (0.29), residues: 766 helix: -0.63 (0.52), residues: 94 sheet: 0.20 (0.32), residues: 231 loop : -1.20 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP F 36 HIS 0.004 0.001 HIS H 108 PHE 0.023 0.002 PHE E 122 TYR 0.024 0.002 TYR G 49 ARG 0.004 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.680 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 95 average time/residue: 0.2067 time to fit residues: 25.4674 Evaluate side-chains 94 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.681 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0566 time to fit residues: 1.0640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.1980 chunk 46 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 36 optimal weight: 0.0670 chunk 6 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95AASN F 39 GLN I 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 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 : 0.004 0.044 6197 Z= 0.250 Angle : 0.619 15.696 8417 Z= 0.325 Chirality : 0.045 0.278 920 Planarity : 0.004 0.044 1087 Dihedral : 5.339 36.596 865 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.90 % Allowed : 18.52 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.14 % 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: -0.88 (0.29), residues: 766 helix: -0.51 (0.52), residues: 94 sheet: 0.38 (0.32), residues: 229 loop : -1.15 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 36 HIS 0.004 0.001 HIS H 108 PHE 0.023 0.001 PHE E 122 TYR 0.025 0.002 TYR G 49 ARG 0.003 0.000 ARG G 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.694 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 98 average time/residue: 0.2138 time to fit residues: 27.0043 Evaluate side-chains 96 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0612 time to fit residues: 1.1273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 20 optimal weight: 0.0060 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95AASN F 6 GLN F 39 GLN I 37 GLN I 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 6197 Z= 0.369 Angle : 0.686 15.082 8417 Z= 0.358 Chirality : 0.047 0.230 920 Planarity : 0.005 0.046 1087 Dihedral : 5.694 40.613 865 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.90 % Allowed : 19.13 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.14 % 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: -0.98 (0.29), residues: 766 helix: -0.53 (0.52), residues: 94 sheet: 0.25 (0.32), residues: 229 loop : -1.19 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP F 36 HIS 0.004 0.001 HIS H 108 PHE 0.026 0.002 PHE E 122 TYR 0.023 0.002 TYR H 50 ARG 0.006 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.676 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 96 average time/residue: 0.1938 time to fit residues: 24.4233 Evaluate side-chains 95 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0609 time to fit residues: 1.1892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.0570 chunk 60 optimal weight: 0.0060 chunk 6 optimal weight: 0.3980 chunk 46 optimal weight: 0.0370 chunk 36 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 overall best weight: 0.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95AASN F 39 GLN I 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6197 Z= 0.179 Angle : 0.598 11.308 8417 Z= 0.309 Chirality : 0.044 0.157 920 Planarity : 0.004 0.044 1087 Dihedral : 5.211 41.360 865 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.30 % Allowed : 18.83 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.14 % 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: -0.69 (0.30), residues: 766 helix: -0.13 (0.52), residues: 92 sheet: 0.45 (0.33), residues: 228 loop : -1.03 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP F 36 HIS 0.002 0.001 HIS H 108 PHE 0.027 0.001 PHE E 122 TYR 0.025 0.002 TYR G 49 ARG 0.004 0.000 ARG F 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.719 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.2135 time to fit residues: 27.3115 Evaluate side-chains 97 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.677 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.0470 chunk 69 optimal weight: 0.3980 chunk 40 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95AASN F 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.165913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.147314 restraints weight = 8929.170| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.18 r_work: 0.3843 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6197 Z= 0.279 Angle : 0.632 10.975 8417 Z= 0.332 Chirality : 0.045 0.170 920 Planarity : 0.005 0.044 1087 Dihedral : 5.305 39.609 865 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.75 % Allowed : 18.37 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.14 % 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: -0.68 (0.30), residues: 766 helix: -0.05 (0.52), residues: 94 sheet: 0.40 (0.33), residues: 228 loop : -1.01 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP F 36 HIS 0.004 0.001 HIS H 108 PHE 0.025 0.001 PHE E 122 TYR 0.024 0.002 TYR G 49 ARG 0.005 0.000 ARG C 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1931.27 seconds wall clock time: 35 minutes 32.08 seconds (2132.08 seconds total)