Starting phenix.real_space_refine on Fri Dec 27 16:48:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tea_41179/12_2024/8tea_41179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tea_41179/12_2024/8tea_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/cci-nas-00/data/ceres_data/8tea_41179/12_2024/8tea_41179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tea_41179/12_2024/8tea_41179.map" model { file = "/net/cci-nas-00/data/ceres_data/8tea_41179/12_2024/8tea_41179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tea_41179/12_2024/8tea_41179.cif" } 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. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.89, per 1000 atoms: 0.81 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 981.7 milliseconds 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: 1.04 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: 1.83 Time building geometry restraints manager: 1.68 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: 0.00 - 1.85: 8124 1.85 - 3.69: 253 3.69 - 5.54: 32 5.54 - 7.38: 6 7.38 - 9.23: 2 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 3.040 nonbonded pdb=" OE1 GLN H 39 " pdb=" OH TYR H 91 " model vdw 2.280 3.040 nonbonded pdb=" N PHE H 29 " pdb=" OH TYR H 32 " model vdw 2.304 3.120 nonbonded pdb=" O GLY I 25 " pdb=" OG1 THR I 69 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR D 169 " pdb=" O TYR F 100 " model vdw 2.332 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.080 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.570 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: C 109 ILE cc_start: 0.7687 (mm) cc_final: 0.7450 (mm) REVERT: F 39 GLN cc_start: 0.5994 (OUTLIER) cc_final: 0.5650 (pt0) REVERT: I 52 ASN cc_start: 0.7523 (t0) cc_final: 0.7281 (t0) outliers start: 2 outliers final: 0 residues processed: 98 average time/residue: 0.1945 time to fit residues: 24.9190 Evaluate side-chains 96 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 39 GLN 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: 0.0980 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6197 Z= 0.321 Angle : 0.612 7.540 8417 Z= 0.334 Chirality : 0.046 0.159 920 Planarity : 0.006 0.075 1087 Dihedral : 5.499 22.207 868 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.36 % Allowed : 9.04 % Favored : 89.61 % 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: -0.78 (0.29), residues: 766 helix: -0.55 (0.55), residues: 88 sheet: 0.33 (0.31), residues: 233 loop : -0.98 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 36 HIS 0.004 0.001 HIS C 82 PHE 0.024 0.002 PHE E 122 TYR 0.017 0.002 TYR H 33 ARG 0.004 0.001 ARG H 71 *********************** 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 103 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: C 109 ILE cc_start: 0.7784 (mm) cc_final: 0.7554 (mm) REVERT: F 100 MET cc_start: 0.6613 (mmt) cc_final: 0.6272 (mmt) REVERT: I 52 ASN cc_start: 0.7532 (t0) cc_final: 0.7105 (t0) outliers start: 9 outliers final: 5 residues processed: 95 average time/residue: 0.2067 time to fit residues: 25.8394 Evaluate side-chains 96 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 22 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 23 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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 37 GLN G 95AASN F 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6197 Z= 0.215 Angle : 0.589 17.886 8417 Z= 0.313 Chirality : 0.044 0.154 920 Planarity : 0.005 0.061 1087 Dihedral : 5.123 23.475 865 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.41 % Allowed : 9.19 % Favored : 88.40 % 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 (0.29), residues: 766 helix: -0.26 (0.55), residues: 94 sheet: 0.41 (0.31), residues: 233 loop : -0.93 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 36 HIS 0.004 0.001 HIS H 108 PHE 0.020 0.001 PHE E 122 TYR 0.025 0.002 TYR G 49 ARG 0.004 0.000 ARG H 71 *********************** 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 108 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.620 Fit side-chains REVERT: D 151 MET cc_start: 0.5821 (mmt) cc_final: 0.5174 (tpp) REVERT: F 100 MET cc_start: 0.6462 (mmt) cc_final: 0.6127 (mmt) REVERT: I 103 MET cc_start: 0.6889 (tmm) cc_final: 0.6438 (tmm) outliers start: 16 outliers final: 8 residues processed: 96 average time/residue: 0.2119 time to fit residues: 26.7243 Evaluate side-chains 96 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 27 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 32 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 65 optimal weight: 0.0470 chunk 19 optimal weight: 0.4980 overall best weight: 0.2278 ------------------------------------------------------------------------------- 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: 0.6605 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6197 Z= 0.181 Angle : 0.559 12.672 8417 Z= 0.298 Chirality : 0.044 0.272 920 Planarity : 0.004 0.054 1087 Dihedral : 4.757 19.120 865 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.41 % Allowed : 11.90 % Favored : 85.69 % 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: -0.46 (0.30), residues: 766 helix: 0.12 (0.56), residues: 94 sheet: 0.43 (0.31), residues: 239 loop : -0.81 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 36 HIS 0.003 0.001 HIS H 108 PHE 0.019 0.001 PHE E 122 TYR 0.021 0.001 TYR G 49 ARG 0.005 0.000 ARG C 57 *********************** 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 to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.669 Fit side-chains REVERT: D 151 MET cc_start: 0.5781 (mmt) cc_final: 0.4295 (mmt) REVERT: F 100 MET cc_start: 0.6359 (mmt) cc_final: 0.6044 (mmt) REVERT: I 103 MET cc_start: 0.6970 (tmm) cc_final: 0.6524 (tmm) outliers start: 16 outliers final: 10 residues processed: 95 average time/residue: 0.1939 time to fit residues: 24.7270 Evaluate side-chains 98 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 27 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 1 optimal weight: 0.0170 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 0.0030 chunk 18 optimal weight: 0.9990 overall best weight: 0.3028 ------------------------------------------------------------------------------- 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: 0.6620 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6197 Z= 0.211 Angle : 0.594 22.614 8417 Z= 0.314 Chirality : 0.045 0.330 920 Planarity : 0.004 0.050 1087 Dihedral : 4.801 21.745 865 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.71 % Allowed : 13.70 % Favored : 83.58 % 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: -0.42 (0.30), residues: 766 helix: 0.26 (0.56), residues: 94 sheet: 0.55 (0.31), residues: 232 loop : -0.86 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 36 HIS 0.003 0.001 HIS H 108 PHE 0.018 0.001 PHE E 122 TYR 0.019 0.002 TYR H 33 ARG 0.002 0.000 ARG H 71 *********************** 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 111 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.656 Fit side-chains REVERT: D 151 MET cc_start: 0.5845 (mmt) cc_final: 0.4387 (mmt) REVERT: F 100 MET cc_start: 0.6363 (mmt) cc_final: 0.6087 (mmt) REVERT: I 103 MET cc_start: 0.6959 (tmm) cc_final: 0.6572 (tmm) outliers start: 18 outliers final: 11 residues processed: 101 average time/residue: 0.1958 time to fit residues: 26.0018 Evaluate side-chains 101 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 27 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 6 optimal weight: 0.2980 chunk 38 optimal weight: 0.1980 chunk 70 optimal weight: 0.0170 overall best weight: 0.2018 ------------------------------------------------------------------------------- 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: 0.6591 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6197 Z= 0.171 Angle : 0.593 20.397 8417 Z= 0.312 Chirality : 0.044 0.307 920 Planarity : 0.004 0.047 1087 Dihedral : 4.717 33.714 865 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.71 % Allowed : 14.16 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.27 (0.30), residues: 766 helix: 0.50 (0.57), residues: 94 sheet: 0.66 (0.32), residues: 232 loop : -0.79 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 36 HIS 0.003 0.001 HIS H 108 PHE 0.017 0.001 PHE E 122 TYR 0.017 0.001 TYR H 33 ARG 0.003 0.000 ARG C 42 *********************** 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 110 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.685 Fit side-chains REVERT: D 151 MET cc_start: 0.5739 (mmt) cc_final: 0.4356 (mmt) REVERT: F 100 MET cc_start: 0.6309 (mmt) cc_final: 0.6092 (mmt) REVERT: I 82 ASP cc_start: 0.6946 (m-30) cc_final: 0.6626 (m-30) REVERT: I 103 MET cc_start: 0.6947 (tmm) cc_final: 0.6577 (tmm) outliers start: 18 outliers final: 12 residues processed: 100 average time/residue: 0.1944 time to fit residues: 25.5987 Evaluate side-chains 101 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 27 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.0470 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6197 Z= 0.330 Angle : 0.659 17.525 8417 Z= 0.351 Chirality : 0.046 0.244 920 Planarity : 0.005 0.045 1087 Dihedral : 5.249 40.218 865 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.01 % Allowed : 14.01 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.51 (0.29), residues: 766 helix: 0.23 (0.55), residues: 94 sheet: 0.39 (0.32), residues: 238 loop : -0.88 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP F 36 HIS 0.004 0.001 HIS H 108 PHE 0.023 0.002 PHE E 122 TYR 0.021 0.002 TYR H 33 ARG 0.005 0.000 ARG G 96 *********************** 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 114 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.784 Fit side-chains REVERT: D 151 MET cc_start: 0.5653 (mmt) cc_final: 0.4101 (mmt) REVERT: F 100 MET cc_start: 0.6610 (mmt) cc_final: 0.6271 (mmt) REVERT: I 103 MET cc_start: 0.6942 (tmm) cc_final: 0.6487 (tmm) outliers start: 20 outliers final: 15 residues processed: 102 average time/residue: 0.1869 time to fit residues: 25.4571 Evaluate side-chains 108 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain F residue 36 TRP Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 27 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.5980 chunk 46 optimal weight: 0.0980 chunk 49 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.6661 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6197 Z= 0.283 Angle : 0.616 15.840 8417 Z= 0.330 Chirality : 0.046 0.219 920 Planarity : 0.005 0.048 1087 Dihedral : 5.234 40.920 865 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.01 % Allowed : 14.31 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.51 (0.29), residues: 766 helix: 0.26 (0.54), residues: 94 sheet: 0.32 (0.32), residues: 238 loop : -0.84 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP F 36 HIS 0.004 0.001 HIS H 108 PHE 0.026 0.001 PHE E 122 TYR 0.019 0.002 TYR H 50 ARG 0.004 0.000 ARG C 74 *********************** 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 115 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: D 151 MET cc_start: 0.5567 (mmt) cc_final: 0.4089 (mmt) REVERT: F 100 MET cc_start: 0.6522 (mmt) cc_final: 0.6267 (mmt) REVERT: I 103 MET cc_start: 0.6959 (tmm) cc_final: 0.6510 (tmm) outliers start: 20 outliers final: 14 residues processed: 105 average time/residue: 0.2308 time to fit residues: 33.1351 Evaluate side-chains 109 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain F residue 36 TRP Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 22 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.6701 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 6197 Z= 0.395 Angle : 0.711 16.910 8417 Z= 0.377 Chirality : 0.048 0.225 920 Planarity : 0.005 0.050 1087 Dihedral : 5.617 39.905 865 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.01 % Allowed : 14.76 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.73 (0.30), residues: 766 helix: -0.12 (0.52), residues: 94 sheet: 0.23 (0.32), residues: 245 loop : -0.99 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP F 36 HIS 0.005 0.001 HIS H 108 PHE 0.029 0.002 PHE E 122 TYR 0.027 0.002 TYR H 50 ARG 0.005 0.001 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 115 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: D 125 MET cc_start: 0.4015 (tpt) cc_final: 0.3483 (tpt) REVERT: D 151 MET cc_start: 0.5592 (mmt) cc_final: 0.4114 (mmt) REVERT: F 100 MET cc_start: 0.6687 (mmt) cc_final: 0.6346 (mmt) REVERT: I 103 MET cc_start: 0.6968 (tmm) cc_final: 0.6503 (tmm) outliers start: 20 outliers final: 14 residues processed: 103 average time/residue: 0.2145 time to fit residues: 28.8687 Evaluate side-chains 109 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain F residue 36 TRP Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 36 optimal weight: 0.1980 chunk 47 optimal weight: 0.0050 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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: 0.6648 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6197 Z= 0.250 Angle : 0.622 13.555 8417 Z= 0.332 Chirality : 0.045 0.191 920 Planarity : 0.004 0.048 1087 Dihedral : 5.291 40.956 865 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.26 % Allowed : 15.96 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.65 (0.30), residues: 766 helix: 0.09 (0.53), residues: 94 sheet: 0.23 (0.32), residues: 238 loop : -0.91 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP F 36 HIS 0.003 0.001 HIS H 108 PHE 0.027 0.001 PHE E 122 TYR 0.021 0.002 TYR H 50 ARG 0.004 0.000 ARG C 74 ********************** 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 109 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: D 125 MET cc_start: 0.4247 (tpt) cc_final: 0.3734 (tpt) REVERT: D 151 MET cc_start: 0.5515 (mmt) cc_final: 0.4123 (mmt) REVERT: I 103 MET cc_start: 0.6970 (tmm) cc_final: 0.6500 (tmm) outliers start: 15 outliers final: 12 residues processed: 99 average time/residue: 0.1793 time to fit residues: 23.7738 Evaluate side-chains 105 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain F residue 36 TRP Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.0040 chunk 25 optimal weight: 0.0970 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 11 optimal weight: 0.0050 chunk 53 optimal weight: 0.4980 chunk 3 optimal weight: 0.0010 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.0410 ------------------------------------------------------------------------------- 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 6 GLN I 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.171708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.153650 restraints weight = 8913.627| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.16 r_work: 0.3930 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6197 Z= 0.142 Angle : 0.549 9.961 8417 Z= 0.292 Chirality : 0.043 0.145 920 Planarity : 0.004 0.046 1087 Dihedral : 4.710 39.100 865 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.51 % Allowed : 17.02 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.14 (0.30), residues: 766 helix: 1.14 (0.58), residues: 84 sheet: 0.42 (0.32), residues: 240 loop : -0.62 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F 36 HIS 0.002 0.000 HIS F 98 PHE 0.024 0.001 PHE E 122 TYR 0.015 0.001 TYR H 32 ARG 0.003 0.000 ARG H 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1914.78 seconds wall clock time: 35 minutes 44.32 seconds (2144.32 seconds total)