Starting phenix.real_space_refine on Tue Aug 4 20:53:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yxv_73618/08_2026/9yxv_73618.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yxv_73618/08_2026/9yxv_73618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yxv_73618/08_2026/9yxv_73618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yxv_73618/08_2026/9yxv_73618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yxv_73618/08_2026/9yxv_73618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yxv_73618/08_2026/9yxv_73618.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 21 5.16 5 C 4110 2.51 5 N 1084 2.21 5 O 1327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6554 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 751 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'RNA': 12} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "C" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 459 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "D" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 963 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "H" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1684 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1609 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DMU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 1.59, per 1000 atoms: 0.24 Number of scatterers: 6554 At special positions: 0 Unit cell: (77.964, 97.188, 110.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 12 15.00 O 1327 8.00 N 1084 7.00 C 4110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 132 " - pdb=" SG CYS L 192 " distance=2.03 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: 0.57 Conformation dependent library (CDL) restraints added in 354.5 milliseconds 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 15 sheets defined 11.9% alpha, 41.2% beta 1 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 61 through 73 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'C' and resid 27 through 42 removed outlier: 3.521A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.900A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 31 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 97 through 100A removed outlier: 4.051A pdb=" N PHE H 100 " --> pdb=" O TRP H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.798A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 125 Processing helix chain 'L' and resid 181 through 185 removed outlier: 4.087A pdb=" N GLU L 185 " --> pdb=" O LYS L 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 181 through 185' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 45 removed outlier: 3.823A pdb=" N ASP A 42 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 83 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 49 through 51 removed outlier: 8.561A pdb=" N PHE C 57 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS C 9 " --> pdb=" O PHE C 57 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL C 59 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C 11 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.205A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.355A pdb=" N SER E 33 " --> pdb=" O ASN E 95 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.098A pdb=" N TYR E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.511A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY H 16 " --> pdb=" O SER H 82B" (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.834A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.369A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.369A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.549A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.515A pdb=" N VAL L 131 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N TYR L 171 " --> pdb=" O ASN L 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 151 through 152 281 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.75 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: 1993 1.34 - 1.46: 1320 1.46 - 1.57: 3366 1.57 - 1.69: 23 1.69 - 1.81: 30 Bond restraints: 6732 Sorted by residual: bond pdb=" C9 DMU A 101 " pdb=" O1 DMU A 101 " ideal model delta sigma weight residual 1.420 1.539 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C11 DMU A 101 " pdb=" C9 DMU A 101 " ideal model delta sigma weight residual 1.513 1.403 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C7 DMU A 101 " pdb=" O4 DMU A 101 " ideal model delta sigma weight residual 1.411 1.485 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C6 DMU A 101 " pdb=" O5 DMU A 101 " ideal model delta sigma weight residual 1.405 1.477 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C4 DMU A 101 " pdb=" O5 DMU A 101 " ideal model delta sigma weight residual 1.411 1.480 -0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 6727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 8940 1.83 - 3.67: 206 3.67 - 5.50: 35 5.50 - 7.33: 12 7.33 - 9.17: 7 Bond angle restraints: 9200 Sorted by residual: angle pdb=" O5' C B1013 " pdb=" C5' C B1013 " pdb=" C4' C B1013 " ideal model delta sigma weight residual 109.40 113.20 -3.80 8.00e-01 1.56e+00 2.26e+01 angle pdb=" CA GLU C 43 " pdb=" CB GLU C 43 " pdb=" CG GLU C 43 " ideal model delta sigma weight residual 114.10 122.73 -8.63 2.00e+00 2.50e-01 1.86e+01 angle pdb=" CA GLU L 141 " pdb=" CB GLU L 141 " pdb=" CG GLU L 141 " ideal model delta sigma weight residual 114.10 122.11 -8.01 2.00e+00 2.50e-01 1.60e+01 angle pdb=" CB LYS H 43 " pdb=" CG LYS H 43 " pdb=" CD LYS H 43 " ideal model delta sigma weight residual 111.30 120.47 -9.17 2.30e+00 1.89e-01 1.59e+01 angle pdb=" CB LYS D 42 " pdb=" CG LYS D 42 " pdb=" CD LYS D 42 " ideal model delta sigma weight residual 111.30 119.75 -8.45 2.30e+00 1.89e-01 1.35e+01 ... (remaining 9195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.38: 3777 26.38 - 52.76: 211 52.76 - 79.13: 47 79.13 - 105.51: 2 105.51 - 131.89: 11 Dihedral angle restraints: 4048 sinusoidal: 1679 harmonic: 2369 Sorted by residual: dihedral pdb=" O5 DMU A 101 " pdb=" C4 DMU A 101 " pdb=" C57 DMU A 101 " pdb=" O61 DMU A 101 " ideal model delta sinusoidal sigma weight residual 65.79 -66.10 131.89 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C3 DMU A 101 " pdb=" C4 DMU A 101 " pdb=" C57 DMU A 101 " pdb=" O61 DMU A 101 " ideal model delta sinusoidal sigma weight residual 186.53 56.12 130.41 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CA TYR L 94 " pdb=" C TYR L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 4045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 745 0.038 - 0.077: 194 0.077 - 0.115: 79 0.115 - 0.154: 22 0.154 - 0.192: 3 Chirality restraints: 1043 Sorted by residual: chirality pdb=" CA TYR L 94 " pdb=" N TYR L 94 " pdb=" C TYR L 94 " pdb=" CB TYR L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA GLU C 43 " pdb=" N GLU C 43 " pdb=" C GLU C 43 " pdb=" CB GLU C 43 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" C10 DMU A 101 " pdb=" C5 DMU A 101 " pdb=" O1 DMU A 101 " pdb=" O7 DMU A 101 " both_signs ideal model delta sigma weight residual False 2.22 2.39 -0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 1040 not shown) Planarity restraints: 1114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 43 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C GLU C 43 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU C 43 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL C 44 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 94 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO D 95 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 24 " 0.133 9.50e-02 1.11e+02 6.02e-02 2.90e+00 pdb=" NE ARG D 24 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 24 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 24 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 24 " 0.000 2.00e-02 2.50e+03 ... (remaining 1111 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 681 2.75 - 3.29: 5886 3.29 - 3.83: 10849 3.83 - 4.36: 12715 4.36 - 4.90: 22820 Nonbonded interactions: 52951 Sorted by model distance: nonbonded pdb=" OG1 THR C 22 " pdb=" O SER H 203 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 48 " pdb=" OP1 C B1014 " model vdw 2.232 3.040 nonbonded pdb=" N GLU L 185 " pdb=" OE1 GLU L 185 " model vdw 2.265 3.120 nonbonded pdb=" O SER L 67 " pdb=" OG SER L 67 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP A 79 " pdb=" OH TYR H 56 " model vdw 2.273 3.040 ... (remaining 52946 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: 3.330 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.350 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 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 0.119 6738 Z= 0.216 Angle : 0.682 9.167 9212 Z= 0.375 Chirality : 0.044 0.192 1043 Planarity : 0.005 0.060 1114 Dihedral : 17.610 131.890 2518 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.29 % Allowed : 21.50 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.30), residues: 799 helix: 0.83 (0.77), residues: 44 sheet: 0.55 (0.28), residues: 354 loop : -0.05 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 18 TYR 0.022 0.001 TYR L 94 PHE 0.006 0.001 PHE A 56 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 ( 6732) covalent geometry : angle 0.68265 / 0.37 ( 9200) SS BOND : bond 0.00135 / 0.06 ( 6) SS BOND : angle 0.39967 / 0.27 ( 12) hydrogen bonds : bond 0.23350 / 15.59 ( 264) hydrogen bonds : angle 8.45800 / 6.16 ( 714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: H 72 ASP cc_start: 0.8066 (t0) cc_final: 0.7627 (t0) outliers start: 2 outliers final: 2 residues processed: 125 average time/residue: 0.6973 time to fit residues: 90.8361 Evaluate side-chains 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain L residue 197 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 GLN C 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.068034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.053402 restraints weight = 15109.924| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.92 r_work: 0.2651 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6738 Z= 0.160 Angle : 0.630 7.649 9212 Z= 0.331 Chirality : 0.044 0.191 1043 Planarity : 0.005 0.069 1114 Dihedral : 14.582 112.197 1127 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.32 % Allowed : 17.60 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.30), residues: 799 helix: 1.28 (0.84), residues: 46 sheet: 0.76 (0.27), residues: 363 loop : 0.07 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 18 TYR 0.026 0.001 TYR L 94 PHE 0.006 0.001 PHE L 118 TRP 0.010 0.001 TRP E 103 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 6732) covalent geometry : angle 0.62599 / 0.33 ( 9200) SS BOND : bond 0.01160 / 0.86 ( 6) SS BOND : angle 2.02598 / 1.50 ( 12) hydrogen bonds : bond 0.04562 / 3.03 ( 264) hydrogen bonds : angle 6.25826 / 4.66 ( 714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.8930 (m) cc_final: 0.8694 (p) REVERT: C 43 GLU cc_start: 0.8793 (pt0) cc_final: 0.8242 (pp20) REVERT: D 24 ARG cc_start: 0.8288 (ttm110) cc_final: 0.8044 (ttm110) REVERT: H 72 ASP cc_start: 0.8495 (t0) cc_final: 0.7976 (t0) REVERT: L 165 ASP cc_start: 0.8483 (t0) cc_final: 0.8185 (t0) REVERT: L 190 TYR cc_start: 0.8640 (m-80) cc_final: 0.8376 (m-80) outliers start: 23 outliers final: 10 residues processed: 127 average time/residue: 0.6680 time to fit residues: 88.5511 Evaluate side-chains 122 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 197 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.067261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.052643 restraints weight = 15153.467| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.90 r_work: 0.2632 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6738 Z= 0.168 Angle : 0.613 8.715 9212 Z= 0.316 Chirality : 0.044 0.202 1043 Planarity : 0.005 0.070 1114 Dihedral : 13.089 111.024 1126 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.88 % Favored : 97.00 % Rotamer: Outliers : 3.32 % Allowed : 18.18 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.30), residues: 799 helix: 0.99 (0.82), residues: 48 sheet: 0.85 (0.27), residues: 365 loop : 0.14 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 18 TYR 0.029 0.001 TYR L 94 PHE 0.007 0.001 PHE L 118 TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 6732) covalent geometry : angle 0.61114 / 0.31 ( 9200) SS BOND : bond 0.00326 / 0.15 ( 6) SS BOND : angle 1.32500 / 0.92 ( 12) hydrogen bonds : bond 0.03993 / 2.70 ( 264) hydrogen bonds : angle 5.53978 / 4.10 ( 714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7996 (pt) REVERT: A 61 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8366 (mm-30) REVERT: A 64 SER cc_start: 0.8920 (m) cc_final: 0.8695 (p) REVERT: C 43 GLU cc_start: 0.8807 (pt0) cc_final: 0.8174 (pp20) REVERT: D 24 ARG cc_start: 0.8281 (ttm110) cc_final: 0.7942 (ttm110) REVERT: D 42 LYS cc_start: 0.8649 (mppt) cc_final: 0.8252 (mppt) REVERT: D 70 ASP cc_start: 0.8567 (m-30) cc_final: 0.8177 (m-30) REVERT: H 72 ASP cc_start: 0.8498 (t0) cc_final: 0.7592 (t0) REVERT: H 75 LYS cc_start: 0.9102 (ptpp) cc_final: 0.8524 (ptpp) REVERT: H 85 GLU cc_start: 0.8961 (pm20) cc_final: 0.8676 (pp20) REVERT: L 94 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7487 (t80) REVERT: L 165 ASP cc_start: 0.8637 (t0) cc_final: 0.8324 (t0) REVERT: L 190 TYR cc_start: 0.8747 (m-80) cc_final: 0.8336 (m-10) outliers start: 23 outliers final: 15 residues processed: 130 average time/residue: 0.6823 time to fit residues: 92.6045 Evaluate side-chains 127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 197 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.065748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.051223 restraints weight = 15361.838| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.88 r_work: 0.2583 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6738 Z= 0.229 Angle : 0.621 7.900 9212 Z= 0.322 Chirality : 0.044 0.226 1043 Planarity : 0.004 0.076 1114 Dihedral : 12.069 109.348 1126 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.00 % Favored : 96.87 % Rotamer: Outliers : 3.03 % Allowed : 18.76 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.30), residues: 799 helix: 0.93 (0.82), residues: 48 sheet: 0.93 (0.27), residues: 362 loop : 0.18 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 18 TYR 0.032 0.002 TYR L 94 PHE 0.009 0.001 PHE L 118 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 ( 6732) covalent geometry : angle 0.61869 / 0.32 ( 9200) SS BOND : bond 0.00504 / 0.31 ( 6) SS BOND : angle 1.73918 / 1.27 ( 12) hydrogen bonds : bond 0.03723 / 2.53 ( 264) hydrogen bonds : angle 5.31959 / 3.96 ( 714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: C 43 GLU cc_start: 0.8839 (pt0) cc_final: 0.8141 (pp20) REVERT: D 24 ARG cc_start: 0.8308 (ttm110) cc_final: 0.8009 (ttm110) REVERT: D 45 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8522 (mtpp) REVERT: D 70 ASP cc_start: 0.8587 (m-30) cc_final: 0.8178 (m-30) REVERT: H 72 ASP cc_start: 0.8513 (t0) cc_final: 0.7531 (t0) REVERT: H 75 LYS cc_start: 0.9184 (ptpp) cc_final: 0.8589 (ptpp) REVERT: H 83 ARG cc_start: 0.8295 (ptt-90) cc_final: 0.8076 (ptt-90) REVERT: H 85 GLU cc_start: 0.8972 (pm20) cc_final: 0.8679 (pp20) REVERT: H 86 ASP cc_start: 0.9273 (m-30) cc_final: 0.8947 (m-30) REVERT: L 94 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7627 (t80) REVERT: L 165 ASP cc_start: 0.8735 (t0) cc_final: 0.8436 (t0) REVERT: L 190 TYR cc_start: 0.8789 (m-80) cc_final: 0.8383 (m-10) outliers start: 21 outliers final: 14 residues processed: 125 average time/residue: 0.6894 time to fit residues: 89.7455 Evaluate side-chains 126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 197 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.065979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.051399 restraints weight = 15506.815| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.89 r_work: 0.2597 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6738 Z= 0.190 Angle : 0.607 8.133 9212 Z= 0.314 Chirality : 0.044 0.220 1043 Planarity : 0.005 0.073 1114 Dihedral : 11.665 106.537 1126 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.00 % Favored : 96.87 % Rotamer: Outliers : 3.32 % Allowed : 19.91 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.31), residues: 799 helix: 1.17 (0.85), residues: 47 sheet: 1.02 (0.27), residues: 360 loop : 0.26 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 18 TYR 0.031 0.001 TYR L 94 PHE 0.020 0.001 PHE D 83 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 6732) covalent geometry : angle 0.60641 / 0.31 ( 9200) SS BOND : bond 0.00402 / 0.23 ( 6) SS BOND : angle 1.10649 / 0.67 ( 12) hydrogen bonds : bond 0.03489 / 2.38 ( 264) hydrogen bonds : angle 5.14606 / 3.83 ( 714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8092 (pt) REVERT: C 43 GLU cc_start: 0.8831 (pt0) cc_final: 0.8124 (pp20) REVERT: D 24 ARG cc_start: 0.8199 (ttm110) cc_final: 0.7909 (ttm110) REVERT: D 70 ASP cc_start: 0.8530 (m-30) cc_final: 0.8076 (m-30) REVERT: D 83 PHE cc_start: 0.7653 (t80) cc_final: 0.7224 (t80) REVERT: D 105 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6105 (tp30) REVERT: D 106 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.7109 (mp) REVERT: H 72 ASP cc_start: 0.8436 (t0) cc_final: 0.7372 (t0) REVERT: H 75 LYS cc_start: 0.9169 (ptpp) cc_final: 0.8515 (ptpp) REVERT: H 85 GLU cc_start: 0.8991 (pm20) cc_final: 0.8666 (pp20) REVERT: L 94 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7481 (t80) REVERT: L 141 GLU cc_start: 0.7794 (pp20) cc_final: 0.7565 (pp20) REVERT: L 165 ASP cc_start: 0.8764 (t0) cc_final: 0.8432 (t0) REVERT: L 190 TYR cc_start: 0.8723 (m-80) cc_final: 0.8332 (m-80) outliers start: 23 outliers final: 10 residues processed: 124 average time/residue: 0.5832 time to fit residues: 75.4148 Evaluate side-chains 123 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 197 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.065660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.051137 restraints weight = 15365.559| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.87 r_work: 0.2580 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6738 Z= 0.197 Angle : 0.611 8.180 9212 Z= 0.317 Chirality : 0.044 0.220 1043 Planarity : 0.004 0.076 1114 Dihedral : 11.573 104.880 1126 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.25 % Favored : 96.62 % Rotamer: Outliers : 3.17 % Allowed : 20.06 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.31), residues: 799 helix: 1.19 (0.84), residues: 47 sheet: 1.05 (0.27), residues: 360 loop : 0.28 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 18 TYR 0.031 0.001 TYR L 94 PHE 0.019 0.001 PHE D 83 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 ( 6732) covalent geometry : angle 0.60994 / 0.32 ( 9200) SS BOND : bond 0.00410 / 0.23 ( 6) SS BOND : angle 1.06179 / 0.63 ( 12) hydrogen bonds : bond 0.03409 / 2.33 ( 264) hydrogen bonds : angle 5.07423 / 3.78 ( 714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8165 (pt) REVERT: C 43 GLU cc_start: 0.8824 (pt0) cc_final: 0.8218 (pp20) REVERT: D 1 ASP cc_start: 0.8463 (p0) cc_final: 0.8243 (p0) REVERT: D 24 ARG cc_start: 0.8258 (ttm110) cc_final: 0.8033 (ttm110) REVERT: D 70 ASP cc_start: 0.8596 (m-30) cc_final: 0.8298 (m-30) REVERT: D 83 PHE cc_start: 0.7533 (t80) cc_final: 0.7075 (t80) REVERT: D 105 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6088 (tp30) REVERT: D 106 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7156 (mp) REVERT: H 43 LYS cc_start: 0.8694 (mppt) cc_final: 0.8478 (mppt) REVERT: H 72 ASP cc_start: 0.8514 (t0) cc_final: 0.7439 (t0) REVERT: H 75 LYS cc_start: 0.9231 (ptpp) cc_final: 0.8529 (ptpp) REVERT: H 85 GLU cc_start: 0.8962 (pm20) cc_final: 0.8636 (pp20) REVERT: L 94 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7535 (t80) REVERT: L 141 GLU cc_start: 0.7908 (pp20) cc_final: 0.7638 (pp20) REVERT: L 159 GLU cc_start: 0.8715 (pt0) cc_final: 0.8207 (mt-10) REVERT: L 165 ASP cc_start: 0.8793 (t0) cc_final: 0.8479 (t0) REVERT: L 190 TYR cc_start: 0.8803 (m-80) cc_final: 0.8426 (m-80) outliers start: 22 outliers final: 12 residues processed: 121 average time/residue: 0.6475 time to fit residues: 81.6003 Evaluate side-chains 125 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 197 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 75 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.066010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.051520 restraints weight = 15237.538| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.87 r_work: 0.2600 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6738 Z= 0.171 Angle : 0.612 8.449 9212 Z= 0.317 Chirality : 0.043 0.212 1043 Planarity : 0.005 0.075 1114 Dihedral : 11.518 103.592 1126 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.88 % Favored : 97.00 % Rotamer: Outliers : 2.74 % Allowed : 20.20 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.31), residues: 799 helix: 1.31 (0.84), residues: 47 sheet: 1.06 (0.27), residues: 360 loop : 0.30 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 18 TYR 0.029 0.001 TYR L 94 PHE 0.018 0.001 PHE D 83 TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 6732) covalent geometry : angle 0.61119 / 0.32 ( 9200) SS BOND : bond 0.00385 / 0.21 ( 6) SS BOND : angle 0.96562 / 0.57 ( 12) hydrogen bonds : bond 0.03264 / 2.23 ( 264) hydrogen bonds : angle 4.97066 / 3.70 ( 714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8109 (pt) REVERT: C 43 GLU cc_start: 0.8829 (pt0) cc_final: 0.8290 (pp20) REVERT: D 1 ASP cc_start: 0.8464 (p0) cc_final: 0.8230 (p0) REVERT: D 24 ARG cc_start: 0.8191 (ttm110) cc_final: 0.7957 (ttm110) REVERT: D 70 ASP cc_start: 0.8541 (m-30) cc_final: 0.8233 (m-30) REVERT: D 83 PHE cc_start: 0.7535 (t80) cc_final: 0.7065 (t80) REVERT: D 105 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6089 (tp30) REVERT: D 106 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.7065 (mp) REVERT: H 46 GLU cc_start: 0.8406 (tt0) cc_final: 0.8029 (pt0) REVERT: H 72 ASP cc_start: 0.8457 (t0) cc_final: 0.7384 (t0) REVERT: H 75 LYS cc_start: 0.9242 (ptpp) cc_final: 0.8542 (ptpp) REVERT: H 85 GLU cc_start: 0.8956 (pm20) cc_final: 0.8636 (pp20) REVERT: H 206 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8791 (ttpp) REVERT: L 4 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8586 (mmt) REVERT: L 94 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7391 (t80) REVERT: L 141 GLU cc_start: 0.7891 (pp20) cc_final: 0.7584 (pp20) REVERT: L 159 GLU cc_start: 0.8748 (pt0) cc_final: 0.8227 (mt-10) REVERT: L 165 ASP cc_start: 0.8782 (t0) cc_final: 0.8446 (t0) REVERT: L 190 TYR cc_start: 0.8724 (m-80) cc_final: 0.8355 (m-80) outliers start: 19 outliers final: 12 residues processed: 122 average time/residue: 0.6171 time to fit residues: 78.3182 Evaluate side-chains 126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 197 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 79 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.065195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.050585 restraints weight = 15473.772| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.89 r_work: 0.2571 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6738 Z= 0.222 Angle : 0.639 8.696 9212 Z= 0.330 Chirality : 0.044 0.222 1043 Planarity : 0.004 0.076 1114 Dihedral : 11.510 103.212 1126 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.50 % Favored : 96.37 % Rotamer: Outliers : 3.03 % Allowed : 20.35 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.30), residues: 799 helix: 1.23 (0.84), residues: 47 sheet: 1.05 (0.27), residues: 360 loop : 0.28 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 18 TYR 0.031 0.002 TYR L 94 PHE 0.016 0.001 PHE D 83 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 ( 6732) covalent geometry : angle 0.63834 / 0.33 ( 9200) SS BOND : bond 0.00416 / 0.24 ( 6) SS BOND : angle 1.11861 / 0.66 ( 12) hydrogen bonds : bond 0.03378 / 2.31 ( 264) hydrogen bonds : angle 4.99864 / 3.73 ( 714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8170 (pt) REVERT: C 43 GLU cc_start: 0.8839 (pt0) cc_final: 0.8300 (pp20) REVERT: D 1 ASP cc_start: 0.8470 (p0) cc_final: 0.8229 (p0) REVERT: D 24 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7969 (ttm110) REVERT: D 42 LYS cc_start: 0.8525 (mppt) cc_final: 0.7988 (mppt) REVERT: D 70 ASP cc_start: 0.8550 (m-30) cc_final: 0.8227 (m-30) REVERT: D 83 PHE cc_start: 0.7587 (t80) cc_final: 0.7096 (t80) REVERT: D 105 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6041 (tp30) REVERT: D 106 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.7084 (mp) REVERT: H 46 GLU cc_start: 0.8448 (tt0) cc_final: 0.8030 (pt0) REVERT: H 72 ASP cc_start: 0.8428 (t0) cc_final: 0.7377 (t0) REVERT: H 75 LYS cc_start: 0.9244 (ptpp) cc_final: 0.8558 (ptpp) REVERT: H 85 GLU cc_start: 0.8969 (pm20) cc_final: 0.8655 (pp20) REVERT: L 94 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.7389 (t80) REVERT: L 141 GLU cc_start: 0.7955 (pp20) cc_final: 0.7642 (pp20) REVERT: L 159 GLU cc_start: 0.8739 (pt0) cc_final: 0.8224 (mt-10) REVERT: L 165 ASP cc_start: 0.8757 (t0) cc_final: 0.8398 (t0) REVERT: L 190 TYR cc_start: 0.8748 (m-80) cc_final: 0.8356 (m-80) outliers start: 21 outliers final: 12 residues processed: 121 average time/residue: 0.5858 time to fit residues: 73.8306 Evaluate side-chains 126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 197 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 0.0370 chunk 47 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.065790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.051405 restraints weight = 15508.362| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.84 r_work: 0.2586 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6738 Z= 0.170 Angle : 0.639 9.013 9212 Z= 0.330 Chirality : 0.043 0.208 1043 Planarity : 0.005 0.074 1114 Dihedral : 11.489 102.534 1126 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.75 % Favored : 97.12 % Rotamer: Outliers : 2.60 % Allowed : 21.07 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.30), residues: 799 helix: 1.35 (0.84), residues: 47 sheet: 1.03 (0.28), residues: 354 loop : 0.29 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 18 TYR 0.029 0.001 TYR L 94 PHE 0.017 0.001 PHE D 83 TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 6732) covalent geometry : angle 0.63862 / 0.33 ( 9200) SS BOND : bond 0.00374 / 0.21 ( 6) SS BOND : angle 0.90436 / 0.52 ( 12) hydrogen bonds : bond 0.03205 / 2.19 ( 264) hydrogen bonds : angle 4.89291 / 3.65 ( 714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.8406 (pt) cc_final: 0.8183 (pt) REVERT: C 43 GLU cc_start: 0.8803 (pt0) cc_final: 0.8303 (pp20) REVERT: D 1 ASP cc_start: 0.8481 (p0) cc_final: 0.8179 (p0) REVERT: D 3 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8179 (mm-40) REVERT: D 24 ARG cc_start: 0.8260 (ttm110) cc_final: 0.8008 (ttm110) REVERT: D 42 LYS cc_start: 0.8636 (mppt) cc_final: 0.8087 (mppt) REVERT: D 70 ASP cc_start: 0.8606 (m-30) cc_final: 0.8267 (m-30) REVERT: D 83 PHE cc_start: 0.7527 (t80) cc_final: 0.7062 (t80) REVERT: D 105 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6230 (tp30) REVERT: D 106 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7120 (mp) REVERT: H 46 GLU cc_start: 0.8494 (tt0) cc_final: 0.8093 (pt0) REVERT: H 72 ASP cc_start: 0.8511 (t0) cc_final: 0.7468 (t0) REVERT: H 75 LYS cc_start: 0.9272 (ptpp) cc_final: 0.8585 (ptpp) REVERT: H 85 GLU cc_start: 0.8946 (pm20) cc_final: 0.8642 (pp20) REVERT: L 141 GLU cc_start: 0.8017 (pp20) cc_final: 0.7723 (pp20) REVERT: L 159 GLU cc_start: 0.8730 (pt0) cc_final: 0.8268 (mt-10) REVERT: L 165 ASP cc_start: 0.8754 (t0) cc_final: 0.8431 (t0) REVERT: L 190 TYR cc_start: 0.8801 (m-80) cc_final: 0.8433 (m-80) outliers start: 18 outliers final: 10 residues processed: 121 average time/residue: 0.5756 time to fit residues: 72.5124 Evaluate side-chains 124 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 197 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.065872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.051387 restraints weight = 15256.362| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.85 r_work: 0.2592 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 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 0.045 6738 Z= 0.179 Angle : 0.646 8.939 9212 Z= 0.332 Chirality : 0.043 0.199 1043 Planarity : 0.004 0.075 1114 Dihedral : 11.480 102.351 1126 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.25 % Favored : 96.62 % Rotamer: Outliers : 2.02 % Allowed : 21.79 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.30), residues: 799 helix: 1.36 (0.84), residues: 47 sheet: 1.02 (0.28), residues: 354 loop : 0.26 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 18 TYR 0.030 0.001 TYR L 94 PHE 0.016 0.001 PHE D 83 TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 6732) covalent geometry : angle 0.64514 / 0.33 ( 9200) SS BOND : bond 0.00365 / 0.19 ( 6) SS BOND : angle 1.09206 / 0.78 ( 12) hydrogen bonds : bond 0.03189 / 2.17 ( 264) hydrogen bonds : angle 4.87728 / 3.63 ( 714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1598 Ramachandran restraints generated. 799 Oldfield, 0 Emsley, 799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8128 (pt) REVERT: C 43 GLU cc_start: 0.8802 (pt0) cc_final: 0.8318 (pp20) REVERT: D 1 ASP cc_start: 0.8413 (p0) cc_final: 0.8176 (p0) REVERT: D 18 ARG cc_start: 0.9031 (mmm160) cc_final: 0.8740 (mmm-85) REVERT: D 24 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7894 (ttm110) REVERT: D 42 LYS cc_start: 0.8554 (mppt) cc_final: 0.7937 (mppt) REVERT: D 70 ASP cc_start: 0.8538 (m-30) cc_final: 0.8210 (m-30) REVERT: D 83 PHE cc_start: 0.7575 (t80) cc_final: 0.7104 (t80) REVERT: D 90 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8334 (tm-30) REVERT: D 105 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6154 (tp30) REVERT: D 106 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.7062 (mp) REVERT: E 73 THR cc_start: 0.9160 (m) cc_final: 0.8951 (m) REVERT: H 46 GLU cc_start: 0.8432 (tt0) cc_final: 0.8002 (pt0) REVERT: H 72 ASP cc_start: 0.8451 (t0) cc_final: 0.7423 (t0) REVERT: H 75 LYS cc_start: 0.9248 (ptpp) cc_final: 0.8557 (ptpp) REVERT: H 85 GLU cc_start: 0.8940 (pm20) cc_final: 0.8635 (pp20) REVERT: L 141 GLU cc_start: 0.7932 (pp20) cc_final: 0.7621 (pp20) REVERT: L 159 GLU cc_start: 0.8752 (pt0) cc_final: 0.8245 (mt-10) REVERT: L 165 ASP cc_start: 0.8748 (t0) cc_final: 0.8398 (t0) REVERT: L 190 TYR cc_start: 0.8719 (m-80) cc_final: 0.8333 (m-80) outliers start: 14 outliers final: 9 residues processed: 119 average time/residue: 0.6085 time to fit residues: 75.3928 Evaluate side-chains 123 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 197 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.065671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.051336 restraints weight = 15275.798| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.84 r_work: 0.2581 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6738 Z= 0.188 Angle : 0.649 8.895 9212 Z= 0.335 Chirality : 0.043 0.202 1043 Planarity : 0.005 0.075 1114 Dihedral : 11.472 102.080 1126 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.13 % Favored : 96.75 % Rotamer: Outliers : 2.02 % Allowed : 21.79 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.30), residues: 799 helix: 1.34 (0.84), residues: 47 sheet: 1.01 (0.28), residues: 344 loop : 0.20 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 18 TYR 0.030 0.001 TYR L 94 PHE 0.016 0.001 PHE D 83 TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS L 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 6732) covalent geometry : angle 0.64767 / 0.33 ( 9200) SS BOND : bond 0.00369 / 0.19 ( 6) SS BOND : angle 1.23207 / 0.92 ( 12) hydrogen bonds : bond 0.03196 / 2.18 ( 264) hydrogen bonds : angle 4.85321 / 3.62 ( 714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.81 seconds wall clock time: 37 minutes 38.38 seconds (2258.38 seconds total)