Starting phenix.real_space_refine on Thu Jul 31 19:20:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfy_43194/07_2025/8vfy_43194.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfy_43194/07_2025/8vfy_43194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vfy_43194/07_2025/8vfy_43194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfy_43194/07_2025/8vfy_43194.map" model { file = "/net/cci-nas-00/data/ceres_data/8vfy_43194/07_2025/8vfy_43194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfy_43194/07_2025/8vfy_43194.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 342 5.49 5 S 21 5.16 5 C 7786 2.51 5 N 2611 2.21 5 O 3286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 14046 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3501 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "J" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3510 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "O" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Time building chain proxies: 8.37, per 1000 atoms: 0.60 Number of scatterers: 14046 At special positions: 0 Unit cell: (84.48, 118.8, 192.72, 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 342 15.00 O 3286 8.00 N 2611 7.00 C 7786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1648 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 11 sheets defined 68.1% alpha, 3.2% beta 171 base pairs and 306 stacking pairs defined. Time for finding SS restraints: 7.24 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.618A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.742A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.370A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.549A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.537A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.809A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.637A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.507A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.323A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.527A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.561A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 186 Processing helix chain 'O' and resid 192 through 204 Processing helix chain 'O' and resid 205 through 209 removed outlier: 3.690A pdb=" N GLN O 209 " --> pdb=" O TYR O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 removed outlier: 4.029A pdb=" N TRP O 214 " --> pdb=" O ASN O 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.804A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.521A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.486A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.723A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.520A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.468A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'O' and resid 228 through 231 436 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 417 hydrogen bonds 834 hydrogen bond angles 0 basepair planarities 171 basepair parallelities 306 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2566 1.33 - 1.45: 4879 1.45 - 1.57: 6846 1.57 - 1.69: 682 1.69 - 1.81: 35 Bond restraints: 15008 Sorted by residual: bond pdb=" N HIS O 168 " pdb=" CA HIS O 168 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N LYS D 30 " pdb=" CA LYS D 30 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N ALA C 10 " pdb=" CA ALA C 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N LYS H 30 " pdb=" CA LYS H 30 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N LYS B 20 " pdb=" CA LYS B 20 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 ... (remaining 15003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 20049 1.17 - 2.33: 1297 2.33 - 3.50: 345 3.50 - 4.66: 34 4.66 - 5.83: 6 Bond angle restraints: 21731 Sorted by residual: angle pdb=" C2' DT J 55 " pdb=" C1' DT J 55 " pdb=" N1 DT J 55 " ideal model delta sigma weight residual 113.50 117.99 -4.49 1.50e+00 4.44e-01 8.98e+00 angle pdb=" C2' DT I 140 " pdb=" C1' DT I 140 " pdb=" N1 DT I 140 " ideal model delta sigma weight residual 113.50 117.92 -4.42 1.50e+00 4.44e-01 8.69e+00 angle pdb=" C2' DC I 110 " pdb=" C1' DC I 110 " pdb=" N1 DC I 110 " ideal model delta sigma weight residual 113.50 117.76 -4.26 1.50e+00 4.44e-01 8.07e+00 angle pdb=" C2' DT I 161 " pdb=" C1' DT I 161 " pdb=" N1 DT I 161 " ideal model delta sigma weight residual 113.50 117.59 -4.09 1.50e+00 4.44e-01 7.43e+00 angle pdb=" C2' DT I 69 " pdb=" C1' DT I 69 " pdb=" N1 DT I 69 " ideal model delta sigma weight residual 113.50 117.55 -4.05 1.50e+00 4.44e-01 7.29e+00 ... (remaining 21726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.36: 6504 31.36 - 62.73: 1665 62.73 - 94.09: 52 94.09 - 125.46: 0 125.46 - 156.82: 2 Dihedral angle restraints: 8223 sinusoidal: 5666 harmonic: 2557 Sorted by residual: dihedral pdb=" C4' DG J 127 " pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " pdb=" P DG J 128 " ideal model delta sinusoidal sigma weight residual 220.00 63.18 156.82 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DC J 93 " pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " pdb=" P DC J 94 " ideal model delta sinusoidal sigma weight residual 220.00 68.58 151.42 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA LYS O 237 " pdb=" C LYS O 237 " pdb=" N PRO O 238 " pdb=" CA PRO O 238 " ideal model delta harmonic sigma weight residual 180.00 162.38 17.62 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 8220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1616 0.032 - 0.064: 525 0.064 - 0.095: 263 0.095 - 0.127: 38 0.127 - 0.159: 5 Chirality restraints: 2447 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE G 111 " pdb=" N ILE G 111 " pdb=" C ILE G 111 " pdb=" CB ILE G 111 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 2444 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS O 237 " -0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO O 238 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO O 238 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO O 238 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 140 " 0.038 2.00e-02 2.50e+03 1.78e-02 7.88e+00 pdb=" N1 DT I 140 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DT I 140 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DT I 140 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 140 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DT I 140 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT I 140 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DT I 140 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 140 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT I 140 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO O 171 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO O 172 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO O 172 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO O 172 " 0.027 5.00e-02 4.00e+02 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1294 2.74 - 3.28: 12610 3.28 - 3.82: 27731 3.82 - 4.36: 32977 4.36 - 4.90: 47101 Nonbonded interactions: 121713 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.203 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 72 " pdb=" OE2 GLU D 76 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR F 72 " pdb=" OE2 GLU H 76 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.275 3.040 ... (remaining 121708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.620 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 39.250 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15008 Z= 0.212 Angle : 0.678 5.829 21731 Z= 0.427 Chirality : 0.039 0.159 2447 Planarity : 0.005 0.073 1565 Dihedral : 26.421 156.825 6575 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.74 % Favored : 98.15 % Rotamer: Outliers : 0.27 % Allowed : 1.21 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.29), residues: 863 helix: 2.21 (0.22), residues: 577 sheet: -1.65 (1.37), residues: 12 loop : -0.34 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 214 HIS 0.003 0.001 HIS D 49 PHE 0.007 0.001 PHE E 104 TYR 0.007 0.001 TYR G 57 ARG 0.003 0.000 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.09755 ( 853) hydrogen bonds : angle 3.64263 ( 2112) covalent geometry : bond 0.00480 (15008) covalent geometry : angle 0.67754 (21731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8872 (p) cc_final: 0.8313 (t) REVERT: A 76 GLN cc_start: 0.8172 (mt0) cc_final: 0.7704 (mt0) REVERT: B 85 ASP cc_start: 0.9143 (m-30) cc_final: 0.8911 (m-30) REVERT: C 90 ASP cc_start: 0.8325 (t0) cc_final: 0.8071 (t0) REVERT: C 95 LYS cc_start: 0.9288 (ttpt) cc_final: 0.9063 (tttm) REVERT: D 108 LYS cc_start: 0.8240 (ptmm) cc_final: 0.8016 (ptpp) REVERT: E 79 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8520 (mtpm) REVERT: G 120 THR cc_start: 0.8473 (p) cc_final: 0.8052 (p) REVERT: H 59 MET cc_start: 0.9127 (tpp) cc_final: 0.8898 (tpt) REVERT: H 113 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8341 (tt0) REVERT: H 115 THR cc_start: 0.9240 (m) cc_final: 0.9030 (p) outliers start: 2 outliers final: 1 residues processed: 186 average time/residue: 1.8162 time to fit residues: 359.8850 Evaluate side-chains 117 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN D 47 GLN E 68 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.105692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069543 restraints weight = 35697.842| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.16 r_work: 0.3091 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15008 Z= 0.203 Angle : 0.615 6.564 21731 Z= 0.370 Chirality : 0.036 0.143 2447 Planarity : 0.005 0.076 1565 Dihedral : 30.323 150.403 4803 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.09 % Favored : 97.80 % Rotamer: Outliers : 2.43 % Allowed : 13.09 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.28), residues: 863 helix: 2.25 (0.21), residues: 589 sheet: -1.54 (1.35), residues: 12 loop : -0.06 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP O 199 HIS 0.003 0.001 HIS F 75 PHE 0.012 0.001 PHE O 254 TYR 0.014 0.001 TYR H 40 ARG 0.007 0.001 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 853) hydrogen bonds : angle 2.95244 ( 2112) covalent geometry : bond 0.00456 (15008) covalent geometry : angle 0.61525 (21731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8769 (p) cc_final: 0.8266 (t) REVERT: A 76 GLN cc_start: 0.8239 (mt0) cc_final: 0.7778 (mt0) REVERT: C 13 LYS cc_start: 0.9146 (tppp) cc_final: 0.8853 (tppp) REVERT: C 90 ASP cc_start: 0.8275 (t0) cc_final: 0.8026 (t0) REVERT: C 91 GLU cc_start: 0.7743 (tp30) cc_final: 0.7523 (tp30) REVERT: D 63 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8135 (m-40) REVERT: D 108 LYS cc_start: 0.8077 (ptmm) cc_final: 0.7794 (ptpp) REVERT: D 119 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8020 (p) REVERT: E 77 ASP cc_start: 0.8937 (m-30) cc_final: 0.8675 (t0) REVERT: G 90 ASP cc_start: 0.8603 (t70) cc_final: 0.8303 (t0) REVERT: G 104 GLN cc_start: 0.8723 (tp40) cc_final: 0.8517 (mm110) REVERT: H 59 MET cc_start: 0.9147 (tpp) cc_final: 0.8817 (tpt) REVERT: H 113 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8417 (tt0) REVERT: O 190 MET cc_start: 0.6650 (ttp) cc_final: 0.5986 (tpp) outliers start: 18 outliers final: 10 residues processed: 136 average time/residue: 1.7515 time to fit residues: 254.6451 Evaluate side-chains 121 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 51 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 107 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN C 38 ASN H 49 HIS ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.106828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.070732 restraints weight = 35565.647| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.27 r_work: 0.3118 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15008 Z= 0.168 Angle : 0.591 9.516 21731 Z= 0.356 Chirality : 0.034 0.130 2447 Planarity : 0.004 0.078 1565 Dihedral : 30.237 148.736 4803 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.09 % Favored : 97.80 % Rotamer: Outliers : 1.35 % Allowed : 16.19 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.28), residues: 863 helix: 2.37 (0.21), residues: 589 sheet: -1.44 (1.37), residues: 12 loop : 0.10 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 199 HIS 0.003 0.001 HIS A 113 PHE 0.011 0.001 PHE E 67 TYR 0.016 0.001 TYR H 40 ARG 0.006 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 853) hydrogen bonds : angle 2.76480 ( 2112) covalent geometry : bond 0.00370 (15008) covalent geometry : angle 0.59058 (21731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.9049 (t80) cc_final: 0.8828 (t80) REVERT: C 90 ASP cc_start: 0.8247 (t0) cc_final: 0.8045 (t0) REVERT: C 91 GLU cc_start: 0.7866 (tp30) cc_final: 0.7421 (tm-30) REVERT: C 92 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8155 (mt-10) REVERT: C 95 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8743 (ttmm) REVERT: D 57 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8929 (mtpt) REVERT: D 63 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8088 (m-40) REVERT: D 108 LYS cc_start: 0.7997 (ptmm) cc_final: 0.7696 (ptpp) REVERT: E 77 ASP cc_start: 0.8903 (m-30) cc_final: 0.8690 (t0) REVERT: G 90 ASP cc_start: 0.8505 (t70) cc_final: 0.8219 (t0) REVERT: G 119 LYS cc_start: 0.8506 (mptt) cc_final: 0.8281 (mmtt) REVERT: H 31 ARG cc_start: 0.8288 (pmt170) cc_final: 0.7690 (ptt90) REVERT: O 190 MET cc_start: 0.6601 (ttp) cc_final: 0.6212 (tpp) outliers start: 10 outliers final: 5 residues processed: 133 average time/residue: 1.7075 time to fit residues: 242.4407 Evaluate side-chains 123 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 116 optimal weight: 0.0000 chunk 88 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS B 25 ASN C 38 ASN G 104 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.105544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.069355 restraints weight = 35424.711| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.22 r_work: 0.3091 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15008 Z= 0.208 Angle : 0.609 8.514 21731 Z= 0.364 Chirality : 0.035 0.154 2447 Planarity : 0.005 0.078 1565 Dihedral : 30.522 149.929 4803 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.32 % Favored : 97.57 % Rotamer: Outliers : 2.56 % Allowed : 16.19 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.28), residues: 863 helix: 2.26 (0.21), residues: 590 sheet: -1.40 (1.33), residues: 12 loop : 0.02 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 199 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.015 0.002 TYR B 88 ARG 0.006 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 853) hydrogen bonds : angle 2.86366 ( 2112) covalent geometry : bond 0.00469 (15008) covalent geometry : angle 0.60949 (21731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8293 (t0) cc_final: 0.8059 (t0) REVERT: C 91 GLU cc_start: 0.7866 (tp30) cc_final: 0.7654 (tm-30) REVERT: D 63 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8139 (m-40) REVERT: D 101 LEU cc_start: 0.9126 (mm) cc_final: 0.8917 (mt) REVERT: D 108 LYS cc_start: 0.8186 (ptmm) cc_final: 0.7915 (ptpp) REVERT: E 63 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7874 (mmm160) REVERT: E 77 ASP cc_start: 0.8953 (m-30) cc_final: 0.8719 (t0) REVERT: G 90 ASP cc_start: 0.8391 (t70) cc_final: 0.8107 (t0) REVERT: G 95 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8659 (ttpp) REVERT: G 116 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8834 (mt) REVERT: H 31 ARG cc_start: 0.8374 (pmt170) cc_final: 0.7856 (ptt90) REVERT: H 76 GLU cc_start: 0.9137 (tp30) cc_final: 0.8875 (mm-30) REVERT: H 101 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8688 (mm) REVERT: O 190 MET cc_start: 0.6759 (ttp) cc_final: 0.6283 (tpp) outliers start: 19 outliers final: 8 residues processed: 130 average time/residue: 1.7970 time to fit residues: 249.4435 Evaluate side-chains 123 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.106161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.070061 restraints weight = 35856.994| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.31 r_work: 0.3122 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15008 Z= 0.183 Angle : 0.598 8.222 21731 Z= 0.358 Chirality : 0.034 0.166 2447 Planarity : 0.004 0.080 1565 Dihedral : 30.487 149.089 4803 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.20 % Favored : 97.68 % Rotamer: Outliers : 2.43 % Allowed : 17.14 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.28), residues: 863 helix: 2.32 (0.21), residues: 590 sheet: -1.22 (1.34), residues: 12 loop : 0.05 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE E 67 TYR 0.018 0.001 TYR B 88 ARG 0.007 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 853) hydrogen bonds : angle 2.78195 ( 2112) covalent geometry : bond 0.00409 (15008) covalent geometry : angle 0.59817 (21731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8504 (p) cc_final: 0.8190 (t) REVERT: A 94 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8369 (mm-30) REVERT: C 13 LYS cc_start: 0.9104 (tppp) cc_final: 0.8816 (tppp) REVERT: C 50 TYR cc_start: 0.9074 (t80) cc_final: 0.8855 (t80) REVERT: C 90 ASP cc_start: 0.8270 (t0) cc_final: 0.8048 (t0) REVERT: C 91 GLU cc_start: 0.7857 (tp30) cc_final: 0.7633 (tm-30) REVERT: D 63 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8079 (m-40) REVERT: D 108 LYS cc_start: 0.8035 (ptmm) cc_final: 0.7736 (ptpp) REVERT: E 63 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7818 (mmm160) REVERT: E 77 ASP cc_start: 0.8972 (m-30) cc_final: 0.8728 (t0) REVERT: G 90 ASP cc_start: 0.8266 (t70) cc_final: 0.7951 (t0) REVERT: G 116 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8816 (mt) REVERT: H 31 ARG cc_start: 0.8172 (pmt170) cc_final: 0.7914 (ptt90) REVERT: H 101 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8676 (mm) REVERT: O 190 MET cc_start: 0.6613 (ttp) cc_final: 0.6187 (tpp) outliers start: 18 outliers final: 9 residues processed: 134 average time/residue: 1.6687 time to fit residues: 239.2116 Evaluate side-chains 132 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.105649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.069298 restraints weight = 35875.131| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.28 r_work: 0.3110 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15008 Z= 0.203 Angle : 0.606 7.182 21731 Z= 0.362 Chirality : 0.035 0.156 2447 Planarity : 0.005 0.080 1565 Dihedral : 30.642 149.929 4803 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.20 % Favored : 97.68 % Rotamer: Outliers : 1.89 % Allowed : 18.89 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.28), residues: 863 helix: 2.22 (0.21), residues: 590 sheet: -1.00 (1.41), residues: 12 loop : 0.01 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 199 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.026 0.002 TYR B 88 ARG 0.007 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 853) hydrogen bonds : angle 2.85974 ( 2112) covalent geometry : bond 0.00456 (15008) covalent geometry : angle 0.60609 (21731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8592 (p) cc_final: 0.8240 (t) REVERT: C 64 GLU cc_start: 0.7970 (tp30) cc_final: 0.7698 (mm-30) REVERT: C 90 ASP cc_start: 0.8232 (t0) cc_final: 0.8007 (t0) REVERT: D 63 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8012 (m-40) REVERT: D 71 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8217 (mt-10) REVERT: D 108 LYS cc_start: 0.8137 (ptmm) cc_final: 0.7843 (ptpp) REVERT: E 63 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7849 (mmm160) REVERT: E 77 ASP cc_start: 0.8980 (m-30) cc_final: 0.8721 (t0) REVERT: G 90 ASP cc_start: 0.8436 (t70) cc_final: 0.8134 (t0) REVERT: G 116 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8800 (mt) REVERT: G 119 LYS cc_start: 0.8651 (mmpt) cc_final: 0.8405 (mmpt) REVERT: H 59 MET cc_start: 0.9233 (tpt) cc_final: 0.8978 (tpt) REVERT: H 101 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8666 (mm) REVERT: H 113 GLU cc_start: 0.8444 (tt0) cc_final: 0.8138 (tm-30) REVERT: O 190 MET cc_start: 0.6687 (ttp) cc_final: 0.6171 (tpp) REVERT: O 253 MET cc_start: 0.6259 (tpt) cc_final: 0.2556 (mtt) outliers start: 14 outliers final: 11 residues processed: 124 average time/residue: 1.7974 time to fit residues: 237.7177 Evaluate side-chains 128 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN G 89 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.105403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069208 restraints weight = 35957.296| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.09 r_work: 0.3110 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15008 Z= 0.203 Angle : 0.614 9.401 21731 Z= 0.364 Chirality : 0.035 0.166 2447 Planarity : 0.005 0.080 1565 Dihedral : 30.650 149.484 4803 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.32 % Favored : 97.57 % Rotamer: Outliers : 1.75 % Allowed : 19.43 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.28), residues: 863 helix: 2.21 (0.21), residues: 589 sheet: -1.23 (1.36), residues: 12 loop : 0.05 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 214 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.028 0.002 TYR B 88 ARG 0.008 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 853) hydrogen bonds : angle 2.83967 ( 2112) covalent geometry : bond 0.00457 (15008) covalent geometry : angle 0.61369 (21731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8575 (p) cc_final: 0.8226 (t) REVERT: C 50 TYR cc_start: 0.9113 (t80) cc_final: 0.8856 (t80) REVERT: C 90 ASP cc_start: 0.8268 (t0) cc_final: 0.8013 (t0) REVERT: D 63 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8112 (m-40) REVERT: D 71 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8225 (mt-10) REVERT: D 108 LYS cc_start: 0.8133 (ptmm) cc_final: 0.7835 (ptpp) REVERT: E 63 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7804 (mmm160) REVERT: E 77 ASP cc_start: 0.8976 (m-30) cc_final: 0.8724 (t0) REVERT: G 90 ASP cc_start: 0.8365 (t70) cc_final: 0.8095 (t0) REVERT: G 116 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8834 (mt) REVERT: H 76 GLU cc_start: 0.9158 (tp30) cc_final: 0.8917 (mm-30) REVERT: H 101 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8670 (mm) REVERT: H 113 GLU cc_start: 0.8445 (tt0) cc_final: 0.8163 (tm-30) REVERT: O 190 MET cc_start: 0.6686 (ttp) cc_final: 0.6102 (tpp) outliers start: 13 outliers final: 10 residues processed: 126 average time/residue: 1.7935 time to fit residues: 241.1491 Evaluate side-chains 127 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.106554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.070360 restraints weight = 35469.045| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.26 r_work: 0.3112 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15008 Z= 0.164 Angle : 0.606 9.843 21731 Z= 0.361 Chirality : 0.034 0.176 2447 Planarity : 0.004 0.080 1565 Dihedral : 30.586 149.054 4803 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.97 % Favored : 97.91 % Rotamer: Outliers : 1.89 % Allowed : 19.84 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.28), residues: 863 helix: 2.30 (0.21), residues: 590 sheet: -1.20 (1.39), residues: 12 loop : 0.12 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 199 HIS 0.002 0.000 HIS H 49 PHE 0.011 0.001 PHE E 67 TYR 0.032 0.001 TYR B 88 ARG 0.008 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 853) hydrogen bonds : angle 2.76574 ( 2112) covalent geometry : bond 0.00363 (15008) covalent geometry : angle 0.60634 (21731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8506 (p) cc_final: 0.8139 (t) REVERT: C 50 TYR cc_start: 0.9045 (t80) cc_final: 0.8843 (t80) REVERT: C 90 ASP cc_start: 0.8224 (t0) cc_final: 0.7991 (t0) REVERT: D 63 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8058 (m-40) REVERT: D 71 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8225 (mt-10) REVERT: D 108 LYS cc_start: 0.8090 (ptmm) cc_final: 0.7764 (ptpp) REVERT: E 77 ASP cc_start: 0.8972 (m-30) cc_final: 0.8724 (t0) REVERT: G 90 ASP cc_start: 0.8342 (t70) cc_final: 0.8030 (t0) REVERT: G 116 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8701 (mt) REVERT: H 40 TYR cc_start: 0.8704 (m-80) cc_final: 0.8317 (m-80) REVERT: H 76 GLU cc_start: 0.9150 (tp30) cc_final: 0.8944 (mm-30) REVERT: H 101 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8681 (mm) REVERT: O 190 MET cc_start: 0.6713 (ttp) cc_final: 0.6355 (tpp) outliers start: 14 outliers final: 9 residues processed: 128 average time/residue: 2.2331 time to fit residues: 306.0730 Evaluate side-chains 128 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.106664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070375 restraints weight = 35468.072| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.30 r_work: 0.3115 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15008 Z= 0.176 Angle : 0.617 12.068 21731 Z= 0.362 Chirality : 0.034 0.151 2447 Planarity : 0.004 0.080 1565 Dihedral : 30.525 149.171 4803 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.09 % Favored : 97.80 % Rotamer: Outliers : 1.89 % Allowed : 19.70 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.28), residues: 863 helix: 2.29 (0.21), residues: 590 sheet: -1.13 (1.39), residues: 12 loop : 0.15 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 214 HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE E 67 TYR 0.037 0.002 TYR B 88 ARG 0.008 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 853) hydrogen bonds : angle 2.76542 ( 2112) covalent geometry : bond 0.00395 (15008) covalent geometry : angle 0.61712 (21731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8056 (t) REVERT: C 50 TYR cc_start: 0.9040 (t80) cc_final: 0.8839 (t80) REVERT: C 91 GLU cc_start: 0.7799 (tp30) cc_final: 0.7576 (tm-30) REVERT: C 95 LYS cc_start: 0.9086 (ttmp) cc_final: 0.8884 (ttmm) REVERT: D 63 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8071 (m-40) REVERT: D 71 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8239 (mt-10) REVERT: D 108 LYS cc_start: 0.8107 (ptmm) cc_final: 0.7777 (ptpp) REVERT: E 77 ASP cc_start: 0.8955 (m-30) cc_final: 0.8740 (t0) REVERT: G 90 ASP cc_start: 0.8354 (t70) cc_final: 0.8045 (t0) REVERT: G 116 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8670 (mt) REVERT: H 31 ARG cc_start: 0.8189 (pmt170) cc_final: 0.7730 (ttp-170) REVERT: H 101 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8670 (mm) REVERT: O 190 MET cc_start: 0.6678 (ttp) cc_final: 0.6296 (tpp) REVERT: O 253 MET cc_start: 0.7016 (tpt) cc_final: 0.3172 (mtt) outliers start: 14 outliers final: 7 residues processed: 130 average time/residue: 1.7308 time to fit residues: 240.6526 Evaluate side-chains 128 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 114 optimal weight: 0.0670 chunk 103 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.107259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071440 restraints weight = 35553.409| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.28 r_work: 0.3134 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15008 Z= 0.159 Angle : 0.614 11.253 21731 Z= 0.362 Chirality : 0.034 0.163 2447 Planarity : 0.004 0.080 1565 Dihedral : 30.465 148.723 4803 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.85 % Favored : 98.03 % Rotamer: Outliers : 0.94 % Allowed : 21.32 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.28), residues: 863 helix: 2.32 (0.21), residues: 590 sheet: -1.04 (1.41), residues: 12 loop : 0.16 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP O 199 HIS 0.002 0.000 HIS H 49 PHE 0.011 0.001 PHE E 67 TYR 0.043 0.002 TYR B 88 ARG 0.008 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 853) hydrogen bonds : angle 2.73839 ( 2112) covalent geometry : bond 0.00352 (15008) covalent geometry : angle 0.61359 (21731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.8301 (p) cc_final: 0.7988 (t) REVERT: C 91 GLU cc_start: 0.7801 (tp30) cc_final: 0.7503 (tm-30) REVERT: C 95 LYS cc_start: 0.9065 (ttmp) cc_final: 0.8860 (ttmm) REVERT: D 63 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8061 (m-40) REVERT: D 71 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8233 (mt-10) REVERT: D 108 LYS cc_start: 0.8082 (ptmm) cc_final: 0.7749 (ptpp) REVERT: E 77 ASP cc_start: 0.8958 (m-30) cc_final: 0.8715 (t0) REVERT: F 24 ASP cc_start: 0.8253 (t0) cc_final: 0.7801 (t0) REVERT: G 90 ASP cc_start: 0.8335 (t70) cc_final: 0.7990 (t0) REVERT: G 116 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8647 (mt) REVERT: H 31 ARG cc_start: 0.8221 (pmt170) cc_final: 0.7712 (ttp-170) REVERT: H 101 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8665 (mm) REVERT: H 113 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7994 (tm-30) REVERT: O 190 MET cc_start: 0.6570 (ttp) cc_final: 0.6174 (tpp) REVERT: O 253 MET cc_start: 0.6395 (tpt) cc_final: 0.2383 (mtt) outliers start: 7 outliers final: 4 residues processed: 124 average time/residue: 2.1915 time to fit residues: 291.2951 Evaluate side-chains 123 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 117 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 2 optimal weight: 0.0050 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.106695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.070696 restraints weight = 35871.426| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.30 r_work: 0.3140 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15008 Z= 0.180 Angle : 0.624 10.466 21731 Z= 0.366 Chirality : 0.035 0.186 2447 Planarity : 0.004 0.080 1565 Dihedral : 30.488 149.218 4803 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.43 % Favored : 97.45 % Rotamer: Outliers : 1.21 % Allowed : 22.27 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.28), residues: 863 helix: 2.23 (0.21), residues: 590 sheet: -1.08 (1.41), residues: 12 loop : 0.12 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP O 199 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.044 0.002 TYR B 88 ARG 0.008 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 853) hydrogen bonds : angle 2.80694 ( 2112) covalent geometry : bond 0.00406 (15008) covalent geometry : angle 0.62357 (21731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12284.88 seconds wall clock time: 215 minutes 49.13 seconds (12949.13 seconds total)