Starting phenix.real_space_refine on Thu Mar 6 02:49:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yc0_39128/03_2025/8yc0_39128.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yc0_39128/03_2025/8yc0_39128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yc0_39128/03_2025/8yc0_39128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yc0_39128/03_2025/8yc0_39128.map" model { file = "/net/cci-nas-00/data/ceres_data/8yc0_39128/03_2025/8yc0_39128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yc0_39128/03_2025/8yc0_39128.cif" } resolution = 4.12 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= -0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3009 2.51 5 N 731 2.21 5 O 858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4635 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 203 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "b" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 218 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 933 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "g" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "m" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 268 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "n" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.38, per 1000 atoms: 0.73 Number of scatterers: 4635 At special positions: 0 Unit cell: (100.004, 86.96, 89.134, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 858 8.00 N 731 7.00 C 3009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.04 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.04 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 522.5 milliseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1084 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 40.0% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'a' and resid 26 through 50 removed outlier: 4.043A pdb=" N LYS a 30 " --> pdb=" O LEU a 26 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU a 31 " --> pdb=" O LEU a 27 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR a 33 " --> pdb=" O PRO a 29 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU a 34 " --> pdb=" O LYS a 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 54 Processing helix chain 'd' and resid 100 through 124 removed outlier: 3.620A pdb=" N VAL d 104 " --> pdb=" O ASP d 100 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA d 105 " --> pdb=" O PRO d 101 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY d 106 " --> pdb=" O ALA d 102 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 152 removed outlier: 3.538A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 154 removed outlier: 3.517A pdb=" N ASN f 154 " --> pdb=" O TYR f 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 80 removed outlier: 3.921A pdb=" N ASP g 80 " --> pdb=" O ASN g 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 137 removed outlier: 3.694A pdb=" N SER g 116 " --> pdb=" O ALA g 112 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY g 117 " --> pdb=" O ALA g 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 257 through 289 removed outlier: 3.582A pdb=" N MET m 261 " --> pdb=" O GLU m 257 " (cutoff:3.500A) Processing helix chain 'n' and resid 253 through 288 Processing sheet with id=AA1, first strand: chain 'd' and resid 32 through 35 removed outlier: 7.525A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU d 60 " --> pdb=" O VAL d 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 41 through 46 removed outlier: 3.843A pdb=" N VAL d 44 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY d 46 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG d 68 " --> pdb=" O GLY d 46 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG e 115 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N HIS d 89 " --> pdb=" O ARG e 115 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL e 97 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR e 99 " --> pdb=" O LEU e 58 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU e 58 " --> pdb=" O TYR e 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 41 removed outlier: 3.705A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY e 76 " --> pdb=" O SER e 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 38 removed outlier: 4.006A pdb=" N LYS f 37 " --> pdb=" O THR f 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR f 48 " --> pdb=" O LYS f 37 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU f 82 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 112 through 115 removed outlier: 5.591A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.960A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY g 75 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU g 44 " --> pdb=" O ASN g 73 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN g 73 " --> pdb=" O LEU g 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 54 through 57 removed outlier: 6.318A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE g 62 " --> pdb=" O TRP g 55 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 1.35 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: 1433 1.34 - 1.47: 1125 1.47 - 1.59: 2115 1.59 - 1.71: 0 1.71 - 1.83: 51 Bond restraints: 4724 Sorted by residual: bond pdb=" C ASP a 28 " pdb=" N PRO a 29 " ideal model delta sigma weight residual 1.333 1.364 -0.031 1.44e-02 4.82e+03 4.62e+00 bond pdb=" CA ASP e 63 " pdb=" CB ASP e 63 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.69e-02 3.50e+03 1.55e+00 bond pdb=" CB PRO f 100 " pdb=" CG PRO f 100 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.46e+00 bond pdb=" N ASN e 121 " pdb=" CA ASN e 121 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.17e+00 bond pdb=" CB ASP f 137 " pdb=" CG ASP f 137 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 ... (remaining 4719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 6304 2.57 - 5.14: 80 5.14 - 7.71: 14 7.71 - 10.28: 4 10.28 - 12.85: 2 Bond angle restraints: 6404 Sorted by residual: angle pdb=" C LEU a 27 " pdb=" CA LEU a 27 " pdb=" CB LEU a 27 " ideal model delta sigma weight residual 115.89 109.41 6.48 1.32e+00 5.74e-01 2.41e+01 angle pdb=" CA CYS f 49 " pdb=" CB CYS f 49 " pdb=" SG CYS f 49 " ideal model delta sigma weight residual 114.40 123.14 -8.74 2.30e+00 1.89e-01 1.44e+01 angle pdb=" CA LEU f 114 " pdb=" CB LEU f 114 " pdb=" CG LEU f 114 " ideal model delta sigma weight residual 116.30 129.15 -12.85 3.50e+00 8.16e-02 1.35e+01 angle pdb=" N GLY d 46 " pdb=" CA GLY d 46 " pdb=" C GLY d 46 " ideal model delta sigma weight residual 111.56 115.25 -3.69 1.01e+00 9.80e-01 1.33e+01 angle pdb=" CB MET m 262 " pdb=" CG MET m 262 " pdb=" SD MET m 262 " ideal model delta sigma weight residual 112.70 123.09 -10.39 3.00e+00 1.11e-01 1.20e+01 ... (remaining 6399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 2343 16.69 - 33.39: 390 33.39 - 50.08: 118 50.08 - 66.78: 20 66.78 - 83.47: 6 Dihedral angle restraints: 2877 sinusoidal: 1184 harmonic: 1693 Sorted by residual: dihedral pdb=" CB CYS d 37 " pdb=" SG CYS d 37 " pdb=" SG CYS d 73 " pdb=" CB CYS d 73 " ideal model delta sinusoidal sigma weight residual 93.00 175.13 -82.13 1 1.00e+01 1.00e-02 8.28e+01 dihedral pdb=" CB CYS e 49 " pdb=" SG CYS e 49 " pdb=" SG CYS e 98 " pdb=" CB CYS e 98 " ideal model delta sinusoidal sigma weight residual -86.00 -15.84 -70.16 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual -86.00 -154.55 68.55 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 2874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 504 0.037 - 0.074: 174 0.074 - 0.111: 55 0.111 - 0.148: 16 0.148 - 0.186: 2 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA ASP e 63 " pdb=" N ASP e 63 " pdb=" C ASP e 63 " pdb=" CB ASP e 63 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA ILE d 70 " pdb=" N ILE d 70 " pdb=" C ILE d 70 " pdb=" CB ILE d 70 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ASN e 121 " pdb=" N ASN e 121 " pdb=" C ASN e 121 " pdb=" CB ASN e 121 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 748 not shown) Planarity restraints: 785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR f 99 " 0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO f 100 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO f 100 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO f 100 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR e 99 " 0.037 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO e 100 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO e 100 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO e 100 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS f 104 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.53e+00 pdb=" N PRO f 105 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO f 105 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO f 105 " 0.017 5.00e-02 4.00e+02 ... (remaining 782 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 95 2.67 - 3.23: 4543 3.23 - 3.79: 7049 3.79 - 4.34: 8421 4.34 - 4.90: 13883 Nonbonded interactions: 33991 Sorted by model distance: nonbonded pdb=" OD1 ASP e 126 " pdb=" N VAL e 127 " model vdw 2.114 3.120 nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.225 3.040 nonbonded pdb=" N GLU f 56 " pdb=" OE1 GLU f 56 " model vdw 2.255 3.120 nonbonded pdb=" NE2 GLN e 60 " pdb=" OD1 ASN e 65 " model vdw 2.258 3.120 nonbonded pdb=" O ILE d 24 " pdb=" OH TYR e 95 " model vdw 2.279 3.040 ... (remaining 33986 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' and resid 28 through 50) selection = (chain 'b' and resid 28 through 50) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'f' and resid 33 through 153) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.870 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 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 0.060 4724 Z= 0.224 Angle : 0.774 12.853 6404 Z= 0.389 Chirality : 0.043 0.186 751 Planarity : 0.005 0.086 785 Dihedral : 17.513 83.473 1766 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.58 % Allowed : 39.73 % Favored : 59.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.34), residues: 565 helix: 2.06 (0.33), residues: 212 sheet: -1.22 (0.64), residues: 74 loop : -2.81 (0.30), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 43 HIS 0.004 0.001 HIS f 61 PHE 0.020 0.001 PHE g 118 TYR 0.016 0.001 TYR b 42 ARG 0.005 0.000 ARG d 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 71 TYR cc_start: 0.7273 (m-80) cc_final: 0.6834 (m-10) REVERT: d 90 TYR cc_start: 0.7388 (m-80) cc_final: 0.6902 (m-80) REVERT: e 36 TYR cc_start: 0.6981 (m-80) cc_final: 0.5299 (m-10) REVERT: e 46 ILE cc_start: 0.8085 (mp) cc_final: 0.7838 (mm) REVERT: e 47 LEU cc_start: 0.8296 (mt) cc_final: 0.8084 (tt) REVERT: e 49 CYS cc_start: 0.6913 (t) cc_final: 0.5597 (t) REVERT: e 85 LYS cc_start: 0.7718 (mptt) cc_final: 0.7517 (mptt) REVERT: e 91 GLU cc_start: 0.8234 (tp30) cc_final: 0.8019 (tm-30) REVERT: e 92 GLN cc_start: 0.7710 (tt0) cc_final: 0.7193 (tt0) REVERT: e 117 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7622 (ttt180) REVERT: e 120 GLU cc_start: 0.8013 (pp20) cc_final: 0.7719 (pp20) REVERT: e 123 MET cc_start: 0.5173 (mtt) cc_final: 0.4753 (ptp) REVERT: g 38 GLU cc_start: 0.8295 (pm20) cc_final: 0.8071 (pm20) REVERT: g 43 LEU cc_start: 0.7667 (mt) cc_final: 0.7448 (mt) REVERT: g 80 ASP cc_start: 0.8028 (m-30) cc_final: 0.7779 (t0) REVERT: g 111 ASN cc_start: 0.7321 (m110) cc_final: 0.6954 (p0) REVERT: m 286 LYS cc_start: 0.7448 (tppt) cc_final: 0.7238 (tptt) outliers start: 3 outliers final: 0 residues processed: 154 average time/residue: 0.1926 time to fit residues: 35.9882 Evaluate side-chains 136 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 21 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.186583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.161178 restraints weight = 8709.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.160990 restraints weight = 14490.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.162143 restraints weight = 10467.376| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4724 Z= 0.236 Angle : 0.682 6.033 6404 Z= 0.358 Chirality : 0.044 0.169 751 Planarity : 0.005 0.057 785 Dihedral : 5.059 50.680 692 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.19 % Allowed : 3.88 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.34), residues: 565 helix: 2.09 (0.33), residues: 217 sheet: -1.32 (0.64), residues: 75 loop : -2.99 (0.29), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP e 59 HIS 0.007 0.001 HIS f 61 PHE 0.023 0.002 PHE b 40 TYR 0.011 0.002 TYR n 264 ARG 0.003 0.001 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 36 TYR cc_start: 0.8070 (m-80) cc_final: 0.6549 (m-80) REVERT: e 49 CYS cc_start: 0.6009 (t) cc_final: 0.5782 (t) REVERT: f 101 ARG cc_start: 0.7993 (mtp85) cc_final: 0.7775 (mtp85) REVERT: f 110 PHE cc_start: 0.8161 (p90) cc_final: 0.7852 (p90) REVERT: f 121 ASN cc_start: 0.8335 (m-40) cc_final: 0.7013 (m-40) REVERT: f 128 MET cc_start: 0.6432 (mpp) cc_final: 0.6224 (mmt) REVERT: g 39 ASP cc_start: 0.8353 (p0) cc_final: 0.7985 (p0) REVERT: g 80 ASP cc_start: 0.8345 (m-30) cc_final: 0.8124 (t0) REVERT: n 259 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7790 (t0) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.1799 time to fit residues: 37.3616 Evaluate side-chains 136 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 50 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 89 HIS e 92 GLN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.181340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.158522 restraints weight = 7675.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.159194 restraints weight = 6471.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.159194 restraints weight = 5844.335| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4724 Z= 0.194 Angle : 0.652 7.617 6404 Z= 0.337 Chirality : 0.043 0.184 751 Planarity : 0.005 0.056 785 Dihedral : 4.957 50.062 692 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.34), residues: 565 helix: 2.29 (0.33), residues: 217 sheet: -1.16 (0.62), residues: 78 loop : -2.93 (0.29), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 43 HIS 0.006 0.002 HIS d 89 PHE 0.035 0.002 PHE b 40 TYR 0.013 0.001 TYR g 34 ARG 0.005 0.001 ARG g 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: e 36 TYR cc_start: 0.7933 (m-80) cc_final: 0.6777 (m-80) REVERT: e 98 CYS cc_start: 0.3221 (p) cc_final: 0.3001 (p) REVERT: e 115 ARG cc_start: 0.8086 (tpt170) cc_final: 0.7868 (tpt170) REVERT: f 110 PHE cc_start: 0.8172 (p90) cc_final: 0.7954 (p90) REVERT: f 115 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.7979 (tpt-90) REVERT: f 117 ARG cc_start: 0.8009 (ptp-170) cc_final: 0.7800 (ptp-170) REVERT: f 120 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7763 (tm-30) REVERT: f 121 ASN cc_start: 0.8172 (m-40) cc_final: 0.7475 (m-40) REVERT: f 125 MET cc_start: 0.8325 (ppp) cc_final: 0.8119 (ppp) REVERT: f 128 MET cc_start: 0.6261 (mpp) cc_final: 0.5882 (mmt) REVERT: g 39 ASP cc_start: 0.8274 (p0) cc_final: 0.7842 (p0) REVERT: g 80 ASP cc_start: 0.8319 (m-30) cc_final: 0.8008 (t0) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1705 time to fit residues: 32.4662 Evaluate side-chains 130 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.172759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.150733 restraints weight = 7859.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.151217 restraints weight = 6955.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.151703 restraints weight = 6359.956| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4724 Z= 0.278 Angle : 0.726 6.762 6404 Z= 0.376 Chirality : 0.045 0.169 751 Planarity : 0.004 0.051 785 Dihedral : 5.103 46.693 692 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.34), residues: 565 helix: 2.00 (0.33), residues: 218 sheet: -1.09 (0.62), residues: 81 loop : -2.98 (0.29), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 72 HIS 0.008 0.002 HIS f 61 PHE 0.028 0.002 PHE b 40 TYR 0.020 0.002 TYR e 99 ARG 0.009 0.001 ARG f 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.505 Fit side-chains REVERT: d 70 ILE cc_start: 0.8731 (mp) cc_final: 0.8380 (tt) REVERT: e 36 TYR cc_start: 0.7971 (m-80) cc_final: 0.6942 (m-10) REVERT: f 110 PHE cc_start: 0.8312 (p90) cc_final: 0.8013 (p90) REVERT: f 120 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7776 (tm-30) REVERT: f 121 ASN cc_start: 0.8158 (m-40) cc_final: 0.7349 (m-40) REVERT: f 128 MET cc_start: 0.6302 (mpp) cc_final: 0.5783 (mmt) REVERT: g 39 ASP cc_start: 0.8392 (p0) cc_final: 0.7823 (p0) REVERT: g 80 ASP cc_start: 0.8329 (m-30) cc_final: 0.7942 (t0) REVERT: n 265 MET cc_start: 0.9180 (tpp) cc_final: 0.8623 (tpp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1801 time to fit residues: 32.6578 Evaluate side-chains 122 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 38 optimal weight: 0.0010 chunk 5 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 259 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 = 0.4006 r_free = 0.4006 target = 0.165213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144874 restraints weight = 8046.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144938 restraints weight = 12213.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.146080 restraints weight = 9176.415| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4724 Z= 0.272 Angle : 0.719 6.979 6404 Z= 0.370 Chirality : 0.045 0.180 751 Planarity : 0.004 0.040 785 Dihedral : 5.320 49.895 692 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.34), residues: 565 helix: 1.90 (0.33), residues: 217 sheet: -1.28 (0.59), residues: 91 loop : -2.97 (0.29), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 72 HIS 0.006 0.002 HIS f 61 PHE 0.013 0.002 PHE m 281 TYR 0.013 0.001 TYR b 42 ARG 0.005 0.001 ARG f 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: d 70 ILE cc_start: 0.8804 (mp) cc_final: 0.8490 (tt) REVERT: e 36 TYR cc_start: 0.8071 (m-80) cc_final: 0.6663 (m-10) REVERT: e 49 CYS cc_start: 0.6494 (t) cc_final: 0.5893 (t) REVERT: f 90 LEU cc_start: 0.9151 (mm) cc_final: 0.8219 (mm) REVERT: f 110 PHE cc_start: 0.8405 (p90) cc_final: 0.8016 (p90) REVERT: f 120 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7625 (tm-30) REVERT: f 121 ASN cc_start: 0.8255 (m-40) cc_final: 0.7183 (m110) REVERT: f 125 MET cc_start: 0.8264 (ppp) cc_final: 0.7962 (ppp) REVERT: f 128 MET cc_start: 0.6218 (mpp) cc_final: 0.5871 (mmt) REVERT: g 39 ASP cc_start: 0.8172 (p0) cc_final: 0.7671 (p0) REVERT: g 80 ASP cc_start: 0.8429 (m-30) cc_final: 0.8050 (t0) REVERT: m 286 LYS cc_start: 0.8739 (tptt) cc_final: 0.8502 (tptt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1612 time to fit residues: 30.5483 Evaluate side-chains 130 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN n 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.169009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.148031 restraints weight = 7902.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.148988 restraints weight = 6536.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.148988 restraints weight = 5666.125| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4724 Z= 0.200 Angle : 0.667 6.592 6404 Z= 0.343 Chirality : 0.043 0.201 751 Planarity : 0.004 0.047 785 Dihedral : 5.255 50.537 692 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.34), residues: 565 helix: 1.99 (0.32), residues: 217 sheet: -1.64 (0.52), residues: 106 loop : -2.69 (0.31), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP f 59 HIS 0.006 0.002 HIS g 29 PHE 0.021 0.001 PHE g 118 TYR 0.012 0.001 TYR g 100 ARG 0.005 0.001 ARG e 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 68 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7134 (mtp-110) REVERT: d 70 ILE cc_start: 0.8765 (mp) cc_final: 0.8347 (tt) REVERT: d 87 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8256 (tm-30) REVERT: e 36 TYR cc_start: 0.7965 (m-80) cc_final: 0.6704 (m-10) REVERT: e 49 CYS cc_start: 0.6517 (t) cc_final: 0.6058 (t) REVERT: e 98 CYS cc_start: 0.3759 (p) cc_final: 0.3262 (p) REVERT: f 101 ARG cc_start: 0.7766 (mtp85) cc_final: 0.7515 (mmp80) REVERT: f 110 PHE cc_start: 0.8286 (p90) cc_final: 0.7932 (p90) REVERT: f 128 MET cc_start: 0.6238 (mpp) cc_final: 0.5920 (mmt) REVERT: g 39 ASP cc_start: 0.8220 (p0) cc_final: 0.7669 (p0) REVERT: g 80 ASP cc_start: 0.8245 (m-30) cc_final: 0.7998 (t0) REVERT: g 82 ARG cc_start: 0.8516 (mtt180) cc_final: 0.8083 (mtt180) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1599 time to fit residues: 29.3862 Evaluate side-chains 122 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 92 GLN f 81 HIS g 86 GLN n 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.165087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.144412 restraints weight = 7984.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.143912 restraints weight = 10180.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.144407 restraints weight = 9825.603| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4724 Z= 0.261 Angle : 0.728 6.677 6404 Z= 0.372 Chirality : 0.045 0.170 751 Planarity : 0.004 0.043 785 Dihedral : 5.293 45.919 692 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.34), residues: 565 helix: 1.88 (0.33), residues: 220 sheet: -1.47 (0.55), residues: 100 loop : -2.57 (0.32), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 72 HIS 0.006 0.002 HIS f 61 PHE 0.014 0.002 PHE n 277 TYR 0.017 0.002 TYR b 42 ARG 0.005 0.001 ARG e 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 98 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7730 (tm-30) REVERT: e 36 TYR cc_start: 0.7903 (m-80) cc_final: 0.6512 (m-10) REVERT: e 49 CYS cc_start: 0.6317 (t) cc_final: 0.5704 (t) REVERT: e 98 CYS cc_start: 0.3679 (p) cc_final: 0.3363 (p) REVERT: f 110 PHE cc_start: 0.8359 (p90) cc_final: 0.8123 (p90) REVERT: f 120 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7580 (tm-30) REVERT: f 121 ASN cc_start: 0.8159 (m-40) cc_final: 0.7447 (m-40) REVERT: f 125 MET cc_start: 0.8309 (ppp) cc_final: 0.7925 (ppp) REVERT: f 128 MET cc_start: 0.6350 (mpp) cc_final: 0.5880 (mmt) REVERT: g 39 ASP cc_start: 0.8170 (p0) cc_final: 0.7677 (p0) REVERT: g 82 ARG cc_start: 0.8651 (mtt180) cc_final: 0.8195 (mtt180) REVERT: m 267 LEU cc_start: 0.9314 (tp) cc_final: 0.9083 (tt) REVERT: n 265 MET cc_start: 0.9051 (mmm) cc_final: 0.8326 (ttm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1538 time to fit residues: 27.5200 Evaluate side-chains 120 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.0470 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS ** n 259 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 = 0.4052 r_free = 0.4052 target = 0.168663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.150482 restraints weight = 7915.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.150212 restraints weight = 7843.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.151081 restraints weight = 8611.970| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4724 Z= 0.195 Angle : 0.682 7.055 6404 Z= 0.348 Chirality : 0.043 0.183 751 Planarity : 0.004 0.042 785 Dihedral : 5.270 52.715 692 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.35), residues: 565 helix: 2.15 (0.33), residues: 217 sheet: -1.65 (0.53), residues: 106 loop : -2.54 (0.33), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g 55 HIS 0.004 0.001 HIS g 29 PHE 0.018 0.001 PHE g 118 TYR 0.010 0.001 TYR g 85 ARG 0.005 0.001 ARG e 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 70 ILE cc_start: 0.8828 (mp) cc_final: 0.8428 (tt) REVERT: e 36 TYR cc_start: 0.7729 (m-80) cc_final: 0.6073 (m-80) REVERT: e 49 CYS cc_start: 0.6439 (t) cc_final: 0.6141 (t) REVERT: f 120 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7504 (tm-30) REVERT: f 121 ASN cc_start: 0.8175 (m-40) cc_final: 0.7442 (m110) REVERT: f 125 MET cc_start: 0.8092 (ppp) cc_final: 0.7760 (ppp) REVERT: f 128 MET cc_start: 0.6228 (mpp) cc_final: 0.5890 (mmt) REVERT: g 39 ASP cc_start: 0.8215 (p0) cc_final: 0.7712 (p0) REVERT: g 61 MET cc_start: 0.2447 (tpt) cc_final: 0.2079 (tpt) REVERT: m 267 LEU cc_start: 0.9288 (tp) cc_final: 0.9058 (tt) REVERT: m 284 THR cc_start: 0.8845 (m) cc_final: 0.8633 (m) REVERT: n 265 MET cc_start: 0.8803 (mmm) cc_final: 0.8213 (ttm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1613 time to fit residues: 28.7482 Evaluate side-chains 115 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN n 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.166889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146562 restraints weight = 7898.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.146876 restraints weight = 8262.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.147193 restraints weight = 7653.202| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4724 Z= 0.232 Angle : 0.708 6.771 6404 Z= 0.364 Chirality : 0.044 0.163 751 Planarity : 0.004 0.043 785 Dihedral : 5.229 47.523 692 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.35), residues: 565 helix: 2.13 (0.32), residues: 218 sheet: -1.59 (0.54), residues: 104 loop : -2.54 (0.33), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 72 HIS 0.005 0.002 HIS f 61 PHE 0.015 0.002 PHE g 118 TYR 0.016 0.001 TYR b 42 ARG 0.006 0.001 ARG f 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: e 36 TYR cc_start: 0.7858 (m-80) cc_final: 0.6295 (m-80) REVERT: e 49 CYS cc_start: 0.6594 (t) cc_final: 0.6107 (t) REVERT: e 59 TRP cc_start: 0.7117 (m100) cc_final: 0.6619 (m100) REVERT: f 120 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7515 (tm-30) REVERT: f 121 ASN cc_start: 0.8143 (m-40) cc_final: 0.7345 (m110) REVERT: f 125 MET cc_start: 0.8140 (ppp) cc_final: 0.7908 (ppp) REVERT: f 128 MET cc_start: 0.6416 (mpp) cc_final: 0.5999 (mmt) REVERT: g 39 ASP cc_start: 0.8367 (p0) cc_final: 0.7927 (p0) REVERT: g 43 LEU cc_start: 0.7895 (mp) cc_final: 0.7687 (mt) REVERT: g 61 MET cc_start: 0.2204 (tpt) cc_final: 0.1718 (tpt) REVERT: m 267 LEU cc_start: 0.9293 (tp) cc_final: 0.9057 (tt) REVERT: m 284 THR cc_start: 0.8934 (m) cc_final: 0.8724 (m) REVERT: m 286 LYS cc_start: 0.8492 (tptt) cc_final: 0.8168 (tptt) REVERT: n 265 MET cc_start: 0.8863 (mmm) cc_final: 0.8165 (ttm) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1558 time to fit residues: 27.5326 Evaluate side-chains 119 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 0.0170 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 29 HIS ** n 259 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 = 0.4054 r_free = 0.4054 target = 0.169288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.148279 restraints weight = 8002.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.147656 restraints weight = 10527.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148309 restraints weight = 9305.722| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4724 Z= 0.210 Angle : 0.710 7.091 6404 Z= 0.361 Chirality : 0.044 0.169 751 Planarity : 0.004 0.040 785 Dihedral : 5.281 50.967 692 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.35), residues: 565 helix: 1.99 (0.32), residues: 224 sheet: -1.65 (0.51), residues: 110 loop : -2.48 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g 72 HIS 0.003 0.001 HIS g 29 PHE 0.019 0.001 PHE g 118 TYR 0.010 0.001 TYR g 100 ARG 0.007 0.001 ARG f 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 28 ASP cc_start: 0.7103 (m-30) cc_final: 0.6546 (p0) REVERT: e 36 TYR cc_start: 0.7735 (m-80) cc_final: 0.6260 (m-80) REVERT: e 49 CYS cc_start: 0.6516 (t) cc_final: 0.6118 (t) REVERT: e 59 TRP cc_start: 0.7091 (m100) cc_final: 0.6603 (m100) REVERT: f 115 ARG cc_start: 0.8779 (tpt-90) cc_final: 0.8384 (tpt90) REVERT: f 120 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7495 (tm-30) REVERT: f 121 ASN cc_start: 0.8146 (m-40) cc_final: 0.7346 (m110) REVERT: f 125 MET cc_start: 0.8178 (ppp) cc_final: 0.7897 (ppp) REVERT: f 128 MET cc_start: 0.6385 (mpp) cc_final: 0.5959 (mmt) REVERT: g 39 ASP cc_start: 0.8230 (p0) cc_final: 0.7848 (p0) REVERT: g 61 MET cc_start: 0.2008 (tpt) cc_final: 0.1588 (tpt) REVERT: m 267 LEU cc_start: 0.9310 (tp) cc_final: 0.9096 (tt) REVERT: n 265 MET cc_start: 0.8876 (mmm) cc_final: 0.8305 (ttm) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1720 time to fit residues: 30.2806 Evaluate side-chains 117 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN ** n 259 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 = 0.3994 r_free = 0.3994 target = 0.163077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144640 restraints weight = 7911.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145150 restraints weight = 13052.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145812 restraints weight = 10299.140| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4724 Z= 0.267 Angle : 0.748 6.530 6404 Z= 0.385 Chirality : 0.045 0.163 751 Planarity : 0.004 0.038 785 Dihedral : 5.416 47.075 692 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.34), residues: 565 helix: 1.72 (0.32), residues: 224 sheet: -1.69 (0.53), residues: 104 loop : -2.54 (0.34), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 72 HIS 0.009 0.003 HIS g 29 PHE 0.019 0.002 PHE m 289 TYR 0.015 0.002 TYR b 42 ARG 0.009 0.001 ARG f 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1721.81 seconds wall clock time: 30 minutes 44.23 seconds (1844.23 seconds total)