Starting phenix.real_space_refine on Tue Sep 24 11:31:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtz_21900/09_2024/6wtz_21900.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtz_21900/09_2024/6wtz_21900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtz_21900/09_2024/6wtz_21900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtz_21900/09_2024/6wtz_21900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtz_21900/09_2024/6wtz_21900.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtz_21900/09_2024/6wtz_21900.cif" } resolution = 3.15 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= 0.085 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 9 5.16 5 C 4962 2.51 5 N 1314 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7917 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2627 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 335} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Restraints were copied for chains: C, B Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASN A 27 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 27 " occ=0.00 residue: pdb=" N ASN B 27 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN B 27 " occ=0.00 residue: pdb=" N ASN C 27 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN C 27 " occ=0.00 Time building chain proxies: 4.97, per 1000 atoms: 0.63 Number of scatterers: 7917 At special positions: 0 Unit cell: (92.88, 95.04, 69.12, 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 9 16.00 O 1632 8.00 N 1314 7.00 C 4962 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: 1.58 Conformation dependent library (CDL) restraints added in 981.2 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1752 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 6 sheets defined 4.4% alpha, 45.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.523A pdb=" N ALA A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 110 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.524A pdb=" N ALA B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 110 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.524A pdb=" N ALA C 202 " --> pdb=" O ASN C 198 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2 through 5 current: chain 'A' and resid 56 through 66 removed outlier: 3.587A pdb=" N LEU A 83 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN A 64 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR A 81 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 95 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR A 139 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP A 97 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA A 137 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY A 99 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 229 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 253 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA A 280 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASP A 290 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP A 282 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASP A 288 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 297 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 15 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2 through 5 current: chain 'B' and resid 56 through 66 removed outlier: 3.587A pdb=" N LEU B 83 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 64 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR B 81 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER B 95 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR B 139 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP B 97 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA B 137 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLY B 99 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 229 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 253 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA B 280 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASP B 290 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 282 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASP B 288 " --> pdb=" O ASP B 282 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 297 " --> pdb=" O TYR B 313 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 15 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 5 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 2 through 5 current: chain 'C' and resid 56 through 66 removed outlier: 3.587A pdb=" N LEU C 83 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN C 64 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR C 81 " --> pdb=" O ASN C 64 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER C 95 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR C 139 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP C 97 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA C 137 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLY C 99 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 229 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS C 253 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA C 280 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASP C 290 " --> pdb=" O ALA C 280 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP C 282 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP C 288 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 297 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 15 " --> pdb=" O PHE C 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 239 through 242 354 hydrogen bonds defined for protein. 999 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: 2.21 Time building geometry restraints manager: 1.91 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: 2631 1.34 - 1.45: 1534 1.45 - 1.57: 3866 1.57 - 1.68: 0 1.68 - 1.80: 18 Bond restraints: 8049 Sorted by residual: bond pdb=" N PHE B 144 " pdb=" CA PHE B 144 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.17e-02 7.31e+03 3.11e+00 bond pdb=" N PHE C 144 " pdb=" CA PHE C 144 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.17e-02 7.31e+03 3.00e+00 bond pdb=" N PHE A 144 " pdb=" CA PHE A 144 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.17e-02 7.31e+03 2.88e+00 bond pdb=" C LYS B 219 " pdb=" N TYR B 220 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.28e-02 6.10e+03 2.58e+00 bond pdb=" C LYS A 219 " pdb=" N TYR A 220 " ideal model delta sigma weight residual 1.330 1.350 -0.020 1.28e-02 6.10e+03 2.53e+00 ... (remaining 8044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 10373 1.73 - 3.45: 439 3.45 - 5.18: 56 5.18 - 6.90: 19 6.90 - 8.63: 3 Bond angle restraints: 10890 Sorted by residual: angle pdb=" C ASP A 127 " pdb=" N PHE A 128 " pdb=" CA PHE A 128 " ideal model delta sigma weight residual 121.54 130.17 -8.63 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C ASP C 127 " pdb=" N PHE C 128 " pdb=" CA PHE C 128 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" C ASP B 127 " pdb=" N PHE B 128 " pdb=" CA PHE B 128 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C ASN A 143 " pdb=" N PHE A 144 " pdb=" CA PHE A 144 " ideal model delta sigma weight residual 121.19 127.38 -6.19 1.59e+00 3.96e-01 1.51e+01 angle pdb=" C ASN C 143 " pdb=" N PHE C 144 " pdb=" CA PHE C 144 " ideal model delta sigma weight residual 121.19 127.33 -6.14 1.59e+00 3.96e-01 1.49e+01 ... (remaining 10885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4038 17.65 - 35.30: 390 35.30 - 52.95: 102 52.95 - 70.60: 27 70.60 - 88.25: 9 Dihedral angle restraints: 4566 sinusoidal: 1710 harmonic: 2856 Sorted by residual: dihedral pdb=" CA ASN A 143 " pdb=" C ASN A 143 " pdb=" N PHE A 144 " pdb=" CA PHE A 144 " ideal model delta harmonic sigma weight residual -180.00 -138.76 -41.24 0 5.00e+00 4.00e-02 6.80e+01 dihedral pdb=" CA ASN B 143 " pdb=" C ASN B 143 " pdb=" N PHE B 144 " pdb=" CA PHE B 144 " ideal model delta harmonic sigma weight residual 180.00 -138.81 -41.19 0 5.00e+00 4.00e-02 6.79e+01 dihedral pdb=" CA ASN C 143 " pdb=" C ASN C 143 " pdb=" N PHE C 144 " pdb=" CA PHE C 144 " ideal model delta harmonic sigma weight residual -180.00 -138.83 -41.17 0 5.00e+00 4.00e-02 6.78e+01 ... (remaining 4563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 828 0.052 - 0.105: 214 0.105 - 0.157: 55 0.157 - 0.209: 4 0.209 - 0.261: 3 Chirality restraints: 1104 Sorted by residual: chirality pdb=" CB ILE C 336 " pdb=" CA ILE C 336 " pdb=" CG1 ILE C 336 " pdb=" CG2 ILE C 336 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE A 336 " pdb=" CA ILE A 336 " pdb=" CG1 ILE A 336 " pdb=" CG2 ILE A 336 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE B 336 " pdb=" CA ILE B 336 " pdb=" CG1 ILE B 336 " pdb=" CG2 ILE B 336 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1101 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 115 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO B 116 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 116 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 116 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 115 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.47e+00 pdb=" N PRO C 116 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 116 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 116 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 115 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO A 116 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " 0.033 5.00e-02 4.00e+02 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2543 2.82 - 3.34: 6096 3.34 - 3.86: 13126 3.86 - 4.38: 15448 4.38 - 4.90: 28034 Nonbonded interactions: 65247 Sorted by model distance: nonbonded pdb=" OH TYR C 32 " pdb=" OD1 ASP C 121 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR B 32 " pdb=" OD1 ASP B 121 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR A 32 " pdb=" OD1 ASP A 121 " model vdw 2.302 3.040 nonbonded pdb=" N ASP A 149 " pdb=" OD1 ASP A 149 " model vdw 2.307 3.120 nonbonded pdb=" N ASP B 149 " pdb=" OD1 ASP B 149 " model vdw 2.307 3.120 ... (remaining 65242 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 'B' selection = chain 'C' } 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=0.00 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.960 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 0.034 8049 Z= 0.266 Angle : 0.839 8.630 10890 Z= 0.496 Chirality : 0.052 0.261 1104 Planarity : 0.005 0.059 1470 Dihedral : 15.731 88.250 2814 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.70 % Allowed : 5.70 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.14 (0.25), residues: 1014 helix: -5.21 (0.18), residues: 18 sheet: 0.12 (0.23), residues: 543 loop : -3.37 (0.22), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 214 HIS 0.003 0.002 HIS B 21 PHE 0.027 0.003 PHE C 128 TYR 0.016 0.002 TYR A 310 ARG 0.002 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 268 time to evaluate : 0.832 Fit side-chains REVERT: A 25 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6986 (ptpt) REVERT: A 62 GLU cc_start: 0.8445 (tt0) cc_final: 0.7943 (tt0) REVERT: A 66 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8191 (mm-40) REVERT: A 210 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.6976 (ttmm) REVERT: A 290 ASP cc_start: 0.7561 (m-30) cc_final: 0.6566 (p0) REVERT: A 312 ASP cc_start: 0.8235 (t0) cc_final: 0.7989 (t0) REVERT: A 329 ASP cc_start: 0.6308 (m-30) cc_final: 0.5931 (m-30) REVERT: B 10 LYS cc_start: 0.7840 (pttm) cc_final: 0.7209 (ptmt) REVERT: B 12 ASP cc_start: 0.6949 (p0) cc_final: 0.6717 (p0) REVERT: B 25 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6754 (mttm) REVERT: B 48 GLU cc_start: 0.7465 (tp30) cc_final: 0.7223 (tp30) REVERT: B 62 GLU cc_start: 0.8484 (tt0) cc_final: 0.7990 (tt0) REVERT: B 95 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8244 (p) REVERT: B 114 MET cc_start: 0.7615 (mmm) cc_final: 0.7401 (mmm) REVERT: B 187 ILE cc_start: 0.7098 (tt) cc_final: 0.6848 (tt) REVERT: B 210 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6861 (ttmm) REVERT: B 219 LYS cc_start: 0.7387 (tttp) cc_final: 0.7071 (tttt) REVERT: B 279 LYS cc_start: 0.7354 (ttpt) cc_final: 0.7144 (ttpt) REVERT: B 290 ASP cc_start: 0.7280 (m-30) cc_final: 0.6354 (p0) REVERT: B 312 ASP cc_start: 0.7987 (t0) cc_final: 0.7593 (t0) REVERT: B 329 ASP cc_start: 0.6396 (m-30) cc_final: 0.6184 (m-30) REVERT: B 339 GLN cc_start: 0.7676 (pt0) cc_final: 0.7456 (pt0) REVERT: C 62 GLU cc_start: 0.8235 (tt0) cc_final: 0.7777 (tt0) REVERT: C 210 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6902 (ttmm) REVERT: C 224 ASN cc_start: 0.7960 (m-40) cc_final: 0.7685 (m-40) REVERT: C 231 TYR cc_start: 0.7717 (t80) cc_final: 0.6991 (t80) REVERT: C 290 ASP cc_start: 0.7350 (m-30) cc_final: 0.6462 (p0) REVERT: C 329 ASP cc_start: 0.6866 (m-30) cc_final: 0.6420 (m-30) outliers start: 45 outliers final: 14 residues processed: 291 average time/residue: 0.1740 time to fit residues: 69.6230 Evaluate side-chains 229 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 328 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS A 170 ASN A 230 ASN A 262 GLN B 170 ASN B 262 GLN C 21 HIS C 170 ASN C 230 ASN C 236 ASN C 262 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8049 Z= 0.413 Angle : 0.731 7.142 10890 Z= 0.405 Chirality : 0.049 0.147 1104 Planarity : 0.005 0.036 1470 Dihedral : 6.638 35.839 1184 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.92 % Allowed : 13.81 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -1.79 (0.26), residues: 1014 helix: -4.96 (0.16), residues: 18 sheet: 0.15 (0.23), residues: 555 loop : -2.91 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 214 HIS 0.004 0.002 HIS C 21 PHE 0.027 0.003 PHE B 153 TYR 0.021 0.002 TYR A 310 ARG 0.004 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 0.803 Fit side-chains REVERT: A 62 GLU cc_start: 0.8533 (tt0) cc_final: 0.8027 (tt0) REVERT: A 98 TYR cc_start: 0.8195 (t80) cc_final: 0.7984 (t80) REVERT: A 210 LYS cc_start: 0.7856 (ttpt) cc_final: 0.7171 (ttmm) REVERT: A 296 GLU cc_start: 0.7667 (tp30) cc_final: 0.7302 (tp30) REVERT: B 50 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7236 (mm-40) REVERT: B 62 GLU cc_start: 0.8394 (tt0) cc_final: 0.7937 (tt0) REVERT: B 182 TYR cc_start: 0.8063 (t80) cc_final: 0.7855 (t80) REVERT: B 210 LYS cc_start: 0.7731 (ttpt) cc_final: 0.6875 (tppt) REVERT: B 219 LYS cc_start: 0.6885 (tttp) cc_final: 0.6425 (tttt) REVERT: B 272 SER cc_start: 0.7265 (m) cc_final: 0.6954 (t) REVERT: C 12 ASP cc_start: 0.7094 (p0) cc_final: 0.6801 (p0) REVERT: C 62 GLU cc_start: 0.8426 (tt0) cc_final: 0.8021 (tt0) REVERT: C 210 LYS cc_start: 0.7606 (ttpt) cc_final: 0.7069 (ttmm) REVERT: C 224 ASN cc_start: 0.7933 (m-40) cc_final: 0.7585 (m-40) REVERT: C 284 GLU cc_start: 0.6757 (mp0) cc_final: 0.6553 (mp0) REVERT: C 312 ASP cc_start: 0.8382 (t0) cc_final: 0.8076 (t0) REVERT: C 329 ASP cc_start: 0.6333 (m-30) cc_final: 0.6023 (m-30) outliers start: 23 outliers final: 16 residues processed: 227 average time/residue: 0.1735 time to fit residues: 54.6136 Evaluate side-chains 218 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 202 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 0.0370 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 82 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN C 152 ASN C 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8049 Z= 0.204 Angle : 0.588 7.162 10890 Z= 0.329 Chirality : 0.045 0.138 1104 Planarity : 0.004 0.039 1470 Dihedral : 5.412 30.165 1141 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.92 % Allowed : 18.25 % Favored : 78.83 % 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: -1.64 (0.26), residues: 1014 helix: -4.78 (0.17), residues: 18 sheet: 0.09 (0.22), residues: 558 loop : -2.58 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 214 HIS 0.004 0.001 HIS C 21 PHE 0.023 0.002 PHE B 153 TYR 0.018 0.001 TYR A 310 ARG 0.002 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8521 (tt0) cc_final: 0.8090 (tt0) REVERT: A 71 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 98 TYR cc_start: 0.8150 (t80) cc_final: 0.7872 (t80) REVERT: A 187 ILE cc_start: 0.6692 (tt) cc_final: 0.6475 (tp) REVERT: A 210 LYS cc_start: 0.7723 (ttpt) cc_final: 0.7041 (ttmm) REVERT: B 62 GLU cc_start: 0.8372 (tt0) cc_final: 0.7989 (tt0) REVERT: B 182 TYR cc_start: 0.7998 (t80) cc_final: 0.7718 (t80) REVERT: B 210 LYS cc_start: 0.7752 (ttpt) cc_final: 0.6905 (tppt) REVERT: B 219 LYS cc_start: 0.6673 (tttp) cc_final: 0.6346 (tttt) REVERT: B 272 SER cc_start: 0.7283 (m) cc_final: 0.7053 (t) REVERT: C 12 ASP cc_start: 0.6869 (p0) cc_final: 0.6623 (p0) REVERT: C 62 GLU cc_start: 0.8460 (tt0) cc_final: 0.8067 (tt0) REVERT: C 210 LYS cc_start: 0.7628 (ttpt) cc_final: 0.7139 (ttmm) outliers start: 23 outliers final: 21 residues processed: 219 average time/residue: 0.1734 time to fit residues: 52.8609 Evaluate side-chains 215 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 0.0370 chunk 55 optimal weight: 1.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 230 ASN C 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8049 Z= 0.218 Angle : 0.583 7.061 10890 Z= 0.326 Chirality : 0.045 0.138 1104 Planarity : 0.003 0.038 1470 Dihedral : 5.251 21.191 1140 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.69 % Allowed : 19.14 % Favored : 76.17 % 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: -1.38 (0.26), residues: 1014 helix: -4.42 (0.23), residues: 18 sheet: 0.20 (0.22), residues: 582 loop : -2.46 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 214 HIS 0.004 0.001 HIS C 21 PHE 0.021 0.002 PHE B 128 TYR 0.017 0.001 TYR A 310 ARG 0.002 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 195 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8527 (tt0) cc_final: 0.8118 (tt0) REVERT: A 71 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7936 (mt-10) REVERT: A 98 TYR cc_start: 0.8194 (t80) cc_final: 0.7887 (t80) REVERT: A 210 LYS cc_start: 0.7657 (ttpt) cc_final: 0.7005 (ttmm) REVERT: B 2 GLU cc_start: 0.7082 (tt0) cc_final: 0.6867 (tt0) REVERT: B 30 ASN cc_start: 0.7801 (t0) cc_final: 0.7380 (t0) REVERT: B 62 GLU cc_start: 0.8384 (tt0) cc_final: 0.8006 (tt0) REVERT: B 182 TYR cc_start: 0.8089 (t80) cc_final: 0.7801 (t80) REVERT: B 210 LYS cc_start: 0.7757 (ttpt) cc_final: 0.6904 (tppt) REVERT: B 219 LYS cc_start: 0.6806 (tttp) cc_final: 0.6395 (tttt) REVERT: B 272 SER cc_start: 0.7249 (m) cc_final: 0.6991 (t) REVERT: C 12 ASP cc_start: 0.6915 (p0) cc_final: 0.6657 (p0) REVERT: C 62 GLU cc_start: 0.8499 (tt0) cc_final: 0.8097 (tt0) REVERT: C 210 LYS cc_start: 0.7537 (ttpt) cc_final: 0.7119 (ttmm) outliers start: 37 outliers final: 28 residues processed: 218 average time/residue: 0.1775 time to fit residues: 54.2439 Evaluate side-chains 225 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 84 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8049 Z= 0.349 Angle : 0.666 7.250 10890 Z= 0.371 Chirality : 0.047 0.166 1104 Planarity : 0.004 0.037 1470 Dihedral : 5.640 26.383 1140 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.58 % Allowed : 21.17 % Favored : 73.26 % 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: -1.36 (0.25), residues: 1014 helix: -4.02 (0.38), residues: 18 sheet: 0.29 (0.22), residues: 567 loop : -2.50 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP C 214 HIS 0.004 0.002 HIS C 21 PHE 0.020 0.002 PHE A 128 TYR 0.019 0.002 TYR B 157 ARG 0.002 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 185 time to evaluate : 0.859 Fit side-chains REVERT: A 62 GLU cc_start: 0.8541 (tt0) cc_final: 0.8084 (tt0) REVERT: A 210 LYS cc_start: 0.7612 (ttpt) cc_final: 0.6958 (ttmm) REVERT: A 219 LYS cc_start: 0.6677 (tttp) cc_final: 0.6416 (tttt) REVERT: B 30 ASN cc_start: 0.7727 (t0) cc_final: 0.7220 (t0) REVERT: B 62 GLU cc_start: 0.8389 (tt0) cc_final: 0.8010 (tt0) REVERT: B 182 TYR cc_start: 0.8153 (t80) cc_final: 0.7764 (t80) REVERT: B 210 LYS cc_start: 0.7789 (ttpt) cc_final: 0.6885 (tppt) REVERT: B 219 LYS cc_start: 0.7085 (tttp) cc_final: 0.6781 (ttmt) REVERT: B 272 SER cc_start: 0.7253 (m) cc_final: 0.6856 (t) REVERT: C 12 ASP cc_start: 0.7065 (p0) cc_final: 0.6801 (p0) REVERT: C 29 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7141 (pm20) REVERT: C 38 MET cc_start: 0.7878 (mtp) cc_final: 0.7621 (ttm) REVERT: C 62 GLU cc_start: 0.8537 (tt0) cc_final: 0.8138 (tt0) REVERT: C 210 LYS cc_start: 0.7551 (ttpt) cc_final: 0.7146 (ttmm) REVERT: C 296 GLU cc_start: 0.7814 (tp30) cc_final: 0.7046 (tp30) outliers start: 44 outliers final: 33 residues processed: 216 average time/residue: 0.1752 time to fit residues: 52.7696 Evaluate side-chains 214 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 180 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8049 Z= 0.241 Angle : 0.603 7.116 10890 Z= 0.337 Chirality : 0.045 0.153 1104 Planarity : 0.003 0.038 1470 Dihedral : 5.315 22.355 1140 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.32 % Allowed : 21.67 % Favored : 73.00 % 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: -1.31 (0.26), residues: 1014 helix: -3.80 (0.41), residues: 18 sheet: 0.24 (0.22), residues: 567 loop : -2.33 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 214 HIS 0.003 0.001 HIS C 21 PHE 0.021 0.002 PHE A 128 TYR 0.016 0.002 TYR A 310 ARG 0.001 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 195 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8540 (tt0) cc_final: 0.8108 (tt0) REVERT: A 210 LYS cc_start: 0.7649 (ttpt) cc_final: 0.6969 (ttmm) REVERT: B 30 ASN cc_start: 0.7703 (t0) cc_final: 0.7199 (t0) REVERT: B 62 GLU cc_start: 0.8372 (tt0) cc_final: 0.7974 (tt0) REVERT: B 210 LYS cc_start: 0.7738 (ttpt) cc_final: 0.6862 (tppt) REVERT: B 219 LYS cc_start: 0.6953 (tttp) cc_final: 0.6659 (ttmt) REVERT: B 272 SER cc_start: 0.7214 (m) cc_final: 0.6920 (t) REVERT: C 12 ASP cc_start: 0.6993 (p0) cc_final: 0.6723 (p0) REVERT: C 62 GLU cc_start: 0.8546 (tt0) cc_final: 0.8141 (tt0) REVERT: C 90 TYR cc_start: 0.7179 (t80) cc_final: 0.6752 (t80) REVERT: C 210 LYS cc_start: 0.7618 (ttpt) cc_final: 0.7210 (ttmm) REVERT: C 312 ASP cc_start: 0.8405 (t0) cc_final: 0.8116 (t0) REVERT: C 314 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6378 (mm) outliers start: 42 outliers final: 35 residues processed: 225 average time/residue: 0.1704 time to fit residues: 53.9464 Evaluate side-chains 223 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8049 Z= 0.223 Angle : 0.592 7.063 10890 Z= 0.332 Chirality : 0.045 0.138 1104 Planarity : 0.003 0.038 1470 Dihedral : 5.208 21.368 1140 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.20 % Allowed : 22.31 % Favored : 72.50 % 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: -1.26 (0.26), residues: 1014 helix: -3.59 (0.43), residues: 18 sheet: 0.24 (0.22), residues: 567 loop : -2.26 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 214 HIS 0.004 0.001 HIS C 21 PHE 0.021 0.002 PHE A 128 TYR 0.016 0.001 TYR A 310 ARG 0.001 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 192 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8537 (tt0) cc_final: 0.8102 (tt0) REVERT: A 210 LYS cc_start: 0.7642 (ttpt) cc_final: 0.7017 (ttmm) REVERT: B 29 GLU cc_start: 0.7312 (pm20) cc_final: 0.7027 (pm20) REVERT: B 30 ASN cc_start: 0.7712 (t0) cc_final: 0.7204 (t0) REVERT: B 62 GLU cc_start: 0.8374 (tt0) cc_final: 0.7979 (tt0) REVERT: B 210 LYS cc_start: 0.7744 (ttpt) cc_final: 0.6879 (tppt) REVERT: B 219 LYS cc_start: 0.6946 (tttp) cc_final: 0.6648 (ttmt) REVERT: B 272 SER cc_start: 0.7197 (m) cc_final: 0.6899 (t) REVERT: C 62 GLU cc_start: 0.8550 (tt0) cc_final: 0.8153 (tt0) REVERT: C 90 TYR cc_start: 0.7165 (t80) cc_final: 0.6753 (t80) REVERT: C 115 LEU cc_start: 0.8347 (mp) cc_final: 0.8107 (mp) REVERT: C 210 LYS cc_start: 0.7616 (ttpt) cc_final: 0.7211 (ttmm) outliers start: 41 outliers final: 36 residues processed: 218 average time/residue: 0.1662 time to fit residues: 50.9167 Evaluate side-chains 226 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 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 230 ASN C 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8049 Z= 0.315 Angle : 0.646 7.241 10890 Z= 0.361 Chirality : 0.047 0.215 1104 Planarity : 0.004 0.037 1470 Dihedral : 5.497 25.454 1140 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.96 % Allowed : 22.05 % Favored : 71.99 % 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: -1.23 (0.25), residues: 1014 helix: -3.44 (0.50), residues: 18 sheet: 0.37 (0.22), residues: 561 loop : -2.38 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 214 HIS 0.003 0.001 HIS C 21 PHE 0.020 0.002 PHE B 128 TYR 0.017 0.002 TYR A 310 ARG 0.002 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 185 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8544 (tt0) cc_final: 0.8083 (tt0) REVERT: A 210 LYS cc_start: 0.7626 (ttpt) cc_final: 0.7010 (ttmm) REVERT: B 29 GLU cc_start: 0.7282 (pm20) cc_final: 0.7039 (pm20) REVERT: B 30 ASN cc_start: 0.7676 (t0) cc_final: 0.7174 (t0) REVERT: B 62 GLU cc_start: 0.8395 (tt0) cc_final: 0.7974 (tt0) REVERT: B 210 LYS cc_start: 0.7720 (ttpt) cc_final: 0.6783 (tppt) REVERT: B 219 LYS cc_start: 0.7021 (tttp) cc_final: 0.6717 (ttmt) REVERT: C 38 MET cc_start: 0.7902 (mtp) cc_final: 0.7663 (ttm) REVERT: C 62 GLU cc_start: 0.8541 (tt0) cc_final: 0.8169 (tt0) REVERT: C 90 TYR cc_start: 0.7094 (t80) cc_final: 0.6657 (t80) REVERT: C 115 LEU cc_start: 0.8379 (mp) cc_final: 0.8140 (mp) REVERT: C 210 LYS cc_start: 0.7612 (ttpt) cc_final: 0.7200 (ttmm) outliers start: 47 outliers final: 41 residues processed: 218 average time/residue: 0.1732 time to fit residues: 53.0308 Evaluate side-chains 226 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 185 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.0570 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8049 Z= 0.266 Angle : 0.619 7.121 10890 Z= 0.347 Chirality : 0.045 0.176 1104 Planarity : 0.003 0.037 1470 Dihedral : 5.351 23.249 1140 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.83 % Allowed : 22.69 % Favored : 71.48 % 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: -1.23 (0.25), residues: 1014 helix: -3.23 (0.55), residues: 18 sheet: 0.30 (0.22), residues: 561 loop : -2.28 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 214 HIS 0.003 0.001 HIS C 21 PHE 0.021 0.002 PHE A 128 TYR 0.017 0.002 TYR A 310 ARG 0.001 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 187 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8547 (tt0) cc_final: 0.8122 (tt0) REVERT: A 210 LYS cc_start: 0.7635 (ttpt) cc_final: 0.7011 (ttmm) REVERT: B 29 GLU cc_start: 0.7278 (pm20) cc_final: 0.7008 (pm20) REVERT: B 30 ASN cc_start: 0.7655 (t0) cc_final: 0.7153 (t0) REVERT: B 62 GLU cc_start: 0.8401 (tt0) cc_final: 0.8013 (tt0) REVERT: B 182 TYR cc_start: 0.8121 (t80) cc_final: 0.7747 (t80) REVERT: B 210 LYS cc_start: 0.7737 (ttpt) cc_final: 0.6863 (tppt) REVERT: B 219 LYS cc_start: 0.6974 (tttp) cc_final: 0.6687 (ttmt) REVERT: B 272 SER cc_start: 0.7259 (m) cc_final: 0.6937 (t) REVERT: C 38 MET cc_start: 0.7870 (mtp) cc_final: 0.7626 (ttm) REVERT: C 62 GLU cc_start: 0.8544 (tt0) cc_final: 0.8160 (tt0) REVERT: C 90 TYR cc_start: 0.7057 (t80) cc_final: 0.6621 (t80) REVERT: C 115 LEU cc_start: 0.8356 (mp) cc_final: 0.8111 (mp) REVERT: C 182 TYR cc_start: 0.8082 (t80) cc_final: 0.7722 (t80) REVERT: C 210 LYS cc_start: 0.7617 (ttpt) cc_final: 0.7205 (ttmm) outliers start: 46 outliers final: 43 residues processed: 219 average time/residue: 0.1597 time to fit residues: 48.9558 Evaluate side-chains 232 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 189 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 80 optimal weight: 0.0670 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 24 optimal weight: 0.0370 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8049 Z= 0.148 Angle : 0.557 6.973 10890 Z= 0.313 Chirality : 0.044 0.163 1104 Planarity : 0.003 0.038 1470 Dihedral : 4.841 20.492 1140 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.93 % Allowed : 24.46 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1014 helix: -3.09 (0.54), residues: 18 sheet: 0.21 (0.22), residues: 555 loop : -2.13 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 214 HIS 0.003 0.001 HIS C 21 PHE 0.021 0.002 PHE A 128 TYR 0.022 0.001 TYR A 182 ARG 0.001 0.000 ARG B 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 203 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8535 (tt0) cc_final: 0.8114 (tt0) REVERT: A 210 LYS cc_start: 0.7646 (ttpt) cc_final: 0.7019 (ttmm) REVERT: B 13 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8251 (tp) REVERT: B 29 GLU cc_start: 0.7268 (pm20) cc_final: 0.7014 (pm20) REVERT: B 30 ASN cc_start: 0.7787 (t0) cc_final: 0.7351 (t0) REVERT: B 62 GLU cc_start: 0.8415 (tt0) cc_final: 0.8095 (tt0) REVERT: B 182 TYR cc_start: 0.8041 (t80) cc_final: 0.7672 (t80) REVERT: B 210 LYS cc_start: 0.7773 (ttpt) cc_final: 0.6887 (tppt) REVERT: B 219 LYS cc_start: 0.6725 (tttp) cc_final: 0.6457 (ttmt) REVERT: B 272 SER cc_start: 0.7128 (m) cc_final: 0.6871 (t) REVERT: C 30 ASN cc_start: 0.7407 (t0) cc_final: 0.6975 (t0) REVERT: C 62 GLU cc_start: 0.8514 (tt0) cc_final: 0.8148 (tt0) REVERT: C 182 TYR cc_start: 0.7895 (t80) cc_final: 0.7309 (t80) REVERT: C 210 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7212 (ttmm) REVERT: C 231 TYR cc_start: 0.7423 (t80) cc_final: 0.6722 (t80) REVERT: C 290 ASP cc_start: 0.7210 (m-30) cc_final: 0.6365 (p0) outliers start: 31 outliers final: 25 residues processed: 221 average time/residue: 0.1696 time to fit residues: 52.4909 Evaluate side-chains 223 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 197 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.0270 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.0980 chunk 54 optimal weight: 0.2980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN C 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.168947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.160070 restraints weight = 8950.178| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.28 r_work: 0.3671 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8049 Z= 0.198 Angle : 0.585 7.077 10890 Z= 0.327 Chirality : 0.045 0.155 1104 Planarity : 0.003 0.037 1470 Dihedral : 4.961 20.482 1140 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.80 % Allowed : 24.71 % Favored : 71.48 % 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: -1.06 (0.26), residues: 1014 helix: -2.92 (0.56), residues: 18 sheet: 0.22 (0.22), residues: 585 loop : -1.99 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 214 HIS 0.003 0.001 HIS C 21 PHE 0.022 0.002 PHE A 128 TYR 0.016 0.001 TYR B 182 ARG 0.001 0.000 ARG A 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2068.18 seconds wall clock time: 37 minutes 23.33 seconds (2243.33 seconds total)