Starting phenix.real_space_refine on Thu Jul 18 23:32:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/07_2024/8vzn_43683.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/07_2024/8vzn_43683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/07_2024/8vzn_43683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/07_2024/8vzn_43683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/07_2024/8vzn_43683.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/07_2024/8vzn_43683.cif" } resolution = 2.77 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= 0.033 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 26 5.16 5 C 3068 2.51 5 N 748 2.21 5 O 814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 119": "OD1" <-> "OD2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4656 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3246 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 15, 'TRANS': 401} Chain breaks: 1 Chain: "B" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 933 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "C" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 470 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.44, per 1000 atoms: 0.95 Number of scatterers: 4656 At special positions: 0 Unit cell: (73.87, 68.06, 118.69, 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 26 16.00 O 814 8.00 N 748 7.00 C 3068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.89 Conformation dependent library (CDL) restraints added in 899.8 milliseconds 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1090 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 62.1% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 106 through 127 removed outlier: 3.504A pdb=" N VAL A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.605A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 158 removed outlier: 3.628A pdb=" N ILE A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 172 through 191 Processing helix chain 'A' and resid 192 through 195 removed outlier: 3.862A pdb=" N LEU A 195 " --> pdb=" O LEU A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 195' Processing helix chain 'A' and resid 199 through 219 removed outlier: 3.503A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.913A pdb=" N ASN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 268 through 295 removed outlier: 3.588A pdb=" N MET A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.540A pdb=" N ALA A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 328 removed outlier: 3.630A pdb=" N ARG A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 353 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 365 through 395 Processing helix chain 'A' and resid 396 through 419 Processing helix chain 'A' and resid 423 through 453 removed outlier: 3.824A pdb=" N VAL A 427 " --> pdb=" O HIS A 423 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 442 " --> pdb=" O MET A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 457 through 488 Processing helix chain 'A' and resid 488 through 508 removed outlier: 3.981A pdb=" N LEU A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 521 removed outlier: 3.771A pdb=" N LYS A 521 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.633A pdb=" N GLY B 13 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE B 37 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER B 53 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA B 43 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.417A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N TYR C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR C 98 " --> pdb=" O GLN C 91 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 873 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: 1.36 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 690 1.29 - 1.42: 1370 1.42 - 1.55: 2680 1.55 - 1.68: 1 1.68 - 1.81: 41 Bond restraints: 4782 Sorted by residual: bond pdb=" CA TYR A 271 " pdb=" C TYR A 271 " ideal model delta sigma weight residual 1.524 1.432 0.092 1.32e-02 5.74e+03 4.81e+01 bond pdb=" CA ALA A 270 " pdb=" CB ALA A 270 " ideal model delta sigma weight residual 1.529 1.424 0.105 1.78e-02 3.16e+03 3.50e+01 bond pdb=" C ARG A 106 " pdb=" O ARG A 106 " ideal model delta sigma weight residual 1.236 1.163 0.073 1.29e-02 6.01e+03 3.18e+01 bond pdb=" C ILE A 126 " pdb=" O ILE A 126 " ideal model delta sigma weight residual 1.235 1.155 0.080 1.45e-02 4.76e+03 3.04e+01 bond pdb=" C LYS B 102 " pdb=" O LYS B 102 " ideal model delta sigma weight residual 1.234 1.168 0.067 1.22e-02 6.72e+03 3.00e+01 ... (remaining 4777 not shown) Histogram of bond angle deviations from ideal: 97.00 - 104.54: 101 104.54 - 112.08: 2222 112.08 - 119.62: 1858 119.62 - 127.16: 2262 127.16 - 134.69: 63 Bond angle restraints: 6506 Sorted by residual: angle pdb=" O CYS A 120 " pdb=" C CYS A 120 " pdb=" N ASN A 121 " ideal model delta sigma weight residual 122.12 114.16 7.96 1.06e+00 8.90e-01 5.64e+01 angle pdb=" N ALA C 33 " pdb=" CA ALA C 33 " pdb=" C ALA C 33 " ideal model delta sigma weight residual 110.88 101.31 9.57 1.28e+00 6.10e-01 5.59e+01 angle pdb=" C GLN B 16 " pdb=" CA GLN B 16 " pdb=" CB GLN B 16 " ideal model delta sigma weight residual 108.68 118.86 -10.18 1.39e+00 5.18e-01 5.36e+01 angle pdb=" CA TRP A 425 " pdb=" C TRP A 425 " pdb=" O TRP A 425 " ideal model delta sigma weight residual 120.24 112.37 7.87 1.11e+00 8.12e-01 5.03e+01 angle pdb=" N TYR A 454 " pdb=" CA TYR A 454 " pdb=" CB TYR A 454 " ideal model delta sigma weight residual 110.42 118.54 -8.12 1.18e+00 7.18e-01 4.74e+01 ... (remaining 6501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2475 17.85 - 35.70: 210 35.70 - 53.55: 35 53.55 - 71.41: 13 71.41 - 89.26: 8 Dihedral angle restraints: 2741 sinusoidal: 1026 harmonic: 1715 Sorted by residual: dihedral pdb=" CD ARG B 70 " pdb=" NE ARG B 70 " pdb=" CZ ARG B 70 " pdb=" NH1 ARG B 70 " ideal model delta sinusoidal sigma weight residual 0.00 88.68 -88.68 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CD ARG B 114 " pdb=" NE ARG B 114 " pdb=" CZ ARG B 114 " pdb=" NH1 ARG B 114 " ideal model delta sinusoidal sigma weight residual 0.00 87.99 -87.99 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CD ARG A 107 " pdb=" NE ARG A 107 " pdb=" CZ ARG A 107 " pdb=" NH1 ARG A 107 " ideal model delta sinusoidal sigma weight residual 0.00 86.98 -86.98 1 1.00e+01 1.00e-02 9.09e+01 ... (remaining 2738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 459 0.067 - 0.134: 198 0.134 - 0.201: 59 0.201 - 0.268: 17 0.268 - 0.335: 3 Chirality restraints: 736 Sorted by residual: chirality pdb=" CB VAL C 34 " pdb=" CA VAL C 34 " pdb=" CG1 VAL C 34 " pdb=" CG2 VAL C 34 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA SER A 104 " pdb=" N SER A 104 " pdb=" C SER A 104 " pdb=" CB SER A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LYS C 40 " pdb=" N LYS C 40 " pdb=" C LYS C 40 " pdb=" CB LYS C 40 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 733 not shown) Planarity restraints: 795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 70 " 1.103 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG B 70 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 70 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 70 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 70 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 107 " -1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 107 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 107 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 107 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 107 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 114 " 1.089 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG B 114 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 114 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 114 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 114 " 0.015 2.00e-02 2.50e+03 ... (remaining 792 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1640 2.84 - 3.36: 4385 3.36 - 3.87: 8138 3.87 - 4.39: 9851 4.39 - 4.90: 16081 Nonbonded interactions: 40095 Sorted by model distance: nonbonded pdb=" O LEU A 195 " pdb=" OH TYR B 104 " model vdw 2.330 2.440 nonbonded pdb=" O THR A 175 " pdb=" OG1 THR A 179 " model vdw 2.335 2.440 nonbonded pdb=" OH TYR A 128 " pdb=" OG1 THR A 203 " model vdw 2.369 2.440 nonbonded pdb=" O ALA A 449 " pdb=" OG1 THR A 453 " model vdw 2.379 2.440 nonbonded pdb=" N LYS B 102 " pdb=" O LYS B 102 " model vdw 2.414 2.496 ... (remaining 40090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 19.690 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.015 0.105 4782 Z= 0.967 Angle : 1.531 10.176 6506 Z= 1.057 Chirality : 0.084 0.335 736 Planarity : 0.039 0.494 795 Dihedral : 15.045 89.256 1645 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.81 % Allowed : 8.82 % Favored : 88.38 % 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: -3.34 (0.29), residues: 586 helix: -1.97 (0.23), residues: 348 sheet: -2.12 (0.55), residues: 67 loop : -2.28 (0.42), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 121 HIS 0.008 0.003 HIS B 112 PHE 0.026 0.004 PHE A 436 TYR 0.019 0.003 TYR A 117 ARG 0.008 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.550 Fit side-chains REVERT: A 102 LYS cc_start: 0.6915 (tttm) cc_final: 0.6684 (ttmm) REVERT: A 253 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.7334 (t80) REVERT: A 381 MET cc_start: 0.8352 (mtm) cc_final: 0.8152 (mtp) REVERT: A 511 LYS cc_start: 0.8079 (tttt) cc_final: 0.7517 (mttp) REVERT: B 106 TRP cc_start: 0.8598 (OUTLIER) cc_final: 0.8396 (t-100) outliers start: 14 outliers final: 1 residues processed: 87 average time/residue: 1.3587 time to fit residues: 122.3898 Evaluate side-chains 64 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 106 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 355 ASN A 422 ASN C 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4782 Z= 0.204 Angle : 0.560 7.231 6506 Z= 0.303 Chirality : 0.040 0.155 736 Planarity : 0.005 0.047 795 Dihedral : 5.922 53.972 651 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.80 % Allowed : 13.63 % Favored : 84.57 % 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: -0.51 (0.34), residues: 586 helix: 0.50 (0.27), residues: 352 sheet: -1.28 (0.60), residues: 65 loop : -1.56 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 50 HIS 0.002 0.001 HIS B 38 PHE 0.018 0.002 PHE A 144 TYR 0.025 0.001 TYR A 117 ARG 0.006 0.001 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8538 (t80) cc_final: 0.8296 (t80) REVERT: A 253 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: A 381 MET cc_start: 0.8175 (mtm) cc_final: 0.7964 (mtp) REVERT: A 511 LYS cc_start: 0.8105 (tttt) cc_final: 0.7498 (mttp) outliers start: 9 outliers final: 4 residues processed: 72 average time/residue: 1.2247 time to fit residues: 92.0990 Evaluate side-chains 65 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 40 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 246 GLN A 422 ASN C 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4782 Z= 0.359 Angle : 0.606 7.136 6506 Z= 0.322 Chirality : 0.043 0.153 736 Planarity : 0.005 0.059 795 Dihedral : 5.280 44.419 647 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.20 % Allowed : 14.43 % Favored : 83.37 % 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: 0.34 (0.35), residues: 586 helix: 1.13 (0.28), residues: 353 sheet: -1.02 (0.61), residues: 65 loop : -1.09 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 108 HIS 0.004 0.001 HIS B 38 PHE 0.018 0.002 PHE A 144 TYR 0.024 0.002 TYR A 117 ARG 0.005 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 511 LYS cc_start: 0.8058 (tttt) cc_final: 0.7455 (mttp) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 1.2581 time to fit residues: 90.1657 Evaluate side-chains 70 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.0030 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.0770 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.2948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 330 ASN A 422 ASN C 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4782 Z= 0.141 Angle : 0.482 6.391 6506 Z= 0.256 Chirality : 0.039 0.145 736 Planarity : 0.004 0.041 795 Dihedral : 4.198 15.596 645 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.80 % Allowed : 17.03 % Favored : 82.16 % 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: 1.14 (0.35), residues: 586 helix: 1.90 (0.28), residues: 352 sheet: -1.15 (0.62), residues: 55 loop : -0.90 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.002 0.001 HIS A 361 PHE 0.016 0.001 PHE A 144 TYR 0.025 0.001 TYR A 117 ARG 0.002 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.537 Fit side-chains REVERT: A 223 ARG cc_start: 0.7980 (ttt-90) cc_final: 0.7401 (ttt90) REVERT: A 253 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8733 (m-80) REVERT: A 447 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7183 (mm-30) REVERT: A 511 LYS cc_start: 0.8030 (tttt) cc_final: 0.7466 (mttp) outliers start: 4 outliers final: 2 residues processed: 68 average time/residue: 1.2389 time to fit residues: 87.7468 Evaluate side-chains 62 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 67 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 330 ASN A 422 ASN C 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4782 Z= 0.217 Angle : 0.519 6.587 6506 Z= 0.274 Chirality : 0.040 0.154 736 Planarity : 0.004 0.045 795 Dihedral : 4.320 16.555 645 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.80 % Allowed : 16.83 % Favored : 81.36 % 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 (0.36), residues: 586 helix: 1.94 (0.27), residues: 352 sheet: -0.92 (0.63), residues: 55 loop : -0.51 (0.49), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 108 HIS 0.003 0.001 HIS B 38 PHE 0.017 0.002 PHE A 144 TYR 0.023 0.001 TYR A 117 ARG 0.001 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7567 (mtt90) REVERT: A 223 ARG cc_start: 0.8024 (ttt-90) cc_final: 0.7433 (ttt90) REVERT: A 447 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7267 (mm-30) REVERT: A 511 LYS cc_start: 0.8066 (tttt) cc_final: 0.7481 (mttp) outliers start: 9 outliers final: 7 residues processed: 65 average time/residue: 1.2140 time to fit residues: 82.1293 Evaluate side-chains 66 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 0.0570 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4782 Z= 0.144 Angle : 0.477 6.320 6506 Z= 0.251 Chirality : 0.039 0.146 736 Planarity : 0.004 0.046 795 Dihedral : 4.055 15.305 645 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.40 % Allowed : 17.03 % Favored : 81.56 % 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: 1.72 (0.36), residues: 586 helix: 2.18 (0.27), residues: 351 sheet: -0.59 (0.63), residues: 56 loop : -0.34 (0.50), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.002 0.001 HIS B 38 PHE 0.015 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7938 (mtt-85) REVERT: A 223 ARG cc_start: 0.7974 (ttt-90) cc_final: 0.7430 (ttt90) REVERT: A 253 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8667 (m-80) REVERT: A 447 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7217 (mm-30) REVERT: A 490 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7104 (ttp) REVERT: A 511 LYS cc_start: 0.8048 (tttt) cc_final: 0.7457 (mttp) outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 1.3296 time to fit residues: 91.0594 Evaluate side-chains 66 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 40 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.0670 chunk 55 optimal weight: 6.9990 chunk 34 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4782 Z= 0.141 Angle : 0.476 6.400 6506 Z= 0.250 Chirality : 0.039 0.148 736 Planarity : 0.004 0.047 795 Dihedral : 3.962 15.038 645 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.60 % Allowed : 17.23 % Favored : 81.16 % 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: 1.89 (0.35), residues: 586 helix: 2.27 (0.27), residues: 353 sheet: -0.24 (0.64), residues: 56 loop : -0.29 (0.50), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.002 0.001 HIS B 38 PHE 0.014 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7941 (mtt-85) REVERT: A 223 ARG cc_start: 0.7984 (ttt-90) cc_final: 0.7451 (ttt90) REVERT: A 444 LEU cc_start: 0.8586 (mm) cc_final: 0.8049 (mt) REVERT: A 511 LYS cc_start: 0.8059 (tttt) cc_final: 0.7460 (mttp) outliers start: 8 outliers final: 5 residues processed: 74 average time/residue: 1.2174 time to fit residues: 93.8239 Evaluate side-chains 69 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 52 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4782 Z= 0.226 Angle : 0.519 6.507 6506 Z= 0.274 Chirality : 0.040 0.153 736 Planarity : 0.004 0.048 795 Dihedral : 4.209 16.490 645 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.40 % Allowed : 18.24 % Favored : 80.36 % 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: 1.72 (0.36), residues: 586 helix: 2.03 (0.27), residues: 352 sheet: -0.11 (0.65), residues: 56 loop : -0.18 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 148 HIS 0.003 0.001 HIS B 38 PHE 0.017 0.002 PHE A 144 TYR 0.023 0.001 TYR A 117 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7586 (mtt90) REVERT: A 223 ARG cc_start: 0.8020 (ttt-90) cc_final: 0.7417 (ttt90) REVERT: A 444 LEU cc_start: 0.8615 (mm) cc_final: 0.8066 (mt) REVERT: A 451 GLU cc_start: 0.8738 (tp30) cc_final: 0.8386 (tp30) REVERT: A 511 LYS cc_start: 0.8063 (tttt) cc_final: 0.7456 (mttp) outliers start: 7 outliers final: 6 residues processed: 67 average time/residue: 1.1819 time to fit residues: 82.5125 Evaluate side-chains 67 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.0010 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 33 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 53 optimal weight: 0.0270 chunk 46 optimal weight: 0.9990 overall best weight: 0.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4782 Z= 0.133 Angle : 0.468 6.318 6506 Z= 0.246 Chirality : 0.038 0.144 736 Planarity : 0.004 0.049 795 Dihedral : 3.913 15.574 645 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.00 % Allowed : 19.04 % Favored : 79.96 % 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: 1.84 (0.35), residues: 586 helix: 2.20 (0.27), residues: 353 sheet: -0.01 (0.66), residues: 54 loop : -0.35 (0.49), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 148 HIS 0.002 0.001 HIS B 38 PHE 0.014 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7982 (ttt-90) cc_final: 0.7392 (tpt90) REVERT: A 444 LEU cc_start: 0.8545 (mm) cc_final: 0.8018 (mt) REVERT: A 447 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7545 (mm-30) REVERT: A 511 LYS cc_start: 0.8055 (tttt) cc_final: 0.7447 (mttp) outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 1.1590 time to fit residues: 77.4421 Evaluate side-chains 66 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 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 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.004 0.036 4782 Z= 0.240 Angle : 0.529 7.266 6506 Z= 0.277 Chirality : 0.041 0.153 736 Planarity : 0.004 0.049 795 Dihedral : 4.192 16.545 645 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.60 % Allowed : 18.44 % Favored : 79.96 % 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: 1.73 (0.35), residues: 586 helix: 2.02 (0.27), residues: 352 sheet: 0.05 (0.65), residues: 56 loop : -0.20 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.003 0.001 HIS B 38 PHE 0.016 0.002 PHE A 144 TYR 0.023 0.001 TYR A 117 ARG 0.002 0.000 ARG A 518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7606 (mtt90) REVERT: A 223 ARG cc_start: 0.7991 (ttt-90) cc_final: 0.7381 (tpt90) REVERT: A 444 LEU cc_start: 0.8608 (mm) cc_final: 0.8068 (mt) REVERT: A 511 LYS cc_start: 0.8059 (tttt) cc_final: 0.7447 (mttp) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 1.1349 time to fit residues: 80.4865 Evaluate side-chains 68 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.165115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114959 restraints weight = 4821.838| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.92 r_work: 0.3079 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4782 Z= 0.207 Angle : 0.513 6.914 6506 Z= 0.269 Chirality : 0.040 0.151 736 Planarity : 0.004 0.048 795 Dihedral : 4.176 16.191 645 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.20 % Allowed : 19.04 % Favored : 79.76 % 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: 1.72 (0.35), residues: 586 helix: 2.01 (0.27), residues: 352 sheet: 0.09 (0.65), residues: 56 loop : -0.19 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 148 HIS 0.003 0.001 HIS B 38 PHE 0.016 0.002 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2304.47 seconds wall clock time: 40 minutes 57.99 seconds (2457.99 seconds total)