Starting phenix.real_space_refine on Mon Sep 23 17:22:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3s_27871/09_2024/8e3s_27871.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3s_27871/09_2024/8e3s_27871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3s_27871/09_2024/8e3s_27871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3s_27871/09_2024/8e3s_27871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3s_27871/09_2024/8e3s_27871.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3s_27871/09_2024/8e3s_27871.cif" } resolution = 3.1 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 32 5.16 5 C 2610 2.51 5 N 672 2.21 5 O 757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4072 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4071 Classifications: {'peptide': 503} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 477} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 158 SG CYS A 20 22.552 25.108 49.930 1.00201.97 S ATOM 180 SG CYS A 23 22.465 22.074 49.200 1.00201.28 S ATOM 754 SG CYS A 94 23.485 21.317 52.197 1.00184.63 S ATOM 760 SG CYS A 95 25.414 23.447 49.428 1.00177.00 S Time building chain proxies: 3.06, per 1000 atoms: 0.75 Number of scatterers: 4072 At special positions: 0 Unit cell: (68.9354, 73.2984, 95.986, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 32 16.00 O 757 8.00 N 672 7.00 C 2610 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: 0.90 Conformation dependent library (CDL) restraints added in 442.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 23 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 95 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 20 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 94 " Number of angles added : 6 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 43.7% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 Processing helix chain 'A' and resid 30 through 35 removed outlier: 3.826A pdb=" N LEU A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE A 35 " --> pdb=" O MET A 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 30 through 35' Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.667A pdb=" N LEU A 107 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 138 through 149 removed outlier: 3.724A pdb=" N ASN A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 removed outlier: 3.894A pdb=" N TYR A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 215 through 218 removed outlier: 3.695A pdb=" N MET A 218 " --> pdb=" O TRP A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 218' Processing helix chain 'A' and resid 262 through 265 removed outlier: 3.620A pdb=" N SER A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 268 through 284 removed outlier: 3.596A pdb=" N LEU A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 353 through 357 removed outlier: 3.763A pdb=" N ARG A 357 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 433 through 443 Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 488 through 494 removed outlier: 3.838A pdb=" N LYS A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.756A pdb=" N GLY A 59 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR A 86 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 79 " --> pdb=" O TYR A 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.756A pdb=" N GLY A 59 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 62 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP A 8 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE A 5 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 498 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE A 7 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 454 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 294 removed outlier: 5.325A pdb=" N TYR A 290 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR A 102 " --> pdb=" O TYR A 290 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY A 292 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N THR A 99 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 101 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 320 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 318 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 158 removed outlier: 3.657A pdb=" N TYR A 154 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 242 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR A 236 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE A 241 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TRP A 260 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE A 243 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE A 258 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL A 245 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 256 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 247 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 254 " --> pdb=" O ASP A 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 338 166 hydrogen bonds defined for protein. 426 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: 1.12 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1301 1.34 - 1.46: 968 1.46 - 1.58: 1857 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 4175 Sorted by residual: bond pdb=" CG GLU A 389 " pdb=" CD GLU A 389 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.31e+00 bond pdb=" CD GLU A 389 " pdb=" OE1 GLU A 389 " ideal model delta sigma weight residual 1.249 1.232 0.017 1.90e-02 2.77e+03 8.04e-01 bond pdb=" C PHE A 361 " pdb=" O PHE A 361 " ideal model delta sigma weight residual 1.248 1.238 0.010 1.26e-02 6.30e+03 6.68e-01 bond pdb=" N GLU A 389 " pdb=" CA GLU A 389 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.28e-02 6.10e+03 5.08e-01 bond pdb=" CA GLU A 389 " pdb=" CB GLU A 389 " ideal model delta sigma weight residual 1.528 1.540 -0.011 1.66e-02 3.63e+03 4.78e-01 ... (remaining 4170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 5484 1.46 - 2.91: 125 2.91 - 4.37: 26 4.37 - 5.82: 6 5.82 - 7.28: 3 Bond angle restraints: 5644 Sorted by residual: angle pdb=" N GLU A 389 " pdb=" CA GLU A 389 " pdb=" CB GLU A 389 " ideal model delta sigma weight residual 110.28 115.74 -5.46 1.55e+00 4.16e-01 1.24e+01 angle pdb=" CA GLU A 389 " pdb=" CB GLU A 389 " pdb=" CG GLU A 389 " ideal model delta sigma weight residual 114.10 119.91 -5.81 2.00e+00 2.50e-01 8.45e+00 angle pdb=" C ASN A 388 " pdb=" N GLU A 389 " pdb=" CA GLU A 389 " ideal model delta sigma weight residual 120.31 116.34 3.97 1.52e+00 4.33e-01 6.84e+00 angle pdb=" N ARG A 79 " pdb=" CA ARG A 79 " pdb=" CB ARG A 79 " ideal model delta sigma weight residual 111.00 115.49 -4.49 1.81e+00 3.05e-01 6.15e+00 angle pdb=" N LYS A 27 " pdb=" CA LYS A 27 " pdb=" C LYS A 27 " ideal model delta sigma weight residual 114.09 110.27 3.82 1.55e+00 4.16e-01 6.06e+00 ... (remaining 5639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 2265 17.84 - 35.68: 210 35.68 - 53.52: 25 53.52 - 71.36: 5 71.36 - 89.20: 2 Dihedral angle restraints: 2507 sinusoidal: 1033 harmonic: 1474 Sorted by residual: dihedral pdb=" CA PHE A 78 " pdb=" C PHE A 78 " pdb=" N ARG A 79 " pdb=" CA ARG A 79 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LEU A 286 " pdb=" C LEU A 286 " pdb=" N GLN A 287 " pdb=" CA GLN A 287 " ideal model delta harmonic sigma weight residual 180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CB GLU A 415 " pdb=" CG GLU A 415 " pdb=" CD GLU A 415 " pdb=" OE1 GLU A 415 " ideal model delta sinusoidal sigma weight residual 0.00 -89.20 89.20 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 2504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 332 0.029 - 0.057: 170 0.057 - 0.086: 50 0.086 - 0.115: 35 0.115 - 0.143: 6 Chirality restraints: 593 Sorted by residual: chirality pdb=" CA GLU A 389 " pdb=" N GLU A 389 " pdb=" C GLU A 389 " pdb=" CB GLU A 389 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE A 424 " pdb=" N ILE A 424 " pdb=" C ILE A 424 " pdb=" CB ILE A 424 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE A 400 " pdb=" N ILE A 400 " pdb=" C ILE A 400 " pdb=" CB ILE A 400 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 590 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 432 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO A 433 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 433 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 433 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 293 " 0.003 2.00e-02 2.50e+03 1.16e-02 2.69e+00 pdb=" CG TYR A 293 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 293 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 293 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 293 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 293 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 293 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 293 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 298 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 299 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.021 5.00e-02 4.00e+02 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 220 2.73 - 3.27: 4234 3.27 - 3.81: 6561 3.81 - 4.36: 7432 4.36 - 4.90: 12749 Nonbonded interactions: 31196 Sorted by model distance: nonbonded pdb=" OH TYR A 44 " pdb=" O TYR A 411 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASP A 247 " pdb=" OG SER A 254 " model vdw 2.244 3.040 nonbonded pdb=" O LEU A 291 " pdb=" NZ LYS A 304 " model vdw 2.253 3.120 nonbonded pdb=" NE1 TRP A 8 " pdb=" OE2 GLU A 63 " model vdw 2.303 3.120 nonbonded pdb=" N GLU A 450 " pdb=" OE1 GLU A 450 " model vdw 2.307 3.120 ... (remaining 31191 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.750 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 : 0.003 0.029 4175 Z= 0.184 Angle : 0.586 7.279 5644 Z= 0.313 Chirality : 0.042 0.143 593 Planarity : 0.004 0.049 726 Dihedral : 13.232 89.198 1567 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.13 (0.39), residues: 501 helix: 0.86 (0.40), residues: 186 sheet: 0.08 (0.90), residues: 28 loop : -0.38 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 40 HIS 0.003 0.001 HIS A 231 PHE 0.007 0.001 PHE A 153 TYR 0.025 0.002 TYR A 293 ARG 0.003 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7273 (mmp) cc_final: 0.6730 (mmm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1647 time to fit residues: 13.3669 Evaluate side-chains 51 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 5.9990 chunk 37 optimal weight: 0.0470 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4175 Z= 0.153 Angle : 0.568 8.572 5644 Z= 0.288 Chirality : 0.043 0.154 593 Planarity : 0.004 0.035 726 Dihedral : 4.195 18.164 556 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.90 % Allowed : 7.64 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.39), residues: 501 helix: 1.23 (0.40), residues: 177 sheet: 0.41 (0.77), residues: 51 loop : -0.29 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 40 HIS 0.003 0.001 HIS A 231 PHE 0.006 0.001 PHE A 84 TYR 0.012 0.001 TYR A 293 ARG 0.002 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7235 (mmp) cc_final: 0.6578 (mmm) REVERT: A 296 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7733 (tm-30) outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.1521 time to fit residues: 12.0540 Evaluate side-chains 56 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.0040 chunk 44 optimal weight: 4.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4175 Z= 0.235 Angle : 0.576 7.326 5644 Z= 0.294 Chirality : 0.043 0.139 593 Planarity : 0.004 0.031 726 Dihedral : 4.411 19.534 556 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.80 % Allowed : 10.79 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.39), residues: 501 helix: 1.27 (0.41), residues: 174 sheet: -0.04 (0.68), residues: 59 loop : -0.38 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 40 HIS 0.003 0.001 HIS A 231 PHE 0.010 0.001 PHE A 78 TYR 0.012 0.001 TYR A 234 ARG 0.002 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7340 (mmp) cc_final: 0.6820 (mmm) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 0.1552 time to fit residues: 12.6828 Evaluate side-chains 59 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4175 Z= 0.197 Angle : 0.564 7.820 5644 Z= 0.283 Chirality : 0.042 0.154 593 Planarity : 0.004 0.035 726 Dihedral : 4.331 19.084 556 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.02 % Allowed : 13.71 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.39), residues: 501 helix: 1.20 (0.40), residues: 175 sheet: -0.06 (0.68), residues: 59 loop : -0.43 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 40 HIS 0.002 0.001 HIS A 231 PHE 0.013 0.001 PHE A 35 TYR 0.010 0.001 TYR A 293 ARG 0.001 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7363 (mmp) cc_final: 0.6872 (mmm) outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 0.1842 time to fit residues: 14.0460 Evaluate side-chains 59 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4175 Z= 0.266 Angle : 0.599 7.508 5644 Z= 0.304 Chirality : 0.044 0.145 593 Planarity : 0.004 0.031 726 Dihedral : 4.505 17.330 556 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.02 % Allowed : 14.61 % 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: 0.01 (0.39), residues: 501 helix: 1.10 (0.40), residues: 174 sheet: -0.72 (0.68), residues: 51 loop : -0.52 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 40 HIS 0.003 0.001 HIS A 231 PHE 0.011 0.002 PHE A 35 TYR 0.014 0.001 TYR A 293 ARG 0.004 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7568 (tt) REVERT: A 148 MET cc_start: 0.7490 (mmp) cc_final: 0.7041 (mmm) outliers start: 9 outliers final: 6 residues processed: 59 average time/residue: 0.1654 time to fit residues: 12.4315 Evaluate side-chains 57 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 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 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4175 Z= 0.162 Angle : 0.559 7.954 5644 Z= 0.279 Chirality : 0.042 0.154 593 Planarity : 0.004 0.035 726 Dihedral : 4.278 17.262 556 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.35 % Allowed : 16.40 % Favored : 82.25 % 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: 0.22 (0.39), residues: 501 helix: 1.27 (0.41), residues: 174 sheet: -0.24 (0.67), residues: 59 loop : -0.47 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 40 HIS 0.003 0.001 HIS A 231 PHE 0.009 0.001 PHE A 35 TYR 0.009 0.001 TYR A 181 ARG 0.002 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7585 (tt) REVERT: A 148 MET cc_start: 0.7432 (mmp) cc_final: 0.6983 (mmm) outliers start: 6 outliers final: 4 residues processed: 56 average time/residue: 0.1768 time to fit residues: 12.6571 Evaluate side-chains 57 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4175 Z= 0.170 Angle : 0.552 8.623 5644 Z= 0.275 Chirality : 0.042 0.148 593 Planarity : 0.004 0.038 726 Dihedral : 4.216 17.090 556 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.57 % Allowed : 17.08 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.40), residues: 501 helix: 1.35 (0.41), residues: 174 sheet: -0.59 (0.68), residues: 51 loop : -0.41 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 40 HIS 0.003 0.001 HIS A 231 PHE 0.008 0.001 PHE A 78 TYR 0.009 0.001 TYR A 293 ARG 0.003 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7559 (tt) REVERT: A 148 MET cc_start: 0.7490 (mmp) cc_final: 0.6967 (mmm) outliers start: 7 outliers final: 6 residues processed: 56 average time/residue: 0.1770 time to fit residues: 12.5888 Evaluate side-chains 59 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4175 Z= 0.196 Angle : 0.560 9.258 5644 Z= 0.278 Chirality : 0.042 0.146 593 Planarity : 0.004 0.037 726 Dihedral : 4.224 17.276 556 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.80 % Allowed : 16.63 % Favored : 81.57 % 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: 0.07 (0.39), residues: 501 helix: 1.24 (0.41), residues: 175 sheet: -0.60 (0.69), residues: 51 loop : -0.57 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 40 HIS 0.003 0.001 HIS A 231 PHE 0.008 0.001 PHE A 78 TYR 0.011 0.001 TYR A 181 ARG 0.002 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7557 (tt) REVERT: A 148 MET cc_start: 0.7466 (mmp) cc_final: 0.6922 (mmm) outliers start: 8 outliers final: 6 residues processed: 57 average time/residue: 0.1747 time to fit residues: 12.5836 Evaluate side-chains 58 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4175 Z= 0.183 Angle : 0.563 9.389 5644 Z= 0.276 Chirality : 0.042 0.148 593 Planarity : 0.004 0.038 726 Dihedral : 4.181 17.251 556 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.25 % Allowed : 16.18 % Favored : 81.57 % 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: 0.03 (0.39), residues: 501 helix: 1.17 (0.41), residues: 175 sheet: -0.60 (0.69), residues: 51 loop : -0.59 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 40 HIS 0.003 0.001 HIS A 231 PHE 0.008 0.001 PHE A 78 TYR 0.007 0.001 TYR A 293 ARG 0.002 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7573 (tt) REVERT: A 148 MET cc_start: 0.7364 (mmp) cc_final: 0.6783 (mmm) outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.1488 time to fit residues: 11.4455 Evaluate side-chains 59 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4175 Z= 0.216 Angle : 0.592 9.639 5644 Z= 0.290 Chirality : 0.043 0.164 593 Planarity : 0.004 0.036 726 Dihedral : 4.262 17.337 556 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.80 % Allowed : 17.08 % Favored : 81.12 % 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: -0.08 (0.39), residues: 501 helix: 0.96 (0.41), residues: 181 sheet: -0.71 (0.68), residues: 51 loop : -0.58 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 40 HIS 0.003 0.001 HIS A 231 PHE 0.009 0.001 PHE A 78 TYR 0.012 0.001 TYR A 181 ARG 0.003 0.000 ARG A 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7581 (tt) outliers start: 8 outliers final: 7 residues processed: 55 average time/residue: 0.1608 time to fit residues: 11.5160 Evaluate side-chains 57 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 484 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 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 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.137550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.108521 restraints weight = 9716.310| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 5.73 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4175 Z= 0.159 Angle : 0.568 9.575 5644 Z= 0.274 Chirality : 0.042 0.168 593 Planarity : 0.004 0.038 726 Dihedral : 4.128 17.052 556 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.57 % Allowed : 17.08 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.39), residues: 501 helix: 1.17 (0.41), residues: 176 sheet: -0.59 (0.68), residues: 51 loop : -0.61 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 40 HIS 0.003 0.001 HIS A 231 PHE 0.007 0.001 PHE A 78 TYR 0.006 0.001 TYR A 293 ARG 0.002 0.000 ARG A 452 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1268.05 seconds wall clock time: 23 minutes 49.34 seconds (1429.34 seconds total)