Starting phenix.real_space_refine on Wed Mar 5 20:25:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qw4_18680/03_2025/8qw4_18680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qw4_18680/03_2025/8qw4_18680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qw4_18680/03_2025/8qw4_18680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qw4_18680/03_2025/8qw4_18680.map" model { file = "/net/cci-nas-00/data/ceres_data/8qw4_18680/03_2025/8qw4_18680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qw4_18680/03_2025/8qw4_18680.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.019 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 27 5.16 5 C 2286 2.51 5 N 564 2.21 5 O 602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3479 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2591 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 4 Chain: "B" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 888 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Time building chain proxies: 5.26, per 1000 atoms: 1.51 Number of scatterers: 3479 At special positions: 0 Unit cell: (93.072, 57.339, 101.382, 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 27 16.00 O 602 8.00 N 564 7.00 C 2286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 264 " distance=2.04 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 98 " distance=2.02 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: 0.82 Conformation dependent library (CDL) restraints added in 443.3 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 808 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 52.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 195 through 225 removed outlier: 3.885A pdb=" N LEU A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 253 removed outlier: 3.963A pdb=" N PHE A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 283 through 313 removed outlier: 3.615A pdb=" N THR A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 290 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 291 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 327 through 345 Proline residue: A 339 - end of helix Processing helix chain 'A' and resid 367 through 375 removed outlier: 3.625A pdb=" N LEU A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 402 removed outlier: 4.147A pdb=" N SER A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 413 through 443 removed outlier: 4.077A pdb=" N PHE A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 445 through 452 removed outlier: 3.647A pdb=" N TRP A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 451 " --> pdb=" O GLY A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.533A pdb=" N LEU A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 removed outlier: 3.598A pdb=" N TYR A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 493 Proline residue: A 493 - end of helix No H-bonds generated for 'chain 'A' and resid 490 through 493' Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'B' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.357A pdb=" N TYR A 177 " --> pdb=" O CYS A 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 27 removed outlier: 4.382A pdb=" N ASP B 79 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.821A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP B 53 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET B 37 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 36 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 94 through 95 156 hydrogen bonds defined for protein. 438 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: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1034 1.34 - 1.46: 921 1.46 - 1.59: 1564 1.59 - 1.71: 0 1.71 - 1.83: 41 Bond restraints: 3560 Sorted by residual: bond pdb=" N GLU A 407 " pdb=" CA GLU A 407 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.50e-02 4.44e+03 2.99e+00 bond pdb=" C ASP A 476 " pdb=" N LEU A 477 " ideal model delta sigma weight residual 1.331 1.307 0.024 1.40e-02 5.10e+03 2.97e+00 bond pdb=" C LEU A 406 " pdb=" N GLU A 407 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.28e-02 6.10e+03 2.77e+00 bond pdb=" CB THR A 276 " pdb=" CG2 THR A 276 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.63e+00 bond pdb=" CB TYR A 177 " pdb=" CG TYR A 177 " ideal model delta sigma weight residual 1.512 1.477 0.035 2.20e-02 2.07e+03 2.48e+00 ... (remaining 3555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 4614 2.38 - 4.76: 169 4.76 - 7.14: 31 7.14 - 9.52: 5 9.52 - 11.91: 3 Bond angle restraints: 4822 Sorted by residual: angle pdb=" C GLU A 235 " pdb=" N ARG A 236 " pdb=" CA ARG A 236 " ideal model delta sigma weight residual 120.09 125.89 -5.80 1.25e+00 6.40e-01 2.15e+01 angle pdb=" N ARG A 459 " pdb=" CA ARG A 459 " pdb=" C ARG A 459 " ideal model delta sigma weight residual 110.80 101.02 9.78 2.13e+00 2.20e-01 2.11e+01 angle pdb=" N GLY A 354 " pdb=" CA GLY A 354 " pdb=" C GLY A 354 " ideal model delta sigma weight residual 112.13 118.02 -5.89 1.34e+00 5.57e-01 1.93e+01 angle pdb=" C ALA B 43 " pdb=" N PRO B 44 " pdb=" CA PRO B 44 " ideal model delta sigma weight residual 127.00 136.73 -9.73 2.40e+00 1.74e-01 1.64e+01 angle pdb=" C CYS A 458 " pdb=" N ARG A 459 " pdb=" CA ARG A 459 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 ... (remaining 4817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 1877 16.29 - 32.57: 177 32.57 - 48.86: 30 48.86 - 65.14: 4 65.14 - 81.43: 6 Dihedral angle restraints: 2094 sinusoidal: 837 harmonic: 1257 Sorted by residual: dihedral pdb=" CB CYS A 189 " pdb=" SG CYS A 189 " pdb=" SG CYS A 264 " pdb=" CB CYS A 264 " ideal model delta sinusoidal sigma weight residual -86.00 -157.10 71.10 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CA TYR A 177 " pdb=" C TYR A 177 " pdb=" N SER A 178 " pdb=" CA SER A 178 " ideal model delta harmonic sigma weight residual -180.00 -145.73 -34.27 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" CA SER A 178 " pdb=" C SER A 178 " pdb=" N PHE A 179 " pdb=" CA PHE A 179 " ideal model delta harmonic sigma weight residual -180.00 -146.92 -33.08 0 5.00e+00 4.00e-02 4.38e+01 ... (remaining 2091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 361 0.048 - 0.096: 136 0.096 - 0.144: 34 0.144 - 0.192: 17 0.192 - 0.241: 2 Chirality restraints: 550 Sorted by residual: chirality pdb=" CA VAL A 316 " pdb=" N VAL A 316 " pdb=" C VAL A 316 " pdb=" CB VAL A 316 " both_signs ideal model delta sigma weight residual False 2.44 2.20 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA PRO B 90 " pdb=" N PRO B 90 " pdb=" C PRO B 90 " pdb=" CB PRO B 90 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO A 405 " pdb=" N PRO A 405 " pdb=" C PRO A 405 " pdb=" CB PRO A 405 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.11e-01 ... (remaining 547 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 316 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO A 317 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 474 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO A 475 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 428 " 0.010 2.00e-02 2.50e+03 1.41e-02 3.99e+00 pdb=" CG TYR A 428 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 428 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 428 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 428 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 428 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 428 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 428 " -0.001 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 75 2.65 - 3.21: 3457 3.21 - 3.78: 5258 3.78 - 4.34: 7053 4.34 - 4.90: 11275 Nonbonded interactions: 27118 Sorted by model distance: nonbonded pdb=" O GLN A 455 " pdb=" NH2 ARG A 459 " model vdw 2.091 3.120 nonbonded pdb=" OH TYR A 241 " pdb=" O VAL A 490 " model vdw 2.209 3.040 nonbonded pdb=" O ASN A 410 " pdb=" N LYS A 413 " model vdw 2.275 3.120 nonbonded pdb=" O ASP A 260 " pdb=" NH1 ARG A 261 " model vdw 2.288 3.120 nonbonded pdb=" O THR A 217 " pdb=" OG1 THR A 220 " model vdw 2.300 3.040 ... (remaining 27113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 6.210 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 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 : 0.007 0.057 3560 Z= 0.479 Angle : 1.098 11.906 4822 Z= 0.608 Chirality : 0.058 0.241 550 Planarity : 0.008 0.116 587 Dihedral : 13.197 81.429 1274 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 0.26 % Allowed : 0.00 % Favored : 99.74 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.29 (0.39), residues: 420 helix: -0.99 (0.37), residues: 189 sheet: -1.69 (0.86), residues: 38 loop : -3.62 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 104 HIS 0.003 0.001 HIS A 282 PHE 0.020 0.003 PHE A 201 TYR 0.034 0.003 TYR A 428 ARG 0.009 0.001 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6980 (tpt90) cc_final: 0.5436 (mtp180) REVERT: A 336 TRP cc_start: 0.7890 (m100) cc_final: 0.7653 (m-10) REVERT: A 349 MET cc_start: 0.4417 (mmt) cc_final: 0.3595 (ptt) REVERT: A 442 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6685 (mp0) REVERT: B 35 ASP cc_start: 0.7720 (m-30) cc_final: 0.7504 (m-30) REVERT: B 55 THR cc_start: 0.7761 (p) cc_final: 0.7495 (m) outliers start: 1 outliers final: 2 residues processed: 119 average time/residue: 0.9080 time to fit residues: 112.0336 Evaluate side-chains 66 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 352 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.185062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.169330 restraints weight = 7913.197| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 3.53 r_work: 0.4256 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3560 Z= 0.287 Angle : 0.879 8.375 4822 Z= 0.448 Chirality : 0.051 0.189 550 Planarity : 0.007 0.069 587 Dihedral : 7.421 36.115 478 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 5.01 % Allowed : 17.94 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.39), residues: 420 helix: -0.77 (0.37), residues: 191 sheet: -1.06 (0.85), residues: 38 loop : -3.34 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 449 HIS 0.001 0.001 HIS A 282 PHE 0.026 0.002 PHE B 32 TYR 0.018 0.002 TYR A 428 ARG 0.006 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.387 Fit side-chains REVERT: A 193 TYR cc_start: 0.5708 (OUTLIER) cc_final: 0.5490 (m-80) REVERT: A 203 ARG cc_start: 0.6724 (tpt90) cc_final: 0.5225 (mtp180) REVERT: A 291 MET cc_start: 0.6460 (ptt) cc_final: 0.6157 (pmm) REVERT: A 336 TRP cc_start: 0.8458 (m100) cc_final: 0.7685 (m-10) REVERT: A 349 MET cc_start: 0.5045 (mmt) cc_final: 0.3572 (ptt) REVERT: A 367 ASP cc_start: 0.7851 (t0) cc_final: 0.7553 (t0) REVERT: A 415 VAL cc_start: 0.6071 (OUTLIER) cc_final: 0.4953 (t) REVERT: A 433 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7813 (tm) REVERT: A 445 TYR cc_start: 0.6776 (t80) cc_final: 0.6512 (t80) REVERT: B 35 ASP cc_start: 0.8733 (m-30) cc_final: 0.8476 (m-30) REVERT: B 109 TYR cc_start: 0.7767 (m-80) cc_final: 0.7357 (m-80) outliers start: 19 outliers final: 7 residues processed: 81 average time/residue: 0.9732 time to fit residues: 81.8835 Evaluate side-chains 75 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 14 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.0050 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.186152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.170877 restraints weight = 8080.436| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 3.54 r_work: 0.4289 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3560 Z= 0.238 Angle : 0.802 8.034 4822 Z= 0.407 Chirality : 0.048 0.274 550 Planarity : 0.006 0.060 587 Dihedral : 6.859 34.612 476 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 3.96 % Allowed : 22.43 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.40), residues: 420 helix: -0.43 (0.38), residues: 190 sheet: -1.02 (0.81), residues: 38 loop : -3.33 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 449 HIS 0.001 0.001 HIS A 282 PHE 0.021 0.002 PHE B 32 TYR 0.020 0.002 TYR A 428 ARG 0.005 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6703 (tpt90) cc_final: 0.5214 (tpt-90) REVERT: A 336 TRP cc_start: 0.8339 (m100) cc_final: 0.7570 (m-10) REVERT: A 349 MET cc_start: 0.4828 (mmt) cc_final: 0.3441 (ptt) REVERT: A 367 ASP cc_start: 0.7700 (t0) cc_final: 0.7275 (t0) REVERT: A 415 VAL cc_start: 0.5885 (OUTLIER) cc_final: 0.4699 (t) REVERT: A 482 MET cc_start: 0.7582 (ppp) cc_final: 0.7361 (pp-130) REVERT: B 35 ASP cc_start: 0.8830 (m-30) cc_final: 0.8528 (m-30) REVERT: B 109 TYR cc_start: 0.7784 (m-80) cc_final: 0.7422 (m-80) outliers start: 15 outliers final: 5 residues processed: 87 average time/residue: 0.8109 time to fit residues: 73.7205 Evaluate side-chains 71 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.0270 chunk 8 optimal weight: 0.3980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.184466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.169184 restraints weight = 8013.277| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 3.59 r_work: 0.4257 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3560 Z= 0.258 Angle : 0.812 9.350 4822 Z= 0.404 Chirality : 0.047 0.175 550 Planarity : 0.005 0.061 587 Dihedral : 6.515 27.046 473 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 5.54 % Allowed : 25.59 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.41), residues: 420 helix: -0.21 (0.39), residues: 189 sheet: -0.87 (0.85), residues: 36 loop : -3.08 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 449 HIS 0.002 0.001 HIS A 282 PHE 0.015 0.002 PHE B 32 TYR 0.023 0.002 TYR A 204 ARG 0.005 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.5204 (tpt-90) REVERT: A 291 MET cc_start: 0.6359 (ptt) cc_final: 0.5606 (pmm) REVERT: A 336 TRP cc_start: 0.8362 (m100) cc_final: 0.7574 (m-10) REVERT: A 349 MET cc_start: 0.4833 (mmt) cc_final: 0.3829 (ptt) REVERT: A 415 VAL cc_start: 0.5972 (OUTLIER) cc_final: 0.4753 (t) REVERT: A 433 LEU cc_start: 0.8176 (tm) cc_final: 0.7671 (pp) REVERT: A 445 TYR cc_start: 0.6613 (t80) cc_final: 0.6347 (t80) REVERT: B 35 ASP cc_start: 0.8871 (m-30) cc_final: 0.8562 (m-30) REVERT: B 109 TYR cc_start: 0.7816 (m-80) cc_final: 0.7511 (m-80) outliers start: 21 outliers final: 6 residues processed: 83 average time/residue: 0.9346 time to fit residues: 80.6009 Evaluate side-chains 72 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.0980 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.184964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.169858 restraints weight = 8101.776| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 3.62 r_work: 0.4267 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3560 Z= 0.241 Angle : 0.819 10.673 4822 Z= 0.400 Chirality : 0.046 0.174 550 Planarity : 0.005 0.059 587 Dihedral : 6.319 27.723 473 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 5.54 % Allowed : 27.70 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.42), residues: 420 helix: -0.20 (0.39), residues: 189 sheet: -0.69 (0.87), residues: 36 loop : -3.01 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 449 HIS 0.001 0.000 HIS A 282 PHE 0.027 0.002 PHE A 224 TYR 0.022 0.002 TYR A 428 ARG 0.005 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6713 (tpt90) cc_final: 0.5254 (tpt-90) REVERT: A 336 TRP cc_start: 0.8318 (m100) cc_final: 0.7527 (m-10) REVERT: A 349 MET cc_start: 0.4904 (mmt) cc_final: 0.3553 (ptt) REVERT: A 367 ASP cc_start: 0.7933 (t0) cc_final: 0.7697 (t0) REVERT: A 415 VAL cc_start: 0.6027 (OUTLIER) cc_final: 0.4738 (t) REVERT: A 433 LEU cc_start: 0.8331 (tm) cc_final: 0.7794 (pp) REVERT: A 445 TYR cc_start: 0.6469 (t80) cc_final: 0.6230 (t80) REVERT: A 482 MET cc_start: 0.7626 (ppp) cc_final: 0.6980 (mtt) REVERT: A 501 LYS cc_start: 0.8631 (tppp) cc_final: 0.8302 (mmmt) REVERT: B 35 ASP cc_start: 0.8833 (m-30) cc_final: 0.8533 (m-30) REVERT: B 103 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7989 (tp30) REVERT: B 109 TYR cc_start: 0.7824 (m-80) cc_final: 0.7443 (m-80) outliers start: 21 outliers final: 11 residues processed: 81 average time/residue: 0.7896 time to fit residues: 66.7611 Evaluate side-chains 78 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.0770 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.184691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.169430 restraints weight = 8147.094| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 3.66 r_work: 0.4260 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3560 Z= 0.248 Angle : 0.828 9.910 4822 Z= 0.403 Chirality : 0.047 0.173 550 Planarity : 0.005 0.060 587 Dihedral : 6.261 28.374 473 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 6.33 % Allowed : 27.44 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.42), residues: 420 helix: -0.19 (0.39), residues: 189 sheet: -0.65 (0.88), residues: 36 loop : -2.95 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 449 HIS 0.003 0.001 HIS A 282 PHE 0.016 0.002 PHE A 253 TYR 0.029 0.002 TYR A 428 ARG 0.007 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.6980 (mmm160) cc_final: 0.6772 (mmm160) REVERT: A 203 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.5211 (tpt-90) REVERT: A 291 MET cc_start: 0.6092 (ptt) cc_final: 0.5340 (pmm) REVERT: A 336 TRP cc_start: 0.8348 (m100) cc_final: 0.7512 (m-10) REVERT: A 349 MET cc_start: 0.4996 (mmt) cc_final: 0.3616 (ptt) REVERT: A 367 ASP cc_start: 0.7931 (t0) cc_final: 0.7662 (t0) REVERT: A 415 VAL cc_start: 0.6111 (OUTLIER) cc_final: 0.4838 (t) REVERT: A 433 LEU cc_start: 0.8407 (tm) cc_final: 0.7885 (pp) REVERT: A 445 TYR cc_start: 0.6543 (t80) cc_final: 0.6288 (t80) REVERT: A 482 MET cc_start: 0.7564 (ppp) cc_final: 0.7028 (mtt) REVERT: A 501 LYS cc_start: 0.8622 (tppp) cc_final: 0.8334 (mmmt) REVERT: B 35 ASP cc_start: 0.8818 (m-30) cc_final: 0.8530 (m-30) REVERT: B 103 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7954 (tp30) REVERT: B 109 TYR cc_start: 0.7813 (m-80) cc_final: 0.7399 (m-80) outliers start: 24 outliers final: 14 residues processed: 83 average time/residue: 0.8779 time to fit residues: 75.8217 Evaluate side-chains 78 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.0270 chunk 26 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.185398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.170352 restraints weight = 8027.273| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 3.56 r_work: 0.4269 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3560 Z= 0.242 Angle : 0.846 10.198 4822 Z= 0.412 Chirality : 0.047 0.173 550 Planarity : 0.005 0.060 587 Dihedral : 6.163 27.948 473 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.28 % Allowed : 27.97 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.42), residues: 420 helix: -0.13 (0.39), residues: 189 sheet: -0.52 (0.87), residues: 35 loop : -2.94 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 449 HIS 0.002 0.001 HIS A 282 PHE 0.014 0.002 PHE A 224 TYR 0.028 0.002 TYR A 428 ARG 0.005 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5196 (tpt-90) REVERT: A 210 SER cc_start: 0.7869 (m) cc_final: 0.7620 (t) REVERT: A 291 MET cc_start: 0.6113 (ptt) cc_final: 0.5333 (pmm) REVERT: A 349 MET cc_start: 0.5001 (mmt) cc_final: 0.3641 (ptt) REVERT: A 367 ASP cc_start: 0.7829 (t0) cc_final: 0.7603 (t0) REVERT: A 433 LEU cc_start: 0.8400 (tm) cc_final: 0.7882 (pp) REVERT: A 445 TYR cc_start: 0.6637 (t80) cc_final: 0.6378 (t80) REVERT: A 482 MET cc_start: 0.7599 (ppp) cc_final: 0.7058 (mtt) REVERT: A 501 LYS cc_start: 0.8611 (tppp) cc_final: 0.8371 (mmmt) REVERT: B 35 ASP cc_start: 0.8826 (m-30) cc_final: 0.8530 (m-30) REVERT: B 103 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8020 (tp30) REVERT: B 109 TYR cc_start: 0.7804 (m-80) cc_final: 0.7429 (m-80) outliers start: 20 outliers final: 13 residues processed: 73 average time/residue: 0.8652 time to fit residues: 65.8184 Evaluate side-chains 75 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 25 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 22 optimal weight: 0.0070 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.184954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.169896 restraints weight = 8202.277| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 3.57 r_work: 0.4269 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3560 Z= 0.244 Angle : 0.850 10.859 4822 Z= 0.408 Chirality : 0.046 0.172 550 Planarity : 0.005 0.061 587 Dihedral : 6.024 27.765 473 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 6.33 % Allowed : 28.23 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.42), residues: 420 helix: -0.05 (0.40), residues: 189 sheet: -0.54 (0.87), residues: 35 loop : -2.91 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.002 0.001 HIS A 181 PHE 0.021 0.002 PHE A 240 TYR 0.030 0.002 TYR A 428 ARG 0.006 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.5185 (tpt-90) REVERT: A 210 SER cc_start: 0.7952 (m) cc_final: 0.7651 (t) REVERT: A 349 MET cc_start: 0.5021 (mmt) cc_final: 0.3681 (ptt) REVERT: A 367 ASP cc_start: 0.7806 (t0) cc_final: 0.7562 (t0) REVERT: A 433 LEU cc_start: 0.8358 (tm) cc_final: 0.7837 (pp) REVERT: A 482 MET cc_start: 0.7583 (ppp) cc_final: 0.7067 (mtt) REVERT: A 501 LYS cc_start: 0.8691 (tppp) cc_final: 0.8413 (mmmt) REVERT: B 35 ASP cc_start: 0.8856 (m-30) cc_final: 0.8565 (m-30) REVERT: B 103 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8056 (tp30) REVERT: B 109 TYR cc_start: 0.7819 (m-80) cc_final: 0.7537 (m-80) outliers start: 24 outliers final: 15 residues processed: 87 average time/residue: 0.8105 time to fit residues: 73.5055 Evaluate side-chains 77 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.183147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.168459 restraints weight = 7837.111| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 3.46 r_work: 0.4248 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3560 Z= 0.273 Angle : 0.939 12.118 4822 Z= 0.446 Chirality : 0.047 0.172 550 Planarity : 0.005 0.061 587 Dihedral : 6.182 29.312 473 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 6.07 % Allowed : 29.29 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.42), residues: 420 helix: 0.07 (0.40), residues: 185 sheet: -0.74 (0.84), residues: 35 loop : -2.95 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 449 HIS 0.001 0.001 HIS A 282 PHE 0.020 0.002 PHE A 240 TYR 0.027 0.002 TYR A 428 ARG 0.007 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 193 TYR cc_start: 0.5794 (m-80) cc_final: 0.3413 (t80) REVERT: A 203 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.5246 (tpt-90) REVERT: A 210 SER cc_start: 0.8016 (m) cc_final: 0.7715 (t) REVERT: A 349 MET cc_start: 0.5180 (mmt) cc_final: 0.3815 (ptt) REVERT: A 367 ASP cc_start: 0.7820 (t0) cc_final: 0.7616 (t0) REVERT: A 433 LEU cc_start: 0.8303 (tm) cc_final: 0.7790 (pp) REVERT: A 445 TYR cc_start: 0.6571 (t80) cc_final: 0.6299 (t80) REVERT: A 449 TRP cc_start: 0.5305 (t60) cc_final: 0.5066 (t60) REVERT: A 482 MET cc_start: 0.7588 (ppp) cc_final: 0.7071 (mtt) REVERT: A 501 LYS cc_start: 0.8672 (tppp) cc_final: 0.8394 (mmmt) REVERT: B 35 ASP cc_start: 0.8827 (m-30) cc_final: 0.8532 (m-30) REVERT: B 103 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8058 (tp30) REVERT: B 109 TYR cc_start: 0.7879 (m-80) cc_final: 0.7564 (m-80) outliers start: 23 outliers final: 15 residues processed: 82 average time/residue: 0.8669 time to fit residues: 74.0792 Evaluate side-chains 79 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 31 optimal weight: 0.0770 chunk 18 optimal weight: 0.0980 chunk 14 optimal weight: 0.0670 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.1454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.185147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.170694 restraints weight = 8236.605| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 3.55 r_work: 0.4269 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3560 Z= 0.235 Angle : 0.929 15.573 4822 Z= 0.440 Chirality : 0.046 0.178 550 Planarity : 0.005 0.060 587 Dihedral : 5.874 28.258 473 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.69 % Allowed : 32.72 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.42), residues: 420 helix: -0.05 (0.39), residues: 186 sheet: -0.60 (0.84), residues: 35 loop : -2.94 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 449 HIS 0.001 0.000 HIS A 332 PHE 0.016 0.002 PHE A 253 TYR 0.019 0.002 TYR A 428 ARG 0.008 0.001 ARG A 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5211 (tpt-90) REVERT: A 210 SER cc_start: 0.7899 (m) cc_final: 0.7587 (t) REVERT: A 349 MET cc_start: 0.4946 (mmt) cc_final: 0.3634 (ptt) REVERT: A 433 LEU cc_start: 0.8408 (tm) cc_final: 0.7903 (pp) REVERT: A 445 TYR cc_start: 0.6540 (t80) cc_final: 0.6315 (t80) REVERT: A 482 MET cc_start: 0.7535 (ppp) cc_final: 0.7075 (mtt) REVERT: B 103 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8099 (tp30) REVERT: B 109 TYR cc_start: 0.7815 (m-80) cc_final: 0.7523 (m-80) outliers start: 14 outliers final: 8 residues processed: 78 average time/residue: 0.9020 time to fit residues: 73.2215 Evaluate side-chains 71 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 10 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.184924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.170165 restraints weight = 8187.351| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 3.61 r_work: 0.4264 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3560 Z= 0.243 Angle : 0.939 13.727 4822 Z= 0.446 Chirality : 0.047 0.174 550 Planarity : 0.005 0.061 587 Dihedral : 5.796 27.992 473 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.43 % Allowed : 33.25 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.95 (0.42), residues: 420 helix: 0.06 (0.40), residues: 186 sheet: -0.36 (0.85), residues: 35 loop : -2.92 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 449 HIS 0.001 0.000 HIS A 282 PHE 0.015 0.002 PHE A 240 TYR 0.017 0.002 TYR A 428 ARG 0.008 0.001 ARG A 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3537.17 seconds wall clock time: 61 minutes 4.17 seconds (3664.17 seconds total)