Starting phenix.real_space_refine on Tue Feb 11 01:20:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qw4_18680/02_2025/8qw4_18680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qw4_18680/02_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_18680/02_2025/8qw4_18680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qw4_18680/02_2025/8qw4_18680.map" model { file = "/net/cci-nas-00/data/ceres_data/8qw4_18680/02_2025/8qw4_18680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qw4_18680/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.79, per 1000 atoms: 1.38 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: 0.79 Conformation dependent library (CDL) restraints added in 380.5 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: 0.33 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: 0.87 Time building geometry restraints manager: 0.94 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: 7.120 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.760 Find NCS groups from input model: 0.030 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:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.220 ------------------------------------------------------------------------------- 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 : 0.369 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: 0.9302 time to fit residues: 114.8077 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 : 0.393 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.169331 restraints weight = 7913.191| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 3.53 r_work: 0.4256 rms_B_bonded: 4.32 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 : 0.406 Fit side-chains REVERT: A 193 TYR cc_start: 0.5710 (OUTLIER) cc_final: 0.5492 (m-80) REVERT: A 203 ARG cc_start: 0.6718 (tpt90) cc_final: 0.5224 (mtp180) REVERT: A 291 MET cc_start: 0.6459 (ptt) cc_final: 0.6157 (pmm) REVERT: A 336 TRP cc_start: 0.8460 (m100) cc_final: 0.7686 (m-10) REVERT: A 349 MET cc_start: 0.5041 (mmt) cc_final: 0.3570 (ptt) REVERT: A 367 ASP cc_start: 0.7853 (t0) cc_final: 0.7554 (t0) REVERT: A 415 VAL cc_start: 0.6072 (OUTLIER) cc_final: 0.4956 (t) REVERT: A 433 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7814 (tm) REVERT: A 445 TYR cc_start: 0.6772 (t80) cc_final: 0.6509 (t80) REVERT: B 35 ASP cc_start: 0.8735 (m-30) cc_final: 0.8478 (m-30) REVERT: B 109 TYR cc_start: 0.7766 (m-80) cc_final: 0.7356 (m-80) outliers start: 19 outliers final: 7 residues processed: 81 average time/residue: 0.9855 time to fit residues: 82.8634 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 : 0.382 ------------------------------------------------------------------------------- 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: 0.0570 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 14 optimal weight: 0.0770 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.0030 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.2266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** 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 = 0.4542 r_free = 0.4542 target = 0.187327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.172088 restraints weight = 8110.493| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 3.55 r_work: 0.4297 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3560 Z= 0.225 Angle : 0.789 8.333 4822 Z= 0.401 Chirality : 0.048 0.278 550 Planarity : 0.006 0.059 587 Dihedral : 6.743 35.450 476 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 3.96 % Allowed : 22.96 % Favored : 73.09 % 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: -2.54 (0.40), residues: 420 helix: -0.38 (0.38), residues: 189 sheet: -1.07 (0.82), residues: 36 loop : -3.25 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 449 HIS 0.001 0.000 HIS A 332 PHE 0.020 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 93 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 326 LYS cc_start: 0.9047 (mtmm) cc_final: 0.8825 (mtmm) REVERT: A 336 TRP cc_start: 0.8320 (m100) cc_final: 0.7567 (m-10) REVERT: A 349 MET cc_start: 0.4775 (mmt) cc_final: 0.3406 (ptt) REVERT: A 367 ASP cc_start: 0.7671 (t0) cc_final: 0.7229 (t0) REVERT: A 415 VAL cc_start: 0.5773 (OUTLIER) cc_final: 0.4559 (t) REVERT: A 433 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7824 (tm) REVERT: A 482 MET cc_start: 0.7558 (ppp) cc_final: 0.7328 (pp-130) REVERT: B 35 ASP cc_start: 0.8821 (m-30) cc_final: 0.8523 (m-30) REVERT: B 109 TYR cc_start: 0.7762 (m-80) cc_final: 0.7448 (m-80) outliers start: 15 outliers final: 5 residues processed: 84 average time/residue: 0.8319 time to fit residues: 72.9652 Evaluate side-chains 72 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 279 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.0870 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4512 r_free = 0.4512 target = 0.184528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.169077 restraints weight = 8057.198| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 3.60 r_work: 0.4257 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.3910 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= 0.269 Angle : 0.811 9.513 4822 Z= 0.406 Chirality : 0.048 0.172 550 Planarity : 0.005 0.062 587 Dihedral : 6.687 34.109 476 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 5.54 % Allowed : 25.07 % Favored : 69.39 % 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: -2.30 (0.41), residues: 420 helix: -0.24 (0.38), residues: 189 sheet: -0.88 (0.84), residues: 36 loop : -3.07 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 449 HIS 0.002 0.001 HIS A 282 PHE 0.015 0.002 PHE B 32 TYR 0.026 0.002 TYR A 428 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 94 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.5191 (tpt-90) REVERT: A 291 MET cc_start: 0.6333 (ptt) cc_final: 0.5601 (pmm) REVERT: A 336 TRP cc_start: 0.8360 (m100) cc_final: 0.7563 (m-10) REVERT: A 349 MET cc_start: 0.4869 (mmt) cc_final: 0.3833 (ptt) REVERT: A 415 VAL cc_start: 0.5995 (OUTLIER) cc_final: 0.4766 (t) REVERT: A 433 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7823 (tm) REVERT: A 445 TYR cc_start: 0.6595 (t80) cc_final: 0.6313 (t80) REVERT: B 35 ASP cc_start: 0.8847 (m-30) cc_final: 0.8533 (m-30) REVERT: B 109 TYR cc_start: 0.7808 (m-80) cc_final: 0.7457 (m-80) outliers start: 21 outliers final: 7 residues processed: 84 average time/residue: 0.9360 time to fit residues: 81.7452 Evaluate side-chains 73 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 A residue 433 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 4 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 8 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.0030 chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 overall best weight: 0.3190 ------------------------------------------------------------------------------- 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 = 0.4530 r_free = 0.4530 target = 0.186442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.171127 restraints weight = 8109.560| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 3.67 r_work: 0.4279 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3560 Z= 0.228 Angle : 0.810 10.458 4822 Z= 0.395 Chirality : 0.046 0.180 550 Planarity : 0.005 0.056 587 Dihedral : 6.183 27.685 473 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 5.01 % Allowed : 27.97 % Favored : 67.02 % 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 (0.41), residues: 420 helix: -0.23 (0.39), residues: 190 sheet: -0.63 (0.88), residues: 36 loop : -3.00 (0.44), residues: 194 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 0.025 0.002 PHE A 224 TYR 0.016 0.001 TYR A 204 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 90 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6670 (tpt90) cc_final: 0.5244 (tpt-90) REVERT: A 250 LEU cc_start: 0.8117 (tt) cc_final: 0.7783 (tt) REVERT: A 349 MET cc_start: 0.4763 (mmt) cc_final: 0.3489 (ptt) REVERT: A 367 ASP cc_start: 0.7951 (t0) cc_final: 0.7723 (t0) REVERT: A 415 VAL cc_start: 0.5903 (OUTLIER) cc_final: 0.4643 (t) REVERT: A 433 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7835 (tm) REVERT: A 445 TYR cc_start: 0.6510 (t80) cc_final: 0.6269 (t80) REVERT: A 482 MET cc_start: 0.7550 (ppp) cc_final: 0.7018 (mtt) REVERT: A 501 LYS cc_start: 0.8541 (tppp) cc_final: 0.8280 (mmmt) REVERT: B 35 ASP cc_start: 0.8867 (m-30) cc_final: 0.8571 (m-30) REVERT: B 103 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7899 (tp30) REVERT: B 109 TYR cc_start: 0.7807 (m-80) cc_final: 0.7423 (m-80) outliers start: 19 outliers final: 9 residues processed: 82 average time/residue: 0.8352 time to fit residues: 71.5568 Evaluate side-chains 75 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU 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 A residue 433 LEU Chi-restraints excluded: chain A residue 485 LEU 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 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: 3.9990 chunk 9 optimal weight: 0.0050 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.4514 r_free = 0.4514 target = 0.184564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.169221 restraints weight = 8185.004| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 3.67 r_work: 0.4260 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.4442 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= 0.257 Angle : 0.823 10.264 4822 Z= 0.400 Chirality : 0.047 0.172 550 Planarity : 0.005 0.059 587 Dihedral : 6.195 28.499 473 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % 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: -2.12 (0.42), residues: 420 helix: -0.14 (0.39), residues: 189 sheet: -0.57 (0.89), residues: 36 loop : -2.96 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 449 HIS 0.001 0.001 HIS A 282 PHE 0.016 0.002 PHE A 253 TYR 0.027 0.002 TYR A 428 ARG 0.006 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 92 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.5291 (tpt-90) REVERT: A 291 MET cc_start: 0.6040 (ptt) cc_final: 0.5311 (pmm) REVERT: A 336 TRP cc_start: 0.8332 (m100) cc_final: 0.7520 (m-10) REVERT: A 349 MET cc_start: 0.4906 (mmt) cc_final: 0.3491 (ptt) REVERT: A 367 ASP cc_start: 0.7909 (t0) cc_final: 0.7643 (t0) REVERT: A 415 VAL cc_start: 0.6119 (OUTLIER) cc_final: 0.4831 (t) REVERT: A 433 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7860 (tm) REVERT: A 445 TYR cc_start: 0.6574 (t80) cc_final: 0.6350 (t80) REVERT: A 482 MET cc_start: 0.7611 (ppp) cc_final: 0.7068 (mtt) REVERT: A 501 LYS cc_start: 0.8634 (tppp) cc_final: 0.8370 (mmmt) REVERT: B 35 ASP cc_start: 0.8840 (m-30) cc_final: 0.8542 (m-30) REVERT: B 103 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7997 (tp30) REVERT: B 109 TYR cc_start: 0.7808 (m-80) cc_final: 0.7474 (m-80) outliers start: 20 outliers final: 10 residues processed: 85 average time/residue: 0.9210 time to fit residues: 81.6319 Evaluate side-chains 76 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 37 MET 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: 0.5980 chunk 39 optimal weight: 0.4980 chunk 33 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4518 r_free = 0.4518 target = 0.184838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.169455 restraints weight = 7914.354| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 3.67 r_work: 0.4259 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.4580 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= 0.254 Angle : 0.856 10.896 4822 Z= 0.414 Chirality : 0.047 0.172 550 Planarity : 0.005 0.059 587 Dihedral : 6.190 27.963 473 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 5.01 % Allowed : 29.55 % 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: -2.10 (0.42), residues: 420 helix: -0.12 (0.39), residues: 189 sheet: -0.48 (0.87), residues: 35 loop : -2.97 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 449 HIS 0.001 0.001 HIS A 282 PHE 0.012 0.002 PHE A 240 TYR 0.029 0.002 TYR A 428 ARG 0.007 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 83 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.5246 (tpt-90) REVERT: A 210 SER cc_start: 0.7871 (m) cc_final: 0.7618 (t) REVERT: A 291 MET cc_start: 0.6112 (ptt) cc_final: 0.5322 (pmm) REVERT: A 349 MET cc_start: 0.4947 (mmt) cc_final: 0.3575 (ptt) REVERT: A 367 ASP cc_start: 0.7861 (t0) cc_final: 0.7612 (t0) REVERT: A 433 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7821 (tm) REVERT: A 445 TYR cc_start: 0.6657 (t80) cc_final: 0.6396 (t80) REVERT: A 482 MET cc_start: 0.7654 (ppp) cc_final: 0.7106 (mtt) REVERT: B 35 ASP cc_start: 0.8850 (m-30) cc_final: 0.8561 (m-30) REVERT: B 103 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8029 (tp30) REVERT: B 109 TYR cc_start: 0.7820 (m-80) cc_final: 0.7480 (m-80) outliers start: 19 outliers final: 11 residues processed: 76 average time/residue: 0.8969 time to fit residues: 71.0267 Evaluate side-chains 77 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 A residue 433 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 66 VAL 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: 0.2980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 22 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.0050 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.2772 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.186500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.171728 restraints weight = 8052.512| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 3.60 r_work: 0.4292 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3560 Z= 0.226 Angle : 0.836 11.251 4822 Z= 0.402 Chirality : 0.045 0.175 550 Planarity : 0.005 0.058 587 Dihedral : 5.814 27.393 473 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.75 % Allowed : 29.02 % 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: -1.95 (0.42), residues: 420 helix: 0.05 (0.40), residues: 189 sheet: -0.31 (0.90), residues: 35 loop : -2.97 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.001 0.000 HIS A 181 PHE 0.009 0.002 PHE A 240 TYR 0.026 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 91 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7189 (mt) REVERT: A 203 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.5228 (tpt-90) REVERT: A 210 SER cc_start: 0.7915 (m) cc_final: 0.7615 (t) REVERT: A 291 MET cc_start: 0.6100 (ptt) cc_final: 0.5302 (pmm) REVERT: A 349 MET cc_start: 0.4886 (mmt) cc_final: 0.3527 (ptt) REVERT: A 367 ASP cc_start: 0.7832 (t0) cc_final: 0.7624 (t0) REVERT: A 433 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7799 (tm) REVERT: A 445 TYR cc_start: 0.6709 (t80) cc_final: 0.6492 (t80) REVERT: A 482 MET cc_start: 0.7534 (ppp) cc_final: 0.7114 (mtt) REVERT: A 501 LYS cc_start: 0.8926 (tptp) cc_final: 0.8670 (tppt) REVERT: B 103 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8078 (tp30) REVERT: B 109 TYR cc_start: 0.7813 (m-80) cc_final: 0.7492 (m-80) outliers start: 18 outliers final: 9 residues processed: 84 average time/residue: 0.9241 time to fit residues: 80.6618 Evaluate side-chains 74 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU 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 A residue 433 LEU 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 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: 0.0980 chunk 34 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 39 optimal weight: 0.3980 chunk 5 optimal weight: 0.4980 chunk 11 optimal weight: 0.0270 chunk 17 optimal weight: 2.9990 overall best weight: 0.1838 ------------------------------------------------------------------------------- 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 = 0.4533 r_free = 0.4533 target = 0.187046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.172589 restraints weight = 7912.597| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 3.56 r_work: 0.4294 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3560 Z= 0.231 Angle : 0.871 12.039 4822 Z= 0.420 Chirality : 0.045 0.176 550 Planarity : 0.005 0.059 587 Dihedral : 5.665 26.340 473 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.17 % Allowed : 31.93 % Favored : 64.91 % 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: -1.88 (0.42), residues: 420 helix: 0.14 (0.40), residues: 187 sheet: -0.42 (0.88), residues: 35 loop : -2.91 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 449 HIS 0.001 0.000 HIS A 332 PHE 0.011 0.002 PHE A 240 TYR 0.032 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 84 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6678 (tpt90) cc_final: 0.5215 (tpt-90) REVERT: A 210 SER cc_start: 0.7854 (m) cc_final: 0.7533 (t) REVERT: A 243 VAL cc_start: 0.8752 (p) cc_final: 0.8529 (p) REVERT: A 349 MET cc_start: 0.4699 (mmt) cc_final: 0.3456 (ptt) REVERT: A 367 ASP cc_start: 0.7735 (t0) cc_final: 0.7497 (t0) REVERT: A 433 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7762 (tm) REVERT: A 482 MET cc_start: 0.7493 (ppp) cc_final: 0.7053 (mtt) REVERT: A 501 LYS cc_start: 0.8867 (tptp) cc_final: 0.8598 (mmmt) REVERT: B 103 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8095 (tp30) REVERT: B 109 TYR cc_start: 0.7816 (m-80) cc_final: 0.7584 (m-80) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.9050 time to fit residues: 76.1832 Evaluate side-chains 72 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU 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 A residue 433 LEU 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 38 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 0.0010 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.0470 overall best weight: 0.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.186629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.172180 restraints weight = 8150.710| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 3.59 r_work: 0.4286 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.5471 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= 0.239 Angle : 0.943 13.881 4822 Z= 0.445 Chirality : 0.047 0.176 550 Planarity : 0.005 0.058 587 Dihedral : 5.610 25.932 473 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.43 % Allowed : 31.66 % Favored : 64.91 % 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: -1.85 (0.42), residues: 420 helix: 0.13 (0.39), residues: 187 sheet: -0.37 (0.90), residues: 35 loop : -2.85 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 449 HIS 0.000 0.000 HIS A 332 PHE 0.014 0.002 PHE A 296 TYR 0.032 0.002 TYR A 428 ARG 0.009 0.001 ARG A 459 ********************** 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 78 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.5110 (tpt-90) REVERT: A 210 SER cc_start: 0.7843 (m) cc_final: 0.7513 (t) REVERT: A 349 MET cc_start: 0.4560 (mmt) cc_final: 0.3297 (ptt) REVERT: A 367 ASP cc_start: 0.7689 (t0) cc_final: 0.7459 (t0) REVERT: A 433 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7843 (tm) REVERT: A 445 TYR cc_start: 0.6387 (t80) cc_final: 0.6144 (t80) REVERT: A 482 MET cc_start: 0.7524 (ppp) cc_final: 0.7140 (mtt) REVERT: A 501 LYS cc_start: 0.8904 (tptp) cc_final: 0.8702 (tppt) REVERT: B 109 TYR cc_start: 0.7769 (m-80) cc_final: 0.7495 (m-80) outliers start: 13 outliers final: 9 residues processed: 74 average time/residue: 0.9283 time to fit residues: 71.4314 Evaluate side-chains 75 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 250 LEU 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 A residue 433 LEU 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: 1.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 13 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** 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 = 0.4495 r_free = 0.4495 target = 0.182927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.168250 restraints weight = 8267.207| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 3.58 r_work: 0.4246 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.5369 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= 0.285 Angle : 0.974 13.630 4822 Z= 0.461 Chirality : 0.048 0.171 550 Planarity : 0.005 0.057 587 Dihedral : 5.926 26.010 473 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 3.17 % Allowed : 32.45 % Favored : 64.38 % 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: -1.92 (0.42), residues: 420 helix: 0.05 (0.39), residues: 189 sheet: -0.25 (0.90), residues: 35 loop : -2.92 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.002 0.001 HIS A 181 PHE 0.009 0.002 PHE A 201 TYR 0.023 0.002 TYR A 428 ARG 0.009 0.001 ARG A 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3479.54 seconds wall clock time: 62 minutes 3.14 seconds (3723.14 seconds total)