Starting phenix.real_space_refine on Sat May 2 10:29:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l19_62738/05_2026/9l19_62738_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l19_62738/05_2026/9l19_62738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l19_62738/05_2026/9l19_62738_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l19_62738/05_2026/9l19_62738_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l19_62738/05_2026/9l19_62738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l19_62738/05_2026/9l19_62738.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.004 sd= 0.068 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 32 5.16 5 C 2937 2.51 5 N 659 2.21 5 O 741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4369 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4334 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 28, 'TRANS': 514} Chain breaks: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.70, per 1000 atoms: 0.16 Number of scatterers: 4369 At special positions: 0 Unit cell: (86.427, 81.092, 69.355, 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 32 16.00 O 741 8.00 N 659 7.00 C 2937 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 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: 0.21 Conformation dependent library (CDL) restraints added in 87.3 milliseconds 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 990 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 1 sheets defined 81.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 removed outlier: 4.031A pdb=" N LYS A 47 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.569A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.517A pdb=" N PHE A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 106 removed outlier: 3.645A pdb=" N VAL A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 117 removed outlier: 3.707A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 138 removed outlier: 3.839A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.311A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 Processing helix chain 'A' and resid 246 through 267 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.692A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 removed outlier: 4.042A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 287' Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.196A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.708A pdb=" N LEU A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.265A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 372 through 381 removed outlier: 3.685A pdb=" N MET A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.731A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 3.504A pdb=" N ARG A 423 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 removed outlier: 3.617A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 449 No H-bonds generated for 'chain 'A' and resid 448 through 449' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.601A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.748A pdb=" N LEU A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.368A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.539A pdb=" N LYS A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.688A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 580 removed outlier: 4.193A pdb=" N VAL A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 593 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 274 hydrogen bonds defined for protein. 813 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: 0.35 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 649 1.31 - 1.43: 1371 1.43 - 1.56: 2449 1.56 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 4515 Sorted by residual: bond pdb=" CA SER A 205 " pdb=" CB SER A 205 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.50e-02 4.44e+03 1.55e+01 bond pdb=" C PRO A 253 " pdb=" O PRO A 253 " ideal model delta sigma weight residual 1.235 1.184 0.051 1.30e-02 5.92e+03 1.52e+01 bond pdb=" N VAL A 59 " pdb=" CA VAL A 59 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.35e+01 bond pdb=" N PRO A 253 " pdb=" CD PRO A 253 " ideal model delta sigma weight residual 1.473 1.427 0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" N GLY A 56 " pdb=" CA GLY A 56 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.02e-02 9.61e+03 9.83e+00 ... (remaining 4510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 5555 1.43 - 2.85: 448 2.85 - 4.28: 116 4.28 - 5.71: 36 5.71 - 7.14: 9 Bond angle restraints: 6164 Sorted by residual: angle pdb=" C PHE A 233 " pdb=" N CYS A 234 " pdb=" CA CYS A 234 " ideal model delta sigma weight residual 120.44 114.79 5.65 1.30e+00 5.92e-01 1.89e+01 angle pdb=" N ALA A 433 " pdb=" CA ALA A 433 " pdb=" C ALA A 433 " ideal model delta sigma weight residual 111.28 115.98 -4.70 1.09e+00 8.42e-01 1.86e+01 angle pdb=" CA ILE A 235 " pdb=" C ILE A 235 " pdb=" O ILE A 235 " ideal model delta sigma weight residual 121.17 116.73 4.44 1.06e+00 8.90e-01 1.75e+01 angle pdb=" CA VAL A 246 " pdb=" C VAL A 246 " pdb=" O VAL A 246 " ideal model delta sigma weight residual 120.95 116.65 4.30 1.04e+00 9.25e-01 1.71e+01 angle pdb=" N TYR A 138 " pdb=" CA TYR A 138 " pdb=" C TYR A 138 " ideal model delta sigma weight residual 113.18 108.23 4.95 1.21e+00 6.83e-01 1.67e+01 ... (remaining 6159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.07: 2365 24.07 - 48.14: 204 48.14 - 72.21: 19 72.21 - 96.28: 8 96.28 - 120.36: 1 Dihedral angle restraints: 2597 sinusoidal: 1033 harmonic: 1564 Sorted by residual: dihedral pdb=" CBC Y01 A 701 " pdb=" CAR Y01 A 701 " pdb=" CAT Y01 A 701 " pdb=" CBH Y01 A 701 " ideal model delta sinusoidal sigma weight residual -57.13 63.23 -120.36 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CA ASP A 293 " pdb=" CB ASP A 293 " pdb=" CG ASP A 293 " pdb=" OD1 ASP A 293 " ideal model delta sinusoidal sigma weight residual -30.00 -89.84 59.84 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CAT Y01 A 701 " pdb=" CAR Y01 A 701 " pdb=" CBC Y01 A 701 " pdb=" OAW Y01 A 701 " ideal model delta sinusoidal sigma weight residual 178.96 84.84 94.12 1 3.00e+01 1.11e-03 1.14e+01 ... (remaining 2594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 465 0.048 - 0.095: 146 0.095 - 0.143: 41 0.143 - 0.191: 20 0.191 - 0.239: 5 Chirality restraints: 677 Sorted by residual: chirality pdb=" CA GLU A 107 " pdb=" N GLU A 107 " pdb=" C GLU A 107 " pdb=" CB GLU A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL A 245 " pdb=" CA VAL A 245 " pdb=" CG1 VAL A 245 " pdb=" CG2 VAL A 245 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA PHE A 431 " pdb=" N PHE A 431 " pdb=" C PHE A 431 " pdb=" CB PHE A 431 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 674 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 50 " 0.026 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C PHE A 50 " -0.092 2.00e-02 2.50e+03 pdb=" O PHE A 50 " 0.035 2.00e-02 2.50e+03 pdb=" N VAL A 51 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 381 " -0.054 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO A 382 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 252 " -0.045 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO A 253 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.039 5.00e-02 4.00e+02 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1192 2.79 - 3.32: 4393 3.32 - 3.85: 7603 3.85 - 4.37: 9083 4.37 - 4.90: 15103 Nonbonded interactions: 37374 Sorted by model distance: nonbonded pdb=" OG SER A 152 " pdb=" OG SER A 388 " model vdw 2.267 3.040 nonbonded pdb=" O CYS A 331 " pdb=" OG SER A 334 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR A 72 " pdb=" O ILE A 359 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR A 168 " pdb=" OE2 GLU A 197 " model vdw 2.295 3.040 nonbonded pdb=" OD2 ASP A 281 " pdb=" OG1 THR A 283 " model vdw 2.295 3.040 ... (remaining 37369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.300 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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 : 0.006 0.059 4516 Z= 0.410 Angle : 0.953 7.136 6166 Z= 0.631 Chirality : 0.058 0.239 677 Planarity : 0.008 0.089 748 Dihedral : 17.154 120.356 1604 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 23.28 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.35), residues: 537 helix: 0.21 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -1.08 (0.49), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.023 0.002 TYR A 69 PHE 0.027 0.002 PHE A 58 TRP 0.015 0.001 TRP A 387 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00637 ( 4515) covalent geometry : angle 0.95325 ( 6164) SS BOND : bond 0.00244 ( 1) SS BOND : angle 1.29321 ( 2) hydrogen bonds : bond 0.19485 ( 274) hydrogen bonds : angle 7.30952 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.083 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.0411 time to fit residues: 10.4781 Evaluate side-chains 123 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.103670 restraints weight = 7790.097| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.07 r_work: 0.3294 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4516 Z= 0.165 Angle : 0.696 7.670 6166 Z= 0.355 Chirality : 0.043 0.160 677 Planarity : 0.005 0.053 748 Dihedral : 6.780 52.294 660 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.39 % Allowed : 21.77 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.37), residues: 537 helix: 0.94 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.82 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 427 TYR 0.025 0.002 TYR A 138 PHE 0.024 0.002 PHE A 522 TRP 0.023 0.002 TRP A 470 HIS 0.010 0.003 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 4515) covalent geometry : angle 0.69631 ( 6164) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.62100 ( 2) hydrogen bonds : bond 0.04417 ( 274) hydrogen bonds : angle 4.90401 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8559 (mm-30) REVERT: A 172 MET cc_start: 0.8355 (ptp) cc_final: 0.8105 (ptp) REVERT: A 317 LYS cc_start: 0.8743 (tppt) cc_final: 0.7955 (mppt) REVERT: A 390 LEU cc_start: 0.9076 (mm) cc_final: 0.8826 (mp) REVERT: A 403 GLN cc_start: 0.9207 (tp40) cc_final: 0.8817 (tp40) REVERT: A 444 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.6903 (tp) REVERT: A 592 ARG cc_start: 0.8559 (ptp-170) cc_final: 0.8051 (ptp-170) outliers start: 25 outliers final: 13 residues processed: 136 average time/residue: 0.0287 time to fit residues: 5.4266 Evaluate side-chains 125 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.0060 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.0470 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.126744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105052 restraints weight = 7683.444| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.07 r_work: 0.3312 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4516 Z= 0.130 Angle : 0.630 6.690 6166 Z= 0.317 Chirality : 0.041 0.163 677 Planarity : 0.005 0.040 748 Dihedral : 6.087 49.481 660 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.09 % Allowed : 23.06 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.37), residues: 537 helix: 1.08 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.35 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 427 TYR 0.020 0.001 TYR A 138 PHE 0.044 0.002 PHE A 522 TRP 0.020 0.001 TRP A 470 HIS 0.007 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4515) covalent geometry : angle 0.63040 ( 6164) SS BOND : bond 0.00144 ( 1) SS BOND : angle 0.47279 ( 2) hydrogen bonds : bond 0.03897 ( 274) hydrogen bonds : angle 4.68427 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7934 (t80) REVERT: A 248 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7339 (t80) REVERT: A 256 MET cc_start: 0.9292 (tpp) cc_final: 0.8901 (mmt) REVERT: A 317 LYS cc_start: 0.8845 (tppt) cc_final: 0.8052 (mppt) REVERT: A 353 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: A 444 LEU cc_start: 0.7524 (tt) cc_final: 0.6827 (tp) REVERT: A 592 ARG cc_start: 0.8431 (ptp-170) cc_final: 0.7835 (mtm110) outliers start: 19 outliers final: 12 residues processed: 135 average time/residue: 0.0336 time to fit residues: 6.0413 Evaluate side-chains 125 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 228 TRP Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 15 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.103964 restraints weight = 7756.584| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.10 r_work: 0.3299 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4516 Z= 0.136 Angle : 0.626 7.796 6166 Z= 0.312 Chirality : 0.041 0.166 677 Planarity : 0.004 0.036 748 Dihedral : 5.700 51.780 660 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.96 % Allowed : 22.63 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.37), residues: 537 helix: 1.16 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.11 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 427 TYR 0.017 0.001 TYR A 578 PHE 0.020 0.001 PHE A 522 TRP 0.016 0.001 TRP A 470 HIS 0.005 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4515) covalent geometry : angle 0.62599 ( 6164) SS BOND : bond 0.00148 ( 1) SS BOND : angle 0.63314 ( 2) hydrogen bonds : bond 0.03681 ( 274) hydrogen bonds : angle 4.55759 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7975 (t80) REVERT: A 107 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8282 (mm-30) REVERT: A 115 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8483 (mtmt) REVERT: A 256 MET cc_start: 0.9227 (tpp) cc_final: 0.8763 (mmt) REVERT: A 263 ARG cc_start: 0.8214 (tpm170) cc_final: 0.7778 (tpm170) REVERT: A 317 LYS cc_start: 0.8888 (tppt) cc_final: 0.8092 (mppt) REVERT: A 353 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: A 440 TYR cc_start: 0.8710 (t80) cc_final: 0.8390 (t80) REVERT: A 444 LEU cc_start: 0.7564 (tt) cc_final: 0.6880 (tp) REVERT: A 506 TYR cc_start: 0.8432 (m-80) cc_final: 0.8197 (m-80) REVERT: A 520 PHE cc_start: 0.9157 (t80) cc_final: 0.8777 (t80) REVERT: A 524 LEU cc_start: 0.9325 (mm) cc_final: 0.8956 (mm) REVERT: A 587 ARG cc_start: 0.8619 (ttp-170) cc_final: 0.8229 (ttm-80) outliers start: 23 outliers final: 17 residues processed: 131 average time/residue: 0.0344 time to fit residues: 5.9716 Evaluate side-chains 126 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 228 TRP Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.0980 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 353 GLN A 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.124320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102534 restraints weight = 7938.448| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.17 r_work: 0.3272 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4516 Z= 0.147 Angle : 0.632 8.124 6166 Z= 0.313 Chirality : 0.041 0.169 677 Planarity : 0.004 0.034 748 Dihedral : 5.445 53.064 660 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.60 % Allowed : 23.49 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.37), residues: 537 helix: 1.23 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.20 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 427 TYR 0.013 0.001 TYR A 323 PHE 0.021 0.002 PHE A 434 TRP 0.014 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4515) covalent geometry : angle 0.63226 ( 6164) SS BOND : bond 0.00180 ( 1) SS BOND : angle 0.62091 ( 2) hydrogen bonds : bond 0.03664 ( 274) hydrogen bonds : angle 4.48458 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7998 (t80) REVERT: A 100 ILE cc_start: 0.8544 (tt) cc_final: 0.8163 (mm) REVERT: A 107 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8316 (mm-30) REVERT: A 115 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8315 (mtmm) REVERT: A 256 MET cc_start: 0.9215 (tpp) cc_final: 0.8679 (mmt) REVERT: A 263 ARG cc_start: 0.8182 (tpm170) cc_final: 0.7787 (tpm170) REVERT: A 317 LYS cc_start: 0.8984 (tppt) cc_final: 0.8185 (mppt) REVERT: A 327 MET cc_start: 0.8107 (mmp) cc_final: 0.7815 (mmt) REVERT: A 353 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: A 440 TYR cc_start: 0.8719 (t80) cc_final: 0.8444 (t80) REVERT: A 444 LEU cc_start: 0.7502 (tt) cc_final: 0.6818 (tp) REVERT: A 464 SER cc_start: 0.8433 (t) cc_final: 0.8177 (m) REVERT: A 506 TYR cc_start: 0.8393 (m-80) cc_final: 0.8158 (m-80) REVERT: A 520 PHE cc_start: 0.9131 (t80) cc_final: 0.8833 (t80) REVERT: A 524 LEU cc_start: 0.9341 (mm) cc_final: 0.9095 (mm) REVERT: A 559 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8472 (tt) REVERT: A 587 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.8237 (ttm-80) outliers start: 26 outliers final: 19 residues processed: 136 average time/residue: 0.0367 time to fit residues: 6.5048 Evaluate side-chains 137 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 228 TRP Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 0.0010 chunk 11 optimal weight: 0.0670 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.105897 restraints weight = 7934.220| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.21 r_work: 0.3320 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4516 Z= 0.119 Angle : 0.618 8.682 6166 Z= 0.305 Chirality : 0.040 0.176 677 Planarity : 0.004 0.034 748 Dihedral : 5.289 53.439 660 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.96 % Allowed : 25.86 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.37), residues: 537 helix: 1.33 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.09 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 427 TYR 0.015 0.001 TYR A 320 PHE 0.019 0.001 PHE A 252 TRP 0.016 0.001 TRP A 236 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4515) covalent geometry : angle 0.61791 ( 6164) SS BOND : bond 0.00207 ( 1) SS BOND : angle 0.53983 ( 2) hydrogen bonds : bond 0.03496 ( 274) hydrogen bonds : angle 4.40543 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7731 (t80) REVERT: A 100 ILE cc_start: 0.8571 (tt) cc_final: 0.8265 (mm) REVERT: A 115 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8504 (mtmm) REVERT: A 256 MET cc_start: 0.9212 (tpp) cc_final: 0.8677 (mmt) REVERT: A 263 ARG cc_start: 0.8167 (tpm170) cc_final: 0.7740 (tpm170) REVERT: A 317 LYS cc_start: 0.8971 (tppt) cc_final: 0.7878 (mppt) REVERT: A 327 MET cc_start: 0.8194 (mmp) cc_final: 0.7850 (mmt) REVERT: A 353 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: A 440 TYR cc_start: 0.8648 (t80) cc_final: 0.8378 (t80) REVERT: A 444 LEU cc_start: 0.7486 (tt) cc_final: 0.6820 (tp) REVERT: A 464 SER cc_start: 0.8239 (t) cc_final: 0.8016 (m) REVERT: A 506 TYR cc_start: 0.8457 (m-80) cc_final: 0.8224 (m-80) REVERT: A 520 PHE cc_start: 0.9063 (t80) cc_final: 0.8802 (t80) REVERT: A 559 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8506 (tt) REVERT: A 587 ARG cc_start: 0.8612 (ttp-170) cc_final: 0.8229 (ttm-80) outliers start: 23 outliers final: 17 residues processed: 141 average time/residue: 0.0327 time to fit residues: 6.1672 Evaluate side-chains 140 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 353 GLN A 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.125531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103459 restraints weight = 7906.483| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.23 r_work: 0.3278 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4516 Z= 0.142 Angle : 0.654 8.595 6166 Z= 0.320 Chirality : 0.042 0.172 677 Planarity : 0.004 0.033 748 Dihedral : 5.239 52.404 660 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.96 % Allowed : 27.37 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.37), residues: 537 helix: 1.24 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -0.20 (0.56), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 427 TYR 0.027 0.001 TYR A 138 PHE 0.019 0.002 PHE A 522 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4515) covalent geometry : angle 0.65434 ( 6164) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.67206 ( 2) hydrogen bonds : bond 0.03591 ( 274) hydrogen bonds : angle 4.45440 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7901 (t80) REVERT: A 100 ILE cc_start: 0.8581 (tt) cc_final: 0.8348 (mm) REVERT: A 105 THR cc_start: 0.9445 (m) cc_final: 0.8815 (m) REVERT: A 107 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8224 (mm-30) REVERT: A 248 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7467 (t80) REVERT: A 256 MET cc_start: 0.9230 (tpp) cc_final: 0.8644 (mmt) REVERT: A 263 ARG cc_start: 0.8039 (tpm170) cc_final: 0.7635 (tpm170) REVERT: A 317 LYS cc_start: 0.8993 (tppt) cc_final: 0.7918 (mppt) REVERT: A 327 MET cc_start: 0.8207 (mmp) cc_final: 0.7849 (mmt) REVERT: A 440 TYR cc_start: 0.8651 (t80) cc_final: 0.8334 (t80) REVERT: A 444 LEU cc_start: 0.7493 (tt) cc_final: 0.6844 (tp) REVERT: A 464 SER cc_start: 0.8295 (t) cc_final: 0.8088 (m) REVERT: A 506 TYR cc_start: 0.8455 (m-80) cc_final: 0.8222 (m-80) REVERT: A 559 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8492 (tt) REVERT: A 587 ARG cc_start: 0.8636 (ttp-170) cc_final: 0.8263 (ttm-80) outliers start: 23 outliers final: 17 residues processed: 131 average time/residue: 0.0331 time to fit residues: 5.8067 Evaluate side-chains 137 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 0.0470 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.125423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.103655 restraints weight = 7849.242| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.21 r_work: 0.3287 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4516 Z= 0.137 Angle : 0.677 9.617 6166 Z= 0.327 Chirality : 0.043 0.283 677 Planarity : 0.004 0.032 748 Dihedral : 5.189 51.546 660 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.60 % Allowed : 26.51 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.37), residues: 537 helix: 1.24 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.15 (0.57), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 427 TYR 0.025 0.001 TYR A 138 PHE 0.020 0.002 PHE A 248 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4515) covalent geometry : angle 0.67707 ( 6164) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.65453 ( 2) hydrogen bonds : bond 0.03726 ( 274) hydrogen bonds : angle 4.46047 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.7904 (t80) REVERT: A 256 MET cc_start: 0.9229 (tpp) cc_final: 0.8649 (mmt) REVERT: A 263 ARG cc_start: 0.7998 (tpm170) cc_final: 0.7594 (tpm170) REVERT: A 317 LYS cc_start: 0.9006 (tppt) cc_final: 0.7943 (mppt) REVERT: A 327 MET cc_start: 0.8191 (mmp) cc_final: 0.7822 (mmt) REVERT: A 440 TYR cc_start: 0.8656 (t80) cc_final: 0.8345 (t80) REVERT: A 444 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6732 (tp) REVERT: A 464 SER cc_start: 0.8274 (t) cc_final: 0.8069 (m) REVERT: A 506 TYR cc_start: 0.8346 (m-80) cc_final: 0.8113 (m-80) REVERT: A 559 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8491 (tt) REVERT: A 587 ARG cc_start: 0.8629 (ttp-170) cc_final: 0.8250 (ttm-80) outliers start: 26 outliers final: 19 residues processed: 130 average time/residue: 0.0327 time to fit residues: 5.7103 Evaluate side-chains 141 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098344 restraints weight = 7835.851| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.35 r_work: 0.3139 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4516 Z= 0.145 Angle : 0.725 10.775 6166 Z= 0.350 Chirality : 0.045 0.343 677 Planarity : 0.004 0.032 748 Dihedral : 5.163 50.439 660 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.96 % Allowed : 29.09 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.38), residues: 537 helix: 1.20 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.13 (0.57), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 427 TYR 0.024 0.001 TYR A 138 PHE 0.024 0.002 PHE A 248 TRP 0.016 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4515) covalent geometry : angle 0.72485 ( 6164) SS BOND : bond 0.00157 ( 1) SS BOND : angle 0.67035 ( 2) hydrogen bonds : bond 0.03946 ( 274) hydrogen bonds : angle 4.48042 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7788 (t80) REVERT: A 263 ARG cc_start: 0.7990 (tpm170) cc_final: 0.7542 (tpm170) REVERT: A 317 LYS cc_start: 0.8909 (tppt) cc_final: 0.7815 (mppt) REVERT: A 327 MET cc_start: 0.8024 (mmp) cc_final: 0.7633 (mmt) REVERT: A 440 TYR cc_start: 0.8583 (t80) cc_final: 0.8257 (t80) REVERT: A 444 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6647 (tp) REVERT: A 464 SER cc_start: 0.8046 (t) cc_final: 0.7822 (m) REVERT: A 506 TYR cc_start: 0.8486 (m-80) cc_final: 0.8234 (m-80) REVERT: A 559 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8484 (tp) REVERT: A 587 ARG cc_start: 0.8674 (ttp-170) cc_final: 0.8336 (ttm-80) outliers start: 23 outliers final: 19 residues processed: 135 average time/residue: 0.0336 time to fit residues: 6.0343 Evaluate side-chains 140 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.0070 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098317 restraints weight = 7742.717| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.35 r_work: 0.3139 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4516 Z= 0.152 Angle : 0.745 11.409 6166 Z= 0.365 Chirality : 0.046 0.345 677 Planarity : 0.004 0.032 748 Dihedral : 5.238 49.245 660 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.79 % Favored : 97.02 % Rotamer: Outliers : 4.96 % Allowed : 28.88 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.38), residues: 537 helix: 1.25 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.23 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 427 TYR 0.017 0.001 TYR A 320 PHE 0.026 0.002 PHE A 248 TRP 0.019 0.001 TRP A 470 HIS 0.005 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 4515) covalent geometry : angle 0.74462 ( 6164) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.65604 ( 2) hydrogen bonds : bond 0.03963 ( 274) hydrogen bonds : angle 4.55088 ( 813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7781 (t80) REVERT: A 263 ARG cc_start: 0.8032 (tpm170) cc_final: 0.7732 (tpm170) REVERT: A 317 LYS cc_start: 0.8916 (tppt) cc_final: 0.7815 (mppt) REVERT: A 327 MET cc_start: 0.8009 (mmp) cc_final: 0.7606 (mmt) REVERT: A 440 TYR cc_start: 0.8581 (t80) cc_final: 0.8244 (t80) REVERT: A 444 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6658 (tp) REVERT: A 464 SER cc_start: 0.7971 (t) cc_final: 0.7743 (m) REVERT: A 506 TYR cc_start: 0.8535 (m-80) cc_final: 0.8270 (m-80) REVERT: A 587 ARG cc_start: 0.8710 (ttp-170) cc_final: 0.8335 (ttm-80) outliers start: 23 outliers final: 16 residues processed: 132 average time/residue: 0.0330 time to fit residues: 5.8736 Evaluate side-chains 136 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.0170 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.124913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.103773 restraints weight = 7973.277| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.24 r_work: 0.3282 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4516 Z= 0.148 Angle : 0.745 11.552 6166 Z= 0.363 Chirality : 0.045 0.317 677 Planarity : 0.004 0.032 748 Dihedral : 5.213 46.714 660 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.98 % Favored : 96.83 % Rotamer: Outliers : 4.09 % Allowed : 29.96 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.38), residues: 537 helix: 1.15 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.10 (0.57), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 427 TYR 0.017 0.001 TYR A 320 PHE 0.026 0.002 PHE A 248 TRP 0.019 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 4515) covalent geometry : angle 0.74488 ( 6164) SS BOND : bond 0.00165 ( 1) SS BOND : angle 0.64636 ( 2) hydrogen bonds : bond 0.03919 ( 274) hydrogen bonds : angle 4.56377 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 635.84 seconds wall clock time: 19 minutes 32.65 seconds (1172.65 seconds total)