Starting phenix.real_space_refine on Fri May 9 16:54:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5e_38067/05_2025/8x5e_38067.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5e_38067/05_2025/8x5e_38067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x5e_38067/05_2025/8x5e_38067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5e_38067/05_2025/8x5e_38067.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5e_38067/05_2025/8x5e_38067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5e_38067/05_2025/8x5e_38067.cif" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 15 5.16 5 C 2178 2.51 5 N 501 2.21 5 O 520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3216 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3134 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 82 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 82 Unusual residues: {'6OU': 6, 'PO4': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'6OU:plan-1': 6, '6OU:plan-2': 6, '6OU:plan-3': 6} Unresolved non-hydrogen planarities: 54 Time building chain proxies: 2.86, per 1000 atoms: 0.89 Number of scatterers: 3216 At special positions: 0 Unit cell: (60.35, 75.65, 74.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 2 15.00 O 520 8.00 N 501 7.00 C 2178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " 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: 0.99 Conformation dependent library (CDL) restraints added in 390.5 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 80.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 230 through 258 removed outlier: 3.597A pdb=" N ILE A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 296 removed outlier: 4.028A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 336 Processing helix chain 'A' and resid 345 through 361 removed outlier: 4.179A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.856A pdb=" N TRP A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.598A pdb=" N ALA A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 419 removed outlier: 3.511A pdb=" N SER A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 removed outlier: 5.573A pdb=" N GLU A 436 " --> pdb=" O ASN A 433 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER A 437 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 439 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS A 440 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 Proline residue: A 455 - end of helix removed outlier: 3.839A pdb=" N ARG A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 502 removed outlier: 3.801A pdb=" N LEU A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 532 removed outlier: 3.629A pdb=" N PHE A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 571 removed outlier: 4.454A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 582 removed outlier: 3.860A pdb=" N SER A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 619 Proline residue: A 598 - end of helix removed outlier: 3.919A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 621 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: 0.76 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 913 1.34 - 1.45: 770 1.45 - 1.57: 1609 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3312 Sorted by residual: bond pdb=" C16 6OU A 703 " pdb=" O18 6OU A 703 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C16 6OU A 707 " pdb=" O18 6OU A 707 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C16 6OU A 705 " pdb=" O18 6OU A 705 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C16 6OU A 706 " pdb=" O18 6OU A 706 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C16 6OU A 708 " pdb=" O18 6OU A 708 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 4428 4.32 - 8.64: 49 8.64 - 12.97: 11 12.97 - 17.29: 0 17.29 - 21.61: 2 Bond angle restraints: 4490 Sorted by residual: angle pdb=" C PRO A 554 " pdb=" CA PRO A 554 " pdb=" CB PRO A 554 " ideal model delta sigma weight residual 111.56 93.15 18.41 1.65e+00 3.67e-01 1.25e+02 angle pdb=" N PRO A 554 " pdb=" CA PRO A 554 " pdb=" C PRO A 554 " ideal model delta sigma weight residual 112.47 134.08 -21.61 2.06e+00 2.36e-01 1.10e+02 angle pdb=" N CYS A 620 " pdb=" CA CYS A 620 " pdb=" C CYS A 620 " ideal model delta sigma weight residual 111.28 122.36 -11.08 1.09e+00 8.42e-01 1.03e+02 angle pdb=" N ASP A 533 " pdb=" CA ASP A 533 " pdb=" C ASP A 533 " ideal model delta sigma weight residual 111.40 123.30 -11.90 1.22e+00 6.72e-01 9.52e+01 angle pdb=" N ILE A 339 " pdb=" CA ILE A 339 " pdb=" C ILE A 339 " ideal model delta sigma weight residual 110.62 117.70 -7.08 1.02e+00 9.61e-01 4.82e+01 ... (remaining 4485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.69: 1825 31.69 - 63.37: 41 63.37 - 95.06: 2 95.06 - 126.74: 3 126.74 - 158.43: 1 Dihedral angle restraints: 1872 sinusoidal: 725 harmonic: 1147 Sorted by residual: dihedral pdb=" C PRO A 554 " pdb=" N PRO A 554 " pdb=" CA PRO A 554 " pdb=" CB PRO A 554 " ideal model delta harmonic sigma weight residual -120.70 -106.85 -13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C15 6OU A 705 " pdb=" C16 6OU A 705 " pdb=" O18 6OU A 705 " pdb=" C19 6OU A 705 " ideal model delta sinusoidal sigma weight residual 175.68 -25.89 -158.43 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C07 6OU A 707 " pdb=" C08 6OU A 707 " pdb=" C09 6OU A 707 " pdb=" C10 6OU A 707 " ideal model delta sinusoidal sigma weight residual 179.90 -62.63 -117.47 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 1869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 417 0.085 - 0.171: 54 0.171 - 0.256: 14 0.256 - 0.341: 7 0.341 - 0.427: 2 Chirality restraints: 494 Sorted by residual: chirality pdb=" CA PRO A 554 " pdb=" N PRO A 554 " pdb=" C PRO A 554 " pdb=" CB PRO A 554 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA HIS A 504 " pdb=" N HIS A 504 " pdb=" C HIS A 504 " pdb=" CB HIS A 504 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA PHE A 610 " pdb=" N PHE A 610 " pdb=" C PHE A 610 " pdb=" CB PHE A 610 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 491 not shown) Planarity restraints: 536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 597 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 598 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 266 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 267 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 503 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" C GLY A 503 " 0.022 2.00e-02 2.50e+03 pdb=" O GLY A 503 " -0.008 2.00e-02 2.50e+03 pdb=" N HIS A 504 " -0.007 2.00e-02 2.50e+03 ... (remaining 533 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 1709 2.93 - 3.42: 3474 3.42 - 3.92: 5053 3.92 - 4.41: 5948 4.41 - 4.90: 8714 Nonbonded interactions: 24898 Sorted by model distance: nonbonded pdb=" O GLY A 286 " pdb=" OG1 THR A 289 " model vdw 2.438 3.040 nonbonded pdb=" O ILE A 271 " pdb=" OH TYR A 352 " model vdw 2.535 3.040 nonbonded pdb=" N TYR A 445 " pdb=" N GLY A 446 " model vdw 2.542 2.560 nonbonded pdb=" N GLY A 621 " pdb=" O GLY A 621 " model vdw 2.546 2.496 nonbonded pdb=" O LEU A 332 " pdb=" N PHE A 335 " model vdw 2.550 3.120 ... (remaining 24893 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.730 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 0.072 3313 Z= 0.502 Angle : 1.268 21.609 4492 Z= 0.851 Chirality : 0.074 0.427 494 Planarity : 0.005 0.047 536 Dihedral : 14.325 158.427 1129 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.53 % Allowed : 7.28 % Favored : 90.19 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.40), residues: 384 helix: -0.06 (0.29), residues: 291 sheet: None (None), residues: 0 loop : -3.29 (0.53), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 373 HIS 0.002 0.001 HIS A 299 PHE 0.010 0.001 PHE A 609 TYR 0.011 0.001 TYR A 558 ARG 0.005 0.001 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.24117 ( 213) hydrogen bonds : angle 8.06105 ( 621) SS BOND : bond 0.00225 ( 1) SS BOND : angle 0.12513 ( 2) covalent geometry : bond 0.00740 ( 3312) covalent geometry : angle 1.26851 ( 4490) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 289 THR cc_start: 0.9175 (p) cc_final: 0.8896 (m) REVERT: A 377 LEU cc_start: 0.8440 (tp) cc_final: 0.7873 (mm) REVERT: A 399 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: A 400 LEU cc_start: 0.8060 (tp) cc_final: 0.7732 (mt) REVERT: A 427 LYS cc_start: 0.6832 (mptt) cc_final: 0.5909 (tttm) REVERT: A 569 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8389 (mm) REVERT: A 573 TRP cc_start: 0.7858 (OUTLIER) cc_final: 0.7010 (p90) outliers start: 8 outliers final: 3 residues processed: 114 average time/residue: 0.1603 time to fit residues: 21.7653 Evaluate side-chains 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 573 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 608 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.145547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127751 restraints weight = 6040.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130764 restraints weight = 3147.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132813 restraints weight = 2033.545| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3313 Z= 0.182 Angle : 0.656 7.027 4492 Z= 0.357 Chirality : 0.040 0.150 494 Planarity : 0.005 0.044 536 Dihedral : 12.202 99.286 490 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.06 % Allowed : 12.97 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.42), residues: 384 helix: 1.68 (0.28), residues: 296 sheet: None (None), residues: 0 loop : -3.34 (0.53), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 292 HIS 0.004 0.001 HIS A 476 PHE 0.025 0.002 PHE A 596 TYR 0.015 0.002 TYR A 483 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.07186 ( 213) hydrogen bonds : angle 5.08631 ( 621) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.27838 ( 2) covalent geometry : bond 0.00382 ( 3312) covalent geometry : angle 0.65607 ( 4490) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 425 GLU cc_start: 0.6648 (mp0) cc_final: 0.6407 (mp0) REVERT: A 427 LYS cc_start: 0.6516 (mptt) cc_final: 0.5574 (tttm) REVERT: A 448 ARG cc_start: 0.6930 (mtp-110) cc_final: 0.6714 (mtp-110) REVERT: A 528 TRP cc_start: 0.9144 (t-100) cc_final: 0.8416 (t-100) REVERT: A 569 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8021 (mm) REVERT: A 573 TRP cc_start: 0.7554 (OUTLIER) cc_final: 0.7263 (p90) outliers start: 16 outliers final: 8 residues processed: 88 average time/residue: 0.1205 time to fit residues: 13.3114 Evaluate side-chains 75 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 617 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128013 restraints weight = 5878.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.131066 restraints weight = 3137.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.133172 restraints weight = 2051.300| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3313 Z= 0.149 Angle : 0.584 6.500 4492 Z= 0.313 Chirality : 0.039 0.153 494 Planarity : 0.004 0.041 536 Dihedral : 10.570 87.093 489 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.38 % Allowed : 15.51 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.42), residues: 384 helix: 2.06 (0.29), residues: 291 sheet: None (None), residues: 0 loop : -3.30 (0.49), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 292 HIS 0.004 0.001 HIS A 616 PHE 0.043 0.002 PHE A 596 TYR 0.011 0.001 TYR A 558 ARG 0.006 0.001 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.05942 ( 213) hydrogen bonds : angle 4.46697 ( 621) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.27236 ( 2) covalent geometry : bond 0.00308 ( 3312) covalent geometry : angle 0.58397 ( 4490) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.356 Fit side-chains REVERT: A 388 LYS cc_start: 0.7859 (mptt) cc_final: 0.7539 (mmtm) REVERT: A 399 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: A 400 LEU cc_start: 0.7782 (tp) cc_final: 0.7148 (mp) REVERT: A 425 GLU cc_start: 0.6886 (mp0) cc_final: 0.6667 (mp0) REVERT: A 528 TRP cc_start: 0.9043 (t-100) cc_final: 0.8739 (t-100) REVERT: A 569 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8058 (mm) REVERT: A 577 ILE cc_start: 0.9160 (tp) cc_final: 0.8888 (tp) outliers start: 17 outliers final: 11 residues processed: 84 average time/residue: 0.1240 time to fit residues: 13.1924 Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 617 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.0070 chunk 14 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 608 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.147994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128933 restraints weight = 6075.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.132136 restraints weight = 3343.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134366 restraints weight = 2225.327| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3313 Z= 0.136 Angle : 0.550 5.627 4492 Z= 0.298 Chirality : 0.038 0.137 494 Planarity : 0.004 0.040 536 Dihedral : 8.991 67.149 487 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.75 % Allowed : 17.09 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.43), residues: 384 helix: 2.13 (0.30), residues: 291 sheet: None (None), residues: 0 loop : -3.06 (0.52), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 528 HIS 0.003 0.001 HIS A 616 PHE 0.054 0.002 PHE A 596 TYR 0.010 0.001 TYR A 558 ARG 0.003 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.05280 ( 213) hydrogen bonds : angle 4.38512 ( 621) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.23710 ( 2) covalent geometry : bond 0.00269 ( 3312) covalent geometry : angle 0.55026 ( 4490) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.361 Fit side-chains REVERT: A 388 LYS cc_start: 0.7839 (mptt) cc_final: 0.7615 (mmtm) REVERT: A 400 LEU cc_start: 0.7619 (tp) cc_final: 0.6963 (mp) REVERT: A 528 TRP cc_start: 0.9066 (t-100) cc_final: 0.8719 (t-100) REVERT: A 569 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8019 (mm) REVERT: A 577 ILE cc_start: 0.9176 (tp) cc_final: 0.8862 (tp) outliers start: 15 outliers final: 13 residues processed: 81 average time/residue: 0.1255 time to fit residues: 12.8492 Evaluate side-chains 81 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 617 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.147193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.128214 restraints weight = 6236.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.131359 restraints weight = 3436.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.133568 restraints weight = 2287.475| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3313 Z= 0.136 Angle : 0.545 6.178 4492 Z= 0.297 Chirality : 0.038 0.166 494 Planarity : 0.004 0.039 536 Dihedral : 8.020 58.909 487 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.38 % Allowed : 18.04 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.43), residues: 384 helix: 2.15 (0.30), residues: 291 sheet: None (None), residues: 0 loop : -3.17 (0.51), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 573 HIS 0.003 0.001 HIS A 616 PHE 0.021 0.001 PHE A 596 TYR 0.009 0.001 TYR A 558 ARG 0.001 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.05202 ( 213) hydrogen bonds : angle 4.27829 ( 621) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.36371 ( 2) covalent geometry : bond 0.00289 ( 3312) covalent geometry : angle 0.54519 ( 4490) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.362 Fit side-chains REVERT: A 399 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.7345 (mp-120) REVERT: A 569 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8013 (mm) outliers start: 17 outliers final: 12 residues processed: 83 average time/residue: 0.1201 time to fit residues: 12.6947 Evaluate side-chains 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 587 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.147314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128260 restraints weight = 6241.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131420 restraints weight = 3407.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133539 restraints weight = 2268.341| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3313 Z= 0.134 Angle : 0.539 6.221 4492 Z= 0.289 Chirality : 0.038 0.173 494 Planarity : 0.004 0.039 536 Dihedral : 7.791 58.313 487 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 6.01 % Allowed : 18.35 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.43), residues: 384 helix: 2.22 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -3.15 (0.51), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 573 HIS 0.003 0.001 HIS A 616 PHE 0.050 0.002 PHE A 596 TYR 0.009 0.001 TYR A 558 ARG 0.002 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 213) hydrogen bonds : angle 4.21820 ( 621) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.23356 ( 2) covalent geometry : bond 0.00285 ( 3312) covalent geometry : angle 0.53938 ( 4490) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.343 Fit side-chains REVERT: A 335 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7525 (t80) REVERT: A 399 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: A 569 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8035 (mm) REVERT: A 577 ILE cc_start: 0.9076 (tp) cc_final: 0.8868 (tp) outliers start: 19 outliers final: 14 residues processed: 84 average time/residue: 0.1236 time to fit residues: 13.2809 Evaluate side-chains 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 617 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 608 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.144854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126312 restraints weight = 6224.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129400 restraints weight = 3361.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131530 restraints weight = 2216.054| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3313 Z= 0.141 Angle : 0.557 8.757 4492 Z= 0.298 Chirality : 0.039 0.160 494 Planarity : 0.004 0.039 536 Dihedral : 7.876 58.006 487 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.01 % Allowed : 19.30 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.43), residues: 384 helix: 2.19 (0.30), residues: 290 sheet: None (None), residues: 0 loop : -3.18 (0.50), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 607 HIS 0.004 0.001 HIS A 616 PHE 0.023 0.001 PHE A 596 TYR 0.009 0.001 TYR A 558 ARG 0.002 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.05183 ( 213) hydrogen bonds : angle 4.27845 ( 621) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.24057 ( 2) covalent geometry : bond 0.00304 ( 3312) covalent geometry : angle 0.55691 ( 4490) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.315 Fit side-chains REVERT: A 335 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7555 (t80) REVERT: A 399 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: A 569 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8103 (mm) REVERT: A 577 ILE cc_start: 0.9080 (tp) cc_final: 0.8873 (tp) outliers start: 19 outliers final: 14 residues processed: 78 average time/residue: 0.1300 time to fit residues: 12.7027 Evaluate side-chains 83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 617 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.144992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126312 restraints weight = 6221.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129399 restraints weight = 3341.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.131503 restraints weight = 2198.513| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3313 Z= 0.134 Angle : 0.548 8.272 4492 Z= 0.290 Chirality : 0.038 0.180 494 Planarity : 0.004 0.038 536 Dihedral : 7.597 56.351 487 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.01 % Allowed : 19.62 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.43), residues: 384 helix: 2.30 (0.30), residues: 283 sheet: None (None), residues: 0 loop : -2.92 (0.51), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 573 HIS 0.003 0.001 HIS A 616 PHE 0.050 0.002 PHE A 596 TYR 0.008 0.001 TYR A 558 ARG 0.002 0.000 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.04997 ( 213) hydrogen bonds : angle 4.19697 ( 621) SS BOND : bond 0.00020 ( 1) SS BOND : angle 0.19697 ( 2) covalent geometry : bond 0.00286 ( 3312) covalent geometry : angle 0.54851 ( 4490) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.353 Fit side-chains REVERT: A 335 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7570 (t80) REVERT: A 399 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.7339 (mp10) REVERT: A 569 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8142 (mm) REVERT: A 577 ILE cc_start: 0.9057 (tp) cc_final: 0.8847 (tp) outliers start: 19 outliers final: 14 residues processed: 81 average time/residue: 0.1363 time to fit residues: 13.8040 Evaluate side-chains 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 617 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 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 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126564 restraints weight = 6168.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129557 restraints weight = 3345.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131705 restraints weight = 2208.678| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3313 Z= 0.136 Angle : 0.563 8.459 4492 Z= 0.301 Chirality : 0.039 0.159 494 Planarity : 0.004 0.039 536 Dihedral : 7.441 57.135 487 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.70 % Allowed : 20.25 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.43), residues: 384 helix: 2.28 (0.30), residues: 283 sheet: None (None), residues: 0 loop : -2.82 (0.52), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 607 HIS 0.003 0.001 HIS A 616 PHE 0.021 0.001 PHE A 596 TYR 0.008 0.001 TYR A 558 ARG 0.003 0.000 ARG A 570 Details of bonding type rmsd hydrogen bonds : bond 0.05003 ( 213) hydrogen bonds : angle 4.27153 ( 621) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.23702 ( 2) covalent geometry : bond 0.00290 ( 3312) covalent geometry : angle 0.56336 ( 4490) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.343 Fit side-chains REVERT: A 335 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7570 (t80) REVERT: A 399 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7266 (mp-120) REVERT: A 569 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8144 (mm) REVERT: A 577 ILE cc_start: 0.9060 (tp) cc_final: 0.8860 (tp) outliers start: 18 outliers final: 15 residues processed: 77 average time/residue: 0.1335 time to fit residues: 12.9118 Evaluate side-chains 81 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 499 HIS A 587 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123838 restraints weight = 6191.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.126834 restraints weight = 3335.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128840 restraints weight = 2184.008| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3313 Z= 0.161 Angle : 0.581 8.231 4492 Z= 0.310 Chirality : 0.040 0.182 494 Planarity : 0.004 0.039 536 Dihedral : 7.739 58.976 487 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 6.01 % Allowed : 20.89 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.43), residues: 384 helix: 2.21 (0.30), residues: 283 sheet: None (None), residues: 0 loop : -2.76 (0.53), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 514 HIS 0.004 0.001 HIS A 616 PHE 0.052 0.002 PHE A 596 TYR 0.009 0.001 TYR A 518 ARG 0.002 0.000 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.05555 ( 213) hydrogen bonds : angle 4.34101 ( 621) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.29867 ( 2) covalent geometry : bond 0.00361 ( 3312) covalent geometry : angle 0.58123 ( 4490) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.367 Fit side-chains REVERT: A 335 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7587 (t80) REVERT: A 399 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.7483 (mp10) REVERT: A 569 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8246 (mm) REVERT: A 577 ILE cc_start: 0.9067 (tp) cc_final: 0.8867 (tp) outliers start: 19 outliers final: 13 residues processed: 75 average time/residue: 0.1364 time to fit residues: 12.7372 Evaluate side-chains 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 587 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125724 restraints weight = 6183.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128696 restraints weight = 3381.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130761 restraints weight = 2253.682| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3313 Z= 0.140 Angle : 0.568 7.919 4492 Z= 0.307 Chirality : 0.039 0.164 494 Planarity : 0.004 0.039 536 Dihedral : 7.152 59.627 485 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 6.33 % Allowed : 20.25 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.43), residues: 384 helix: 2.23 (0.30), residues: 283 sheet: None (None), residues: 0 loop : -2.71 (0.53), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 607 HIS 0.003 0.001 HIS A 616 PHE 0.020 0.002 PHE A 596 TYR 0.008 0.001 TYR A 483 ARG 0.004 0.000 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.05198 ( 213) hydrogen bonds : angle 4.31096 ( 621) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.27850 ( 2) covalent geometry : bond 0.00300 ( 3312) covalent geometry : angle 0.56801 ( 4490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1363.12 seconds wall clock time: 24 minutes 41.37 seconds (1481.37 seconds total)