Starting phenix.real_space_refine on Mon Jan 13 16:11:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5e_38067/01_2025/8x5e_38067.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5e_38067/01_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_38067/01_2025/8x5e_38067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5e_38067/01_2025/8x5e_38067.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5e_38067/01_2025/8x5e_38067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5e_38067/01_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-5571/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: 2.74, per 1000 atoms: 0.85 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: 1.00 Conformation dependent library (CDL) restraints added in 378.3 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: 0.26 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: 0.72 Time building geometry restraints manager: 1.05 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.910 Find NCS groups from input model: 0.020 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- 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 3312 Z= 0.499 Angle : 1.269 21.609 4490 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 *********************** 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 : 0.366 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: 0.1634 time to fit residues: 22.2365 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 : 0.344 ------------------------------------------------------------------------------- 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 3312 Z= 0.249 Angle : 0.656 7.027 4490 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 *********************** 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 : 0.371 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: 0.1276 time to fit residues: 14.1382 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 : 0.419 ------------------------------------------------------------------------------- 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: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 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 = 0.3794 r_free = 0.3794 target = 0.146050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127862 restraints weight = 5892.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.130889 restraints weight = 3149.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.132962 restraints weight = 2062.242| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3312 Z= 0.204 Angle : 0.587 6.503 4490 Z= 0.315 Chirality : 0.039 0.146 494 Planarity : 0.004 0.041 536 Dihedral : 10.575 87.239 489 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % 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 : -3.29 (0.49), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 292 HIS 0.004 0.001 HIS A 616 PHE 0.044 0.002 PHE A 596 TYR 0.011 0.001 TYR A 558 ARG 0.004 0.000 ARG A 548 *********************** 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 : 0.364 Fit side-chains REVERT: A 388 LYS cc_start: 0.7860 (mptt) cc_final: 0.7537 (mmtm) REVERT: A 399 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.7348 (mp10) REVERT: A 400 LEU cc_start: 0.7767 (tp) cc_final: 0.7116 (mp) REVERT: A 425 GLU cc_start: 0.6882 (mp0) cc_final: 0.6665 (mp0) REVERT: A 528 TRP cc_start: 0.9047 (t-100) cc_final: 0.8743 (t-100) REVERT: A 569 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8064 (mm) REVERT: A 577 ILE cc_start: 0.9161 (tp) cc_final: 0.8888 (tp) outliers start: 17 outliers final: 11 residues processed: 84 average time/residue: 0.1292 time to fit residues: 13.6342 Evaluate side-chains 77 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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: 0.8980 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 0.0070 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.146846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127858 restraints weight = 6099.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131043 restraints weight = 3359.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133192 restraints weight = 2241.742| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3312 Z= 0.188 Angle : 0.559 5.616 4490 Z= 0.302 Chirality : 0.038 0.133 494 Planarity : 0.004 0.040 536 Dihedral : 9.091 69.533 487 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.75 % Allowed : 16.77 % Favored : 78.48 % 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 : -3.07 (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 0.049 0.002 PHE A 596 TYR 0.010 0.001 TYR A 558 ARG 0.002 0.000 ARG A 548 *********************** 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 84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.378 Fit side-chains REVERT: A 388 LYS cc_start: 0.7813 (mptt) cc_final: 0.7573 (mmtm) REVERT: A 400 LEU cc_start: 0.7708 (tp) cc_final: 0.7030 (mp) REVERT: A 528 TRP cc_start: 0.9090 (t-100) cc_final: 0.8792 (t-100) REVERT: A 569 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8070 (mm) REVERT: A 577 ILE cc_start: 0.9180 (tp) cc_final: 0.8867 (tp) outliers start: 15 outliers final: 13 residues processed: 79 average time/residue: 0.1364 time to fit residues: 13.4206 Evaluate side-chains 79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.147346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128386 restraints weight = 6234.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131546 restraints weight = 3451.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133514 restraints weight = 2303.974| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3312 Z= 0.174 Angle : 0.541 5.531 4490 Z= 0.294 Chirality : 0.038 0.150 494 Planarity : 0.004 0.039 536 Dihedral : 7.956 59.104 487 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.06 % Allowed : 17.72 % Favored : 77.22 % 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: 2.16 (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 0.011 0.001 TRP A 573 HIS 0.003 0.001 HIS A 616 PHE 0.020 0.001 PHE A 596 TYR 0.009 0.001 TYR A 558 ARG 0.002 0.000 ARG A 603 *********************** 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 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.375 Fit side-chains REVERT: A 399 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7356 (mp-120) REVERT: A 400 LEU cc_start: 0.7728 (tp) cc_final: 0.7031 (mp) REVERT: A 569 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8052 (mm) outliers start: 16 outliers final: 11 residues processed: 81 average time/residue: 0.1193 time to fit residues: 12.3223 Evaluate side-chains 75 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 38 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.146683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128201 restraints weight = 6155.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.131241 restraints weight = 3307.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133357 restraints weight = 2177.672| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3312 Z= 0.201 Angle : 0.540 6.182 4490 Z= 0.291 Chirality : 0.038 0.170 494 Planarity : 0.004 0.039 536 Dihedral : 7.843 59.297 487 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.38 % Allowed : 18.67 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.43), residues: 384 helix: 2.17 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -3.15 (0.52), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 514 HIS 0.004 0.001 HIS A 616 PHE 0.047 0.002 PHE A 596 TYR 0.009 0.001 TYR A 558 ARG 0.002 0.000 ARG A 603 *********************** 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 84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.350 Fit side-chains REVERT: A 335 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7498 (t80) REVERT: A 399 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: A 569 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8151 (mm) REVERT: A 577 ILE cc_start: 0.9092 (tp) cc_final: 0.8876 (tp) outliers start: 17 outliers final: 14 residues processed: 78 average time/residue: 0.1233 time to fit residues: 12.3388 Evaluate side-chains 85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 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 587 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 = 0.3800 r_free = 0.3800 target = 0.145992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127134 restraints weight = 6149.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130251 restraints weight = 3338.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.132376 restraints weight = 2203.066| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3312 Z= 0.175 Angle : 0.541 8.609 4490 Z= 0.291 Chirality : 0.038 0.140 494 Planarity : 0.004 0.038 536 Dihedral : 7.788 59.200 487 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.01 % Allowed : 18.99 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.43), residues: 384 helix: 2.24 (0.30), residues: 290 sheet: None (None), residues: 0 loop : -3.03 (0.51), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 573 HIS 0.003 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 603 *********************** 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 84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.393 Fit side-chains REVERT: A 335 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7555 (t80) REVERT: A 399 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7279 (mp10) REVERT: A 569 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8122 (mm) REVERT: A 577 ILE cc_start: 0.9086 (tp) cc_final: 0.8869 (tp) outliers start: 19 outliers final: 13 residues processed: 76 average time/residue: 0.1218 time to fit residues: 11.8712 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 617 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.146076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127291 restraints weight = 6193.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.130393 restraints weight = 3330.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132488 restraints weight = 2197.386| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3312 Z= 0.172 Angle : 0.531 8.297 4490 Z= 0.284 Chirality : 0.037 0.148 494 Planarity : 0.004 0.039 536 Dihedral : 7.531 57.513 487 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.70 % Allowed : 19.94 % 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: 1.44 (0.43), residues: 384 helix: 2.10 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -3.31 (0.51), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 573 HIS 0.003 0.001 HIS A 616 PHE 0.048 0.002 PHE A 596 TYR 0.008 0.001 TYR A 558 ARG 0.002 0.000 ARG A 603 *********************** 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 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.345 Fit side-chains REVERT: A 335 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7566 (t80) REVERT: A 399 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: A 400 LEU cc_start: 0.7697 (tp) cc_final: 0.7070 (mp) REVERT: A 569 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8124 (mm) REVERT: A 577 ILE cc_start: 0.9055 (tp) cc_final: 0.8839 (tp) outliers start: 18 outliers final: 14 residues processed: 75 average time/residue: 0.1461 time to fit residues: 13.6335 Evaluate side-chains 79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 0.6980 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 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: 0.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.145033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126219 restraints weight = 6156.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129293 restraints weight = 3338.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131427 restraints weight = 2203.182| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3312 Z= 0.193 Angle : 0.544 8.420 4490 Z= 0.295 Chirality : 0.038 0.156 494 Planarity : 0.004 0.039 536 Dihedral : 7.458 58.405 487 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.38 % Allowed : 20.57 % 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: 1.38 (0.43), residues: 384 helix: 2.05 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -3.28 (0.51), residues: 88 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 0.020 0.001 PHE A 596 TYR 0.008 0.001 TYR A 558 ARG 0.003 0.000 ARG A 604 *********************** 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 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.393 Fit side-chains REVERT: A 335 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7586 (t80) REVERT: A 399 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.7270 (mp-120) REVERT: A 569 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8145 (mm) REVERT: A 577 ILE cc_start: 0.9042 (tp) cc_final: 0.8839 (tp) outliers start: 17 outliers final: 13 residues processed: 75 average time/residue: 0.1414 time to fit residues: 13.2219 Evaluate side-chains 79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.0030 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.145872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127120 restraints weight = 6133.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130201 restraints weight = 3323.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.132360 restraints weight = 2186.643| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3312 Z= 0.177 Angle : 0.549 9.203 4490 Z= 0.289 Chirality : 0.038 0.161 494 Planarity : 0.004 0.038 536 Dihedral : 7.231 59.090 487 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.70 % Allowed : 20.57 % Favored : 73.73 % 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: 1.43 (0.43), residues: 384 helix: 2.06 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -3.21 (0.51), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 573 HIS 0.003 0.001 HIS A 616 PHE 0.049 0.002 PHE A 596 TYR 0.008 0.001 TYR A 558 ARG 0.002 0.000 ARG A 603 ********************** 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 83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.334 Fit side-chains REVERT: A 335 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7645 (t80) REVERT: A 400 LEU cc_start: 0.7816 (tp) cc_final: 0.7166 (mp) REVERT: A 569 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8210 (mm) REVERT: A 577 ILE cc_start: 0.9034 (tp) cc_final: 0.8818 (tp) outliers start: 18 outliers final: 15 residues processed: 75 average time/residue: 0.1323 time to fit residues: 12.4059 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 582 THR 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: 0.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126203 restraints weight = 6071.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129294 restraints weight = 3269.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.131382 restraints weight = 2144.365| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3312 Z= 0.198 Angle : 0.564 9.206 4490 Z= 0.301 Chirality : 0.039 0.150 494 Planarity : 0.004 0.039 536 Dihedral : 7.296 59.384 487 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.38 % Allowed : 19.94 % 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: 1.43 (0.43), residues: 384 helix: 2.05 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -3.16 (0.51), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 514 HIS 0.003 0.001 HIS A 616 PHE 0.020 0.001 PHE A 596 TYR 0.008 0.001 TYR A 558 ARG 0.004 0.000 ARG A 603 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1300.16 seconds wall clock time: 24 minutes 21.54 seconds (1461.54 seconds total)