Starting phenix.real_space_refine on Tue Feb 11 04:01:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fil_31602/02_2025/7fil_31602.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fil_31602/02_2025/7fil_31602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fil_31602/02_2025/7fil_31602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fil_31602/02_2025/7fil_31602.map" model { file = "/net/cci-nas-00/data/ceres_data/7fil_31602/02_2025/7fil_31602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fil_31602/02_2025/7fil_31602.cif" } resolution = 3.0 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2551 2.51 5 N 673 2.21 5 O 747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3993 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3993 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 22, 'TRANS': 481} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 2.70, per 1000 atoms: 0.68 Number of scatterers: 3993 At special positions: 0 Unit cell: (76.285, 77.672, 102.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 747 8.00 N 673 7.00 C 2551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.92 Conformation dependent library (CDL) restraints added in 446.7 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 67.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 222 through 243 removed outlier: 4.095A pdb=" N LYS A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 removed outlier: 3.565A pdb=" N LYS A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.452A pdb=" N VAL A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 325 removed outlier: 3.654A pdb=" N ALA A 322 " --> pdb=" O CYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 362 Processing helix chain 'A' and resid 366 through 375 removed outlier: 3.800A pdb=" N SER A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 390 removed outlier: 4.342A pdb=" N PHE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 427 removed outlier: 3.880A pdb=" N SER A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.683A pdb=" N TRP A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 502 removed outlier: 3.536A pdb=" N LEU A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 539 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.940A pdb=" N LEU A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 588 " --> pdb=" O THR A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 614 removed outlier: 4.195A pdb=" N GLU A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) Proline residue: A 610 - end of helix removed outlier: 3.555A pdb=" N LEU A 614 " --> pdb=" O PRO A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 659 Processing helix chain 'A' and resid 662 through 671 removed outlier: 3.511A pdb=" N ILE A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 690 removed outlier: 3.508A pdb=" N TYR A 679 " --> pdb=" O ASN A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 713 removed outlier: 3.824A pdb=" N GLU A 701 " --> pdb=" O CYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 3.683A pdb=" N ALA A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) Proline residue: A 728 - end of helix 235 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1056 1.33 - 1.45: 701 1.45 - 1.57: 2286 1.57 - 1.69: 1 1.69 - 1.82: 31 Bond restraints: 4075 Sorted by residual: bond pdb=" N PRO A 314 " pdb=" CA PRO A 314 " ideal model delta sigma weight residual 1.469 1.692 -0.223 1.28e-02 6.10e+03 3.05e+02 bond pdb=" C LYS A 327 " pdb=" N PRO A 328 " ideal model delta sigma weight residual 1.333 1.499 -0.167 1.17e-02 7.31e+03 2.03e+02 bond pdb=" C VAL A 325 " pdb=" N PRO A 326 " ideal model delta sigma weight residual 1.332 1.509 -0.177 1.32e-02 5.74e+03 1.80e+02 bond pdb=" C GLU A 313 " pdb=" N PRO A 314 " ideal model delta sigma weight residual 1.334 1.450 -0.116 2.34e-02 1.83e+03 2.48e+01 bond pdb=" N LYS A 365 " pdb=" CA LYS A 365 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 9.02e+00 ... (remaining 4070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 5452 3.43 - 6.86: 61 6.86 - 10.28: 2 10.28 - 13.71: 2 13.71 - 17.14: 4 Bond angle restraints: 5521 Sorted by residual: angle pdb=" C LYS A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta sigma weight residual 119.90 136.48 -16.58 1.05e+00 9.07e-01 2.49e+02 angle pdb=" C VAL A 325 " pdb=" N PRO A 326 " pdb=" CA PRO A 326 " ideal model delta sigma weight residual 119.76 134.51 -14.75 1.00e+00 1.00e+00 2.18e+02 angle pdb=" C GLU A 313 " pdb=" N PRO A 314 " pdb=" CA PRO A 314 " ideal model delta sigma weight residual 119.84 136.98 -17.14 1.25e+00 6.40e-01 1.88e+02 angle pdb=" N PRO A 314 " pdb=" CA PRO A 314 " pdb=" C PRO A 314 " ideal model delta sigma weight residual 112.47 97.38 15.09 2.06e+00 2.36e-01 5.37e+01 angle pdb=" CA PRO A 314 " pdb=" N PRO A 314 " pdb=" CD PRO A 314 " ideal model delta sigma weight residual 112.00 101.88 10.12 1.40e+00 5.10e-01 5.23e+01 ... (remaining 5516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 2098 17.76 - 35.52: 261 35.52 - 53.28: 80 53.28 - 71.04: 23 71.04 - 88.80: 7 Dihedral angle restraints: 2469 sinusoidal: 982 harmonic: 1487 Sorted by residual: dihedral pdb=" CA GLN A 564 " pdb=" C GLN A 564 " pdb=" N GLU A 565 " pdb=" CA GLU A 565 " ideal model delta harmonic sigma weight residual 180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" C TYR A 597 " pdb=" N TYR A 597 " pdb=" CA TYR A 597 " pdb=" CB TYR A 597 " ideal model delta harmonic sigma weight residual -122.60 -133.07 10.47 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" CA PRO A 462 " pdb=" C PRO A 462 " pdb=" N ARG A 463 " pdb=" CA ARG A 463 " ideal model delta harmonic sigma weight residual 180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 2466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 607 0.128 - 0.257: 15 0.257 - 0.385: 3 0.385 - 0.513: 0 0.513 - 0.641: 1 Chirality restraints: 626 Sorted by residual: chirality pdb=" CA PRO A 314 " pdb=" N PRO A 314 " pdb=" C PRO A 314 " pdb=" CB PRO A 314 " both_signs ideal model delta sigma weight residual False 2.72 3.36 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA TYR A 597 " pdb=" N TYR A 597 " pdb=" C TYR A 597 " pdb=" CB TYR A 597 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA LYS A 327 " pdb=" N LYS A 327 " pdb=" C LYS A 327 " pdb=" CB LYS A 327 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 623 not shown) Planarity restraints: 705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 322 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C ALA A 322 " -0.043 2.00e-02 2.50e+03 pdb=" O ALA A 322 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 323 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 360 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C THR A 360 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 360 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 361 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 314 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C PRO A 314 " 0.037 2.00e-02 2.50e+03 pdb=" O PRO A 314 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 315 " -0.012 2.00e-02 2.50e+03 ... (remaining 702 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 597 2.75 - 3.29: 4096 3.29 - 3.83: 6537 3.83 - 4.36: 7249 4.36 - 4.90: 12045 Nonbonded interactions: 30524 Sorted by model distance: nonbonded pdb=" O PHE A 632 " pdb=" N ASN A 634 " model vdw 2.213 3.120 nonbonded pdb=" O SER A 478 " pdb=" OG SER A 478 " model vdw 2.218 3.040 nonbonded pdb=" OG SER A 352 " pdb=" OD1 ASP A 423 " model vdw 2.224 3.040 nonbonded pdb=" ND2 ASN A 474 " pdb=" OG1 THR A 559 " model vdw 2.237 3.120 nonbonded pdb=" OE1 GLN A 324 " pdb=" NH1 ARG A 412 " model vdw 2.253 3.120 ... (remaining 30519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.150 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 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 : 0.008 0.223 4075 Z= 0.513 Angle : 1.046 17.138 5521 Z= 0.706 Chirality : 0.062 0.641 626 Planarity : 0.005 0.040 705 Dihedral : 18.460 88.802 1497 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 1.21 % Allowed : 7.66 % Favored : 91.13 % Rotamer: Outliers : 8.76 % Allowed : 25.58 % Favored : 65.67 % Cbeta Deviations : 0.41 % 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: -1.82 (0.36), residues: 496 helix: -0.21 (0.27), residues: 318 sheet: None (None), residues: 0 loop : -3.06 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 439 HIS 0.004 0.001 HIS A 631 PHE 0.025 0.002 PHE A 376 TYR 0.011 0.002 TYR A 597 ARG 0.003 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 70 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6202 (mpp) cc_final: 0.5826 (mpt) REVERT: A 232 LEU cc_start: 0.8611 (tp) cc_final: 0.8389 (tp) REVERT: A 251 LYS cc_start: 0.7725 (tppp) cc_final: 0.7515 (mtmt) REVERT: A 363 HIS cc_start: 0.7800 (OUTLIER) cc_final: 0.7519 (t70) REVERT: A 393 ASN cc_start: 0.7785 (t0) cc_final: 0.7265 (t0) REVERT: A 397 GLN cc_start: 0.8108 (mt0) cc_final: 0.7762 (tm-30) REVERT: A 446 PHE cc_start: 0.7953 (m-80) cc_final: 0.7607 (m-10) REVERT: A 472 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7012 (pp20) REVERT: A 559 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8297 (m) REVERT: A 622 PRO cc_start: 0.6401 (Cg_exo) cc_final: 0.5544 (Cg_endo) REVERT: A 631 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7656 (t70) REVERT: A 632 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: A 716 PHE cc_start: 0.6143 (m-10) cc_final: 0.5756 (m-10) outliers start: 38 outliers final: 15 residues processed: 106 average time/residue: 0.9761 time to fit residues: 107.7334 Evaluate side-chains 78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 631 HIS Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain A residue 727 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 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 378 ASN A 397 GLN A 430 HIS A 436 HIS A 466 GLN A 500 GLN A 555 GLN A 556 HIS ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.152497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.130834 restraints weight = 6375.700| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.93 r_work: 0.3873 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4075 Z= 0.222 Angle : 0.691 9.923 5521 Z= 0.351 Chirality : 0.042 0.189 626 Planarity : 0.005 0.054 705 Dihedral : 10.300 59.089 567 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.26 % Favored : 92.54 % Rotamer: Outliers : 10.14 % Allowed : 26.04 % Favored : 63.82 % 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: -0.11 (0.39), residues: 496 helix: 1.08 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.35 (0.49), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 530 HIS 0.005 0.001 HIS A 582 PHE 0.019 0.002 PHE A 629 TYR 0.017 0.002 TYR A 323 ARG 0.006 0.001 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 66 time to evaluate : 0.491 Fit side-chains REVERT: A 225 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.5736 (mmm) REVERT: A 233 LEU cc_start: 0.4572 (OUTLIER) cc_final: 0.4094 (mp) REVERT: A 285 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7141 (mpt) REVERT: A 393 ASN cc_start: 0.8085 (t0) cc_final: 0.7809 (t0) REVERT: A 397 GLN cc_start: 0.8200 (mt0) cc_final: 0.7826 (tm-30) REVERT: A 448 SER cc_start: 0.7639 (OUTLIER) cc_final: 0.7253 (p) REVERT: A 466 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: A 569 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7770 (mp) REVERT: A 631 HIS cc_start: 0.7838 (OUTLIER) cc_final: 0.6711 (m90) REVERT: A 632 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: A 648 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7500 (mm-30) REVERT: A 651 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7524 (tt) REVERT: A 716 PHE cc_start: 0.6380 (m-10) cc_final: 0.5769 (m-10) outliers start: 44 outliers final: 12 residues processed: 96 average time/residue: 0.9113 time to fit residues: 91.3499 Evaluate side-chains 80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 631 HIS Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 697 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.152230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.130352 restraints weight = 6308.406| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.99 r_work: 0.3860 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4075 Z= 0.229 Angle : 0.692 10.490 5521 Z= 0.349 Chirality : 0.041 0.198 626 Planarity : 0.005 0.056 705 Dihedral : 8.511 55.473 548 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.66 % Favored : 92.14 % Rotamer: Outliers : 9.45 % Allowed : 27.19 % Favored : 63.36 % 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: 0.38 (0.39), residues: 496 helix: 1.55 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.39 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 530 HIS 0.005 0.001 HIS A 582 PHE 0.016 0.002 PHE A 629 TYR 0.010 0.001 TYR A 323 ARG 0.003 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 61 time to evaluate : 0.434 Fit side-chains REVERT: A 225 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.5737 (mmm) REVERT: A 285 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7189 (mpt) REVERT: A 391 GLU cc_start: 0.7137 (pm20) cc_final: 0.6771 (tt0) REVERT: A 397 GLN cc_start: 0.8177 (mt0) cc_final: 0.7807 (tm-30) REVERT: A 446 PHE cc_start: 0.7936 (m-80) cc_final: 0.7721 (m-10) REVERT: A 466 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: A 569 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7903 (mp) REVERT: A 631 HIS cc_start: 0.7817 (OUTLIER) cc_final: 0.6757 (m90) REVERT: A 632 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: A 651 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7503 (tt) outliers start: 41 outliers final: 13 residues processed: 93 average time/residue: 0.8454 time to fit residues: 82.3558 Evaluate side-chains 76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 631 HIS Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 697 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.151919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.128860 restraints weight = 6730.182| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.16 r_work: 0.3880 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4075 Z= 0.204 Angle : 0.665 11.517 5521 Z= 0.330 Chirality : 0.040 0.189 626 Planarity : 0.005 0.053 705 Dihedral : 7.757 55.547 546 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.66 % Favored : 92.14 % Rotamer: Outliers : 6.91 % Allowed : 31.34 % Favored : 61.75 % 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: 0.86 (0.39), residues: 496 helix: 1.98 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.36 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 530 HIS 0.004 0.001 HIS A 582 PHE 0.014 0.001 PHE A 629 TYR 0.013 0.001 TYR A 323 ARG 0.003 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.480 Fit side-chains REVERT: A 225 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5664 (mmm) REVERT: A 233 LEU cc_start: 0.4532 (OUTLIER) cc_final: 0.4010 (mp) REVERT: A 285 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7308 (mpt) REVERT: A 379 GLN cc_start: 0.7366 (mm110) cc_final: 0.7119 (mp10) REVERT: A 391 GLU cc_start: 0.7107 (pm20) cc_final: 0.6796 (tt0) REVERT: A 466 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: A 512 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7757 (mpp-170) REVERT: A 520 LYS cc_start: 0.7248 (ttmm) cc_final: 0.6950 (tttp) REVERT: A 569 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8051 (mp) REVERT: A 632 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6744 (m-80) outliers start: 30 outliers final: 11 residues processed: 84 average time/residue: 0.8672 time to fit residues: 76.2673 Evaluate side-chains 74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 697 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0670 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.0060 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.1338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.149644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.126574 restraints weight = 7087.021| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 3.22 r_work: 0.3831 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4075 Z= 0.261 Angle : 0.686 11.460 5521 Z= 0.342 Chirality : 0.042 0.183 626 Planarity : 0.005 0.051 705 Dihedral : 7.510 57.629 544 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.46 % Favored : 92.34 % Rotamer: Outliers : 8.06 % Allowed : 31.34 % Favored : 60.60 % 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: 0.82 (0.39), residues: 496 helix: 1.97 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -2.40 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 577 HIS 0.005 0.001 HIS A 582 PHE 0.017 0.002 PHE A 376 TYR 0.011 0.002 TYR A 323 ARG 0.002 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 56 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.5693 (mmm) REVERT: A 410 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7709 (mm-30) REVERT: A 466 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: A 520 LYS cc_start: 0.7337 (ttmm) cc_final: 0.7038 (tttm) REVERT: A 600 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.6939 (mmt90) REVERT: A 632 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6733 (m-80) REVERT: A 651 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7628 (mt) outliers start: 35 outliers final: 20 residues processed: 84 average time/residue: 0.9309 time to fit residues: 81.5160 Evaluate side-chains 80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 709 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.0970 chunk 14 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.152848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.129895 restraints weight = 6702.821| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 3.12 r_work: 0.3884 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4075 Z= 0.196 Angle : 0.653 11.389 5521 Z= 0.325 Chirality : 0.040 0.179 626 Planarity : 0.004 0.051 705 Dihedral : 7.151 57.915 541 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.45 % Favored : 93.35 % Rotamer: Outliers : 6.45 % Allowed : 32.49 % Favored : 61.06 % 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: 1.16 (0.39), residues: 496 helix: 2.24 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.31 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 577 HIS 0.004 0.001 HIS A 582 PHE 0.012 0.001 PHE A 629 TYR 0.011 0.001 TYR A 323 ARG 0.002 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5581 (mmm) REVERT: A 233 LEU cc_start: 0.4599 (OUTLIER) cc_final: 0.4022 (mp) REVERT: A 285 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7182 (mmt) REVERT: A 393 ASN cc_start: 0.7878 (t0) cc_final: 0.7639 (t0) REVERT: A 410 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7606 (mm-30) REVERT: A 520 LYS cc_start: 0.7283 (ttmm) cc_final: 0.6989 (tttp) REVERT: A 557 ASP cc_start: 0.6534 (m-30) cc_final: 0.6073 (m-30) REVERT: A 600 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.6878 (mmt90) REVERT: A 626 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: A 632 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6891 (m-80) outliers start: 28 outliers final: 13 residues processed: 82 average time/residue: 0.9144 time to fit residues: 78.3439 Evaluate side-chains 73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 709 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.149901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.126759 restraints weight = 6946.507| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.15 r_work: 0.3839 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4075 Z= 0.250 Angle : 0.678 10.519 5521 Z= 0.341 Chirality : 0.042 0.180 626 Planarity : 0.005 0.048 705 Dihedral : 6.676 56.329 538 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.86 % Favored : 91.94 % Rotamer: Outliers : 6.22 % Allowed : 33.18 % Favored : 60.60 % 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: 1.01 (0.39), residues: 496 helix: 2.15 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.43 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 530 HIS 0.004 0.001 HIS A 582 PHE 0.012 0.002 PHE A 629 TYR 0.009 0.001 TYR A 323 ARG 0.003 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5642 (mmm) REVERT: A 241 PHE cc_start: 0.5750 (t80) cc_final: 0.5303 (t80) REVERT: A 393 ASN cc_start: 0.8079 (t0) cc_final: 0.7834 (t0) REVERT: A 410 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7579 (mm-30) REVERT: A 600 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.6947 (mmt90) REVERT: A 626 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7868 (m-30) outliers start: 27 outliers final: 15 residues processed: 78 average time/residue: 0.9877 time to fit residues: 80.2772 Evaluate side-chains 77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 709 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.150599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.127142 restraints weight = 6852.361| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 3.17 r_work: 0.3856 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4075 Z= 0.231 Angle : 0.683 10.174 5521 Z= 0.343 Chirality : 0.041 0.200 626 Planarity : 0.004 0.050 705 Dihedral : 6.577 56.278 538 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.06 % Favored : 92.74 % Rotamer: Outliers : 7.37 % Allowed : 31.80 % Favored : 60.83 % 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: 1.09 (0.39), residues: 496 helix: 2.22 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.41 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 530 HIS 0.003 0.001 HIS A 582 PHE 0.011 0.001 PHE A 629 TYR 0.010 0.001 TYR A 323 ARG 0.002 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.6184 (OUTLIER) cc_final: 0.5604 (mmm) REVERT: A 233 LEU cc_start: 0.4672 (OUTLIER) cc_final: 0.4103 (mp) REVERT: A 385 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7833 (tm) REVERT: A 393 ASN cc_start: 0.8108 (t0) cc_final: 0.7890 (t0) REVERT: A 410 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 520 LYS cc_start: 0.7360 (ttmm) cc_final: 0.7073 (tttp) REVERT: A 557 ASP cc_start: 0.6571 (m-30) cc_final: 0.6071 (m-30) REVERT: A 600 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.6915 (mmt90) REVERT: A 626 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: A 632 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6924 (m-80) outliers start: 32 outliers final: 18 residues processed: 85 average time/residue: 0.9738 time to fit residues: 86.2989 Evaluate side-chains 84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 719 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 26 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.154237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.131217 restraints weight = 6950.039| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 3.18 r_work: 0.3898 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4075 Z= 0.205 Angle : 0.682 9.818 5521 Z= 0.340 Chirality : 0.040 0.209 626 Planarity : 0.004 0.050 705 Dihedral : 6.366 56.720 538 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.45 % Favored : 93.35 % Rotamer: Outliers : 5.76 % Allowed : 33.87 % Favored : 60.37 % 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: 1.29 (0.39), residues: 496 helix: 2.37 (0.27), residues: 324 sheet: None (None), residues: 0 loop : -2.33 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 680 HIS 0.002 0.001 HIS A 582 PHE 0.010 0.001 PHE A 629 TYR 0.009 0.001 TYR A 323 ARG 0.008 0.001 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6116 (OUTLIER) cc_final: 0.5755 (mmm) REVERT: A 233 LEU cc_start: 0.4688 (OUTLIER) cc_final: 0.4082 (mp) REVERT: A 324 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7423 (mt0) REVERT: A 385 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7714 (tm) REVERT: A 410 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7359 (mm-30) REVERT: A 520 LYS cc_start: 0.7333 (ttmm) cc_final: 0.7047 (tttp) REVERT: A 557 ASP cc_start: 0.6681 (m-30) cc_final: 0.6049 (m-30) REVERT: A 565 GLU cc_start: 0.7236 (mp0) cc_final: 0.6908 (pm20) REVERT: A 595 LYS cc_start: 0.7529 (tmmm) cc_final: 0.7170 (tmmm) REVERT: A 600 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6970 (mmt90) REVERT: A 632 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7131 (m-80) outliers start: 25 outliers final: 12 residues processed: 80 average time/residue: 1.0365 time to fit residues: 86.1749 Evaluate side-chains 72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 709 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.151530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.127853 restraints weight = 6994.782| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 3.26 r_work: 0.3864 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4075 Z= 0.236 Angle : 0.690 9.562 5521 Z= 0.345 Chirality : 0.041 0.204 626 Planarity : 0.004 0.050 705 Dihedral : 6.415 56.661 538 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.85 % Favored : 92.94 % Rotamer: Outliers : 5.30 % Allowed : 35.48 % Favored : 59.22 % 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: 1.26 (0.39), residues: 496 helix: 2.36 (0.27), residues: 324 sheet: None (None), residues: 0 loop : -2.38 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 680 HIS 0.004 0.001 HIS A 582 PHE 0.010 0.001 PHE A 629 TYR 0.009 0.001 TYR A 289 ARG 0.003 0.000 ARG A 528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.5687 (mmm) REVERT: A 233 LEU cc_start: 0.4681 (OUTLIER) cc_final: 0.4116 (mp) REVERT: A 385 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7725 (tm) REVERT: A 410 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7535 (mm-30) REVERT: A 520 LYS cc_start: 0.7319 (ttmm) cc_final: 0.7008 (tttp) REVERT: A 557 ASP cc_start: 0.6574 (m-30) cc_final: 0.6123 (m-30) REVERT: A 565 GLU cc_start: 0.7416 (mp0) cc_final: 0.7154 (pm20) REVERT: A 600 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.6956 (mmt90) REVERT: A 632 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7323 (m-80) outliers start: 23 outliers final: 11 residues processed: 76 average time/residue: 1.1427 time to fit residues: 90.3424 Evaluate side-chains 70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 605 TRP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 709 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 34 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 31 optimal weight: 0.0040 chunk 42 optimal weight: 4.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.154240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.131237 restraints weight = 6846.074| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 3.15 r_work: 0.3906 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4075 Z= 0.209 Angle : 0.679 9.703 5521 Z= 0.341 Chirality : 0.040 0.206 626 Planarity : 0.004 0.049 705 Dihedral : 6.286 56.962 538 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.05 % Favored : 93.75 % Rotamer: Outliers : 4.61 % Allowed : 36.18 % Favored : 59.22 % 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: 1.45 (0.39), residues: 496 helix: 2.52 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.34 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 680 HIS 0.002 0.000 HIS A 582 PHE 0.009 0.001 PHE A 629 TYR 0.007 0.001 TYR A 323 ARG 0.009 0.001 ARG A 463 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3280.11 seconds wall clock time: 58 minutes 27.75 seconds (3507.75 seconds total)