Starting phenix.real_space_refine on Wed Mar 5 23:14:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fil_31602/03_2025/7fil_31602.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fil_31602/03_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_31602/03_2025/7fil_31602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fil_31602/03_2025/7fil_31602.map" model { file = "/net/cci-nas-00/data/ceres_data/7fil_31602/03_2025/7fil_31602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fil_31602/03_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-5624/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: 3.47, per 1000 atoms: 0.87 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: 1.02 Conformation dependent library (CDL) restraints added in 477.0 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: 0.35 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: 1.15 Time building geometry restraints manager: 1.21 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: 0.700 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:16.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- 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 : 0.471 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: 1.0287 time to fit residues: 113.2070 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 : 0.529 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.130834 restraints weight = 6375.701| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.93 r_work: 0.3872 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 : 0.421 Fit side-chains REVERT: A 225 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.5737 (mmm) REVERT: A 233 LEU cc_start: 0.4573 (OUTLIER) cc_final: 0.4095 (mp) REVERT: A 285 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7139 (mpt) REVERT: A 393 ASN cc_start: 0.8086 (t0) cc_final: 0.7809 (t0) REVERT: A 397 GLN cc_start: 0.8197 (mt0) cc_final: 0.7825 (tm-30) REVERT: A 448 SER cc_start: 0.7639 (OUTLIER) cc_final: 0.7253 (p) REVERT: A 466 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: A 569 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7770 (mp) REVERT: A 631 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.6713 (m90) REVERT: A 632 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7041 (m-80) REVERT: A 648 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7501 (mm-30) REVERT: A 651 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7523 (tt) REVERT: A 716 PHE cc_start: 0.6380 (m-10) cc_final: 0.5771 (m-10) outliers start: 44 outliers final: 12 residues processed: 96 average time/residue: 0.9192 time to fit residues: 92.0737 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 : 0.407 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS A 707 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.146734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.124172 restraints weight = 6812.929| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.10 r_work: 0.3826 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2513 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= 0.270 Angle : 0.713 10.398 5521 Z= 0.362 Chirality : 0.043 0.198 626 Planarity : 0.005 0.055 705 Dihedral : 8.707 56.384 548 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.66 % Favored : 92.14 % Rotamer: Outliers : 9.91 % Allowed : 26.73 % 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: 0.21 (0.39), residues: 496 helix: 1.39 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.40 (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 0.017 0.002 PHE A 629 TYR 0.011 0.002 TYR A 289 ARG 0.004 0.001 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 103 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 60 time to evaluate : 0.425 Fit side-chains REVERT: A 225 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.5902 (mmm) REVERT: A 285 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7277 (mpt) REVERT: A 391 GLU cc_start: 0.7180 (pm20) cc_final: 0.6795 (tt0) REVERT: A 397 GLN cc_start: 0.8193 (mt0) cc_final: 0.7835 (tm-30) REVERT: A 448 SER cc_start: 0.7294 (OUTLIER) cc_final: 0.7035 (p) REVERT: A 466 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: A 569 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7899 (mp) REVERT: A 631 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.6875 (m90) REVERT: A 632 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: A 651 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7628 (tt) outliers start: 43 outliers final: 18 residues processed: 94 average time/residue: 0.8705 time to fit residues: 85.5675 Evaluate side-chains 83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 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 285 MET Chi-restraints excluded: chain A residue 308 TRP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 448 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: 0.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.148625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.125472 restraints weight = 6758.177| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 3.14 r_work: 0.3841 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4075 Z= 0.239 Angle : 0.698 12.916 5521 Z= 0.349 Chirality : 0.042 0.186 626 Planarity : 0.005 0.053 705 Dihedral : 8.080 56.823 546 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.86 % Favored : 91.94 % Rotamer: Outliers : 9.45 % Allowed : 27.88 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.39), residues: 496 helix: 1.78 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -2.35 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 530 HIS 0.005 0.001 HIS A 582 PHE 0.015 0.002 PHE A 629 TYR 0.009 0.001 TYR A 289 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 102 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 61 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.5878 (mmm) REVERT: A 285 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7332 (mpt) REVERT: A 323 TYR cc_start: 0.7107 (t80) cc_final: 0.6849 (t80) REVERT: A 466 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: A 512 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7752 (mpp-170) REVERT: A 569 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7927 (mp) REVERT: A 632 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6705 (m-80) REVERT: A 648 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7546 (mm-30) REVERT: A 651 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7467 (tt) outliers start: 41 outliers final: 19 residues processed: 91 average time/residue: 0.8804 time to fit residues: 83.7480 Evaluate side-chains 81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 361 LEU Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 383 SER 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 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 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 614 LEU Chi-restraints excluded: chain A residue 621 ILE 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 673 VAL 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: 0.9980 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.151090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.127393 restraints weight = 7065.721| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 3.23 r_work: 0.3853 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4075 Z= 0.224 Angle : 0.678 11.342 5521 Z= 0.338 Chirality : 0.041 0.178 626 Planarity : 0.005 0.052 705 Dihedral : 7.516 57.519 544 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.26 % Favored : 92.54 % Rotamer: Outliers : 7.37 % Allowed : 30.65 % Favored : 61.98 % 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: 0.92 (0.39), residues: 496 helix: 2.05 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -2.32 (0.50), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 577 HIS 0.004 0.001 HIS A 582 PHE 0.016 0.002 PHE A 376 TYR 0.008 0.001 TYR A 323 ARG 0.003 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 89 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6198 (OUTLIER) cc_final: 0.5734 (mmm) REVERT: A 233 LEU cc_start: 0.4591 (OUTLIER) cc_final: 0.3986 (mp) REVERT: A 323 TYR cc_start: 0.7342 (t80) cc_final: 0.7102 (t80) REVERT: A 393 ASN cc_start: 0.8160 (t0) cc_final: 0.7668 (t0) REVERT: A 466 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: A 520 LYS cc_start: 0.7297 (ttmm) cc_final: 0.6995 (tttm) REVERT: A 632 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6739 (m-80) outliers start: 32 outliers final: 15 residues processed: 79 average time/residue: 0.9179 time to fit residues: 75.8088 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 : 0.470 ------------------------------------------------------------------------------- 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 361 LEU Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 453 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 14 optimal weight: 0.0040 chunk 34 optimal weight: 0.1980 chunk 22 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.3392 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.156880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.134443 restraints weight = 6386.273| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 3.07 r_work: 0.3912 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4075 Z= 0.185 Angle : 0.666 10.603 5521 Z= 0.325 Chirality : 0.039 0.178 626 Planarity : 0.004 0.051 705 Dihedral : 6.989 56.949 541 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.85 % Favored : 93.95 % Rotamer: Outliers : 5.99 % Allowed : 32.03 % Favored : 61.98 % 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 (0.39), residues: 496 helix: 2.36 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.29 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 577 HIS 0.003 0.001 HIS A 582 PHE 0.012 0.001 PHE A 376 TYR 0.007 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 91 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5641 (mmm) REVERT: A 227 MET cc_start: 0.7631 (tpt) cc_final: 0.7232 (tpt) REVERT: A 233 LEU cc_start: 0.4601 (OUTLIER) cc_final: 0.4083 (mp) REVERT: A 241 PHE cc_start: 0.5443 (t80) cc_final: 0.5114 (t80) REVERT: A 323 TYR cc_start: 0.7242 (t80) cc_final: 0.7031 (t80) REVERT: A 393 ASN cc_start: 0.8038 (t0) cc_final: 0.7750 (t0) REVERT: A 520 LYS cc_start: 0.7264 (ttmm) cc_final: 0.6980 (tttp) REVERT: A 557 ASP cc_start: 0.6762 (m-30) cc_final: 0.6126 (m-30) REVERT: A 632 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6423 (m-80) outliers start: 26 outliers final: 13 residues processed: 86 average time/residue: 0.9593 time to fit residues: 86.1445 Evaluate side-chains 74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 308 TRP Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 420 SER 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 609 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.0000 chunk 48 optimal weight: 0.0000 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.153738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.130383 restraints weight = 6695.401| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 3.13 r_work: 0.3898 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4075 Z= 0.206 Angle : 0.681 10.135 5521 Z= 0.338 Chirality : 0.041 0.199 626 Planarity : 0.004 0.049 705 Dihedral : 6.365 56.828 538 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.85 % Favored : 92.94 % Rotamer: Outliers : 6.91 % Allowed : 32.72 % 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: 1.32 (0.39), residues: 496 helix: 2.37 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.25 (0.48), 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 0.001 PHE A 446 TYR 0.006 0.001 TYR A 289 ARG 0.006 0.001 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 92 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5602 (mmm) REVERT: A 233 LEU cc_start: 0.4669 (OUTLIER) cc_final: 0.4115 (mp) REVERT: A 323 TYR cc_start: 0.7222 (t80) cc_final: 0.6904 (t80) REVERT: A 393 ASN cc_start: 0.7918 (t0) cc_final: 0.7667 (t0) REVERT: A 410 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7500 (mm-30) REVERT: A 520 LYS cc_start: 0.7279 (ttmm) cc_final: 0.6979 (tttp) REVERT: A 557 ASP cc_start: 0.6564 (m-30) cc_final: 0.6089 (m-30) REVERT: A 600 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7908 (mmt90) REVERT: A 632 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6966 (m-80) outliers start: 30 outliers final: 15 residues processed: 84 average time/residue: 0.9862 time to fit residues: 86.2331 Evaluate side-chains 74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 308 TRP Chi-restraints excluded: chain A residue 361 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 453 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 609 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 45 optimal weight: 0.0470 chunk 41 optimal weight: 0.6980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.156343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.133810 restraints weight = 6362.510| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 3.05 r_work: 0.3905 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4075 Z= 0.210 Angle : 0.689 9.746 5521 Z= 0.342 Chirality : 0.042 0.205 626 Planarity : 0.004 0.050 705 Dihedral : 6.317 56.993 538 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.65 % Favored : 93.15 % Rotamer: Outliers : 5.76 % Allowed : 34.33 % Favored : 59.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.47 (0.39), residues: 496 helix: 2.47 (0.27), residues: 324 sheet: None (None), residues: 0 loop : -2.18 (0.48), 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 446 TYR 0.006 0.001 TYR A 727 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 84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.5668 (mmm) REVERT: A 233 LEU cc_start: 0.4689 (OUTLIER) cc_final: 0.4135 (mp) REVERT: A 385 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7622 (tm) REVERT: A 520 LYS cc_start: 0.7277 (ttmm) cc_final: 0.6990 (tttp) REVERT: A 557 ASP cc_start: 0.6746 (m-30) cc_final: 0.6106 (m-30) REVERT: A 565 GLU cc_start: 0.7255 (mp0) cc_final: 0.6947 (pm20) REVERT: A 595 LYS cc_start: 0.7538 (tmmm) cc_final: 0.7185 (tmmm) REVERT: A 632 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6860 (m-80) outliers start: 25 outliers final: 16 residues processed: 77 average time/residue: 1.0826 time to fit residues: 86.7932 Evaluate side-chains 74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 308 TRP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 385 LEU 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 427 LEU Chi-restraints excluded: chain A residue 453 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.1980 chunk 4 optimal weight: 0.0170 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.155639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.133150 restraints weight = 6401.656| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.07 r_work: 0.3900 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4075 Z= 0.218 Angle : 0.698 9.621 5521 Z= 0.344 Chirality : 0.041 0.201 626 Planarity : 0.004 0.050 705 Dihedral : 6.285 57.012 538 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.65 % Favored : 93.15 % Rotamer: Outliers : 6.22 % Allowed : 33.87 % Favored : 59.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.39), residues: 496 helix: 2.44 (0.27), residues: 326 sheet: None (None), residues: 0 loop : -2.17 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 680 HIS 0.003 0.001 HIS A 582 PHE 0.012 0.001 PHE A 629 TYR 0.006 0.001 TYR A 727 ARG 0.002 0.000 ARG A 688 *********************** 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: 27 poor density : 59 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6208 (OUTLIER) cc_final: 0.5691 (mmm) REVERT: A 233 LEU cc_start: 0.4608 (OUTLIER) cc_final: 0.4106 (mp) REVERT: A 385 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7499 (tm) REVERT: A 520 LYS cc_start: 0.7278 (ttmm) cc_final: 0.6986 (tttp) REVERT: A 557 ASP cc_start: 0.6754 (m-30) cc_final: 0.6143 (m-30) REVERT: A 565 GLU cc_start: 0.7357 (mp0) cc_final: 0.7053 (pm20) REVERT: A 619 LYS cc_start: 0.7904 (pmtt) cc_final: 0.7636 (tttp) REVERT: A 632 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.7296 (m-80) outliers start: 27 outliers final: 15 residues processed: 77 average time/residue: 1.0143 time to fit residues: 81.3495 Evaluate side-chains 70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 308 TRP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 385 LEU 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 427 LEU Chi-restraints excluded: chain A residue 514 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 629 PHE 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: 1.9990 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.151348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.127851 restraints weight = 6801.852| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 3.16 r_work: 0.3868 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4178 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= 0.240 Angle : 0.721 9.568 5521 Z= 0.357 Chirality : 0.042 0.207 626 Planarity : 0.004 0.048 705 Dihedral : 6.372 56.947 538 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.06 % Favored : 92.74 % Rotamer: Outliers : 4.61 % Allowed : 35.48 % Favored : 59.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.38), residues: 496 helix: 2.42 (0.27), residues: 326 sheet: None (None), residues: 0 loop : -2.25 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 680 HIS 0.004 0.001 HIS A 582 PHE 0.009 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 76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.5648 (mmm) REVERT: A 227 MET cc_start: 0.8094 (tpt) cc_final: 0.7582 (ttt) REVERT: A 233 LEU cc_start: 0.4617 (OUTLIER) cc_final: 0.4081 (mp) REVERT: A 385 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7523 (tm) REVERT: A 393 ASN cc_start: 0.7992 (t0) cc_final: 0.7727 (t0) REVERT: A 520 LYS cc_start: 0.7332 (ttmm) cc_final: 0.7038 (tttp) REVERT: A 557 ASP cc_start: 0.6657 (m-30) cc_final: 0.6037 (m-30) REVERT: A 565 GLU cc_start: 0.7213 (mp0) cc_final: 0.6889 (pm20) REVERT: A 632 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7215 (m-80) outliers start: 20 outliers final: 14 residues processed: 72 average time/residue: 1.1813 time to fit residues: 88.4999 Evaluate side-chains 71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 308 TRP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 385 LEU 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 427 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 598 MET 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: 0.0060 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.0020 chunk 42 optimal weight: 3.9990 overall best weight: 0.3004 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.158258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.135843 restraints weight = 6311.047| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.09 r_work: 0.3914 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4075 Z= 0.206 Angle : 0.708 9.599 5521 Z= 0.351 Chirality : 0.041 0.210 626 Planarity : 0.004 0.049 705 Dihedral : 6.229 57.515 538 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.65 % Favored : 94.15 % Rotamer: Outliers : 4.15 % Allowed : 36.18 % Favored : 59.68 % 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: 1.65 (0.39), residues: 496 helix: 2.62 (0.27), residues: 326 sheet: None (None), residues: 0 loop : -2.18 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 680 HIS 0.002 0.001 HIS A 603 PHE 0.008 0.001 PHE A 629 TYR 0.006 0.001 TYR A 727 ARG 0.002 0.000 ARG A 528 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3870.26 seconds wall clock time: 68 minutes 39.21 seconds (4119.21 seconds total)