Starting phenix.real_space_refine on Tue Mar 3 12:15:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fil_31602/03_2026/7fil_31602.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fil_31602/03_2026/7fil_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 { model { file = "/net/cci-nas-00/data/ceres_data/7fil_31602/03_2026/7fil_31602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fil_31602/03_2026/7fil_31602.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fil_31602/03_2026/7fil_31602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fil_31602/03_2026/7fil_31602.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 0.92, per 1000 atoms: 0.23 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: 0.32 Conformation dependent library (CDL) restraints added in 110.5 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: 0.15 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: 0.61 Time building geometry restraints manager: 0.44 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: 0.010 Normalize map: mean=0, sd=1: 0.680 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.280 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.870 ------------------------------------------------------------------------------- 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= 0.550 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 : 19.22 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (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 ARG 0.003 0.001 ARG A 350 TYR 0.011 0.002 TYR A 597 PHE 0.025 0.002 PHE A 376 TRP 0.008 0.002 TRP A 439 HIS 0.004 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00810 ( 4075) covalent geometry : angle 1.04605 ( 5521) hydrogen bonds : bond 0.14798 ( 235) hydrogen bonds : angle 5.74139 ( 705) *********************** 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 : 0.123 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: 0.7018 (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: 0.5739 (m-10) outliers start: 38 outliers final: 15 residues processed: 106 average time/residue: 0.4798 time to fit residues: 52.5941 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 : 0.177 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.0060 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.3974 ------------------------------------------------------------------------------- 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 = 0.4306 r_free = 0.4306 target = 0.154228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.132773 restraints weight = 6358.320| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.92 r_work: 0.3895 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4075 Z= 0.144 Angle : 0.687 10.162 5521 Z= 0.348 Chirality : 0.041 0.181 626 Planarity : 0.005 0.055 705 Dihedral : 10.138 59.345 567 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.06 % Favored : 92.74 % Rotamer: Outliers : 9.45 % Allowed : 26.04 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.39), residues: 496 helix: 1.18 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.39 (0.49), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 688 TYR 0.018 0.001 TYR A 323 PHE 0.022 0.001 PHE A 629 TRP 0.008 0.001 TRP A 530 HIS 0.004 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4075) covalent geometry : angle 0.68695 ( 5521) hydrogen bonds : bond 0.04795 ( 235) hydrogen bonds : angle 4.02434 ( 705) *********************** 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 111 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 70 time to evaluate : 0.106 Fit side-chains REVERT: A 225 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.5700 (mmm) REVERT: A 232 LEU cc_start: 0.8533 (tp) cc_final: 0.8323 (tp) REVERT: A 233 LEU cc_start: 0.4592 (OUTLIER) cc_final: 0.4158 (mp) REVERT: A 285 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7185 (mpt) REVERT: A 291 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.7085 (ttm) REVERT: A 393 ASN cc_start: 0.8049 (t0) cc_final: 0.7772 (t0) REVERT: A 397 GLN cc_start: 0.8188 (mt0) cc_final: 0.7823 (tm-30) REVERT: A 448 SER cc_start: 0.7735 (OUTLIER) cc_final: 0.7238 (p) REVERT: A 466 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: A 472 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7622 (pp20) REVERT: A 569 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7741 (mp) REVERT: A 631 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.6705 (m90) REVERT: A 632 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: A 648 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7639 (mm-30) REVERT: A 651 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7460 (tt) REVERT: A 716 PHE cc_start: 0.6413 (m-10) cc_final: 0.5829 (m-10) outliers start: 41 outliers final: 12 residues processed: 97 average time/residue: 0.3861 time to fit residues: 38.9080 Evaluate side-chains 85 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 291 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 442 LEU Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 472 GLU 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 614 LEU 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 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 GLN A 445 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.154409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.132571 restraints weight = 6262.423| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.97 r_work: 0.3895 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2742 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= 0.141 Angle : 0.673 9.126 5521 Z= 0.336 Chirality : 0.040 0.193 626 Planarity : 0.005 0.055 705 Dihedral : 8.601 55.180 551 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.46 % Favored : 92.34 % Rotamer: Outliers : 7.37 % Allowed : 29.72 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.40), residues: 496 helix: 1.70 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -2.39 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 688 TYR 0.010 0.001 TYR A 323 PHE 0.016 0.001 PHE A 629 TRP 0.008 0.001 TRP A 530 HIS 0.004 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4075) covalent geometry : angle 0.67266 ( 5521) hydrogen bonds : bond 0.04283 ( 235) hydrogen bonds : angle 3.75036 ( 705) *********************** 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 92 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.145 Fit side-chains REVERT: A 225 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5687 (mmm) REVERT: A 285 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7154 (mpt) REVERT: A 323 TYR cc_start: 0.6893 (t80) cc_final: 0.6678 (t80) REVERT: A 391 GLU cc_start: 0.7035 (pm20) cc_final: 0.6706 (tt0) REVERT: A 397 GLN cc_start: 0.8160 (mt0) cc_final: 0.7803 (tm-30) REVERT: A 446 PHE cc_start: 0.7949 (m-80) cc_final: 0.7653 (m-10) REVERT: A 466 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: A 569 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8008 (mp) REVERT: A 632 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6892 (m-80) outliers start: 32 outliers final: 9 residues processed: 83 average time/residue: 0.4109 time to fit residues: 35.4973 Evaluate side-chains 71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 427 LEU Chi-restraints excluded: chain A residue 466 GLN 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.156317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.134329 restraints weight = 6284.445| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.01 r_work: 0.3907 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4075 Z= 0.130 Angle : 0.673 12.948 5521 Z= 0.330 Chirality : 0.040 0.191 626 Planarity : 0.004 0.053 705 Dihedral : 7.256 55.496 544 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.46 % Favored : 92.34 % Rotamer: Outliers : 6.45 % Allowed : 30.65 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.39), residues: 496 helix: 2.13 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.38 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 688 TYR 0.008 0.001 TYR A 323 PHE 0.012 0.001 PHE A 629 TRP 0.009 0.001 TRP A 530 HIS 0.005 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4075) covalent geometry : angle 0.67285 ( 5521) hydrogen bonds : bond 0.03941 ( 235) hydrogen bonds : angle 3.48725 ( 705) *********************** 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 86 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5619 (mmm) REVERT: A 233 LEU cc_start: 0.4451 (OUTLIER) cc_final: 0.3888 (mp) REVERT: A 285 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7243 (mpt) REVERT: A 391 GLU cc_start: 0.7303 (pm20) cc_final: 0.6915 (tt0) REVERT: A 397 GLN cc_start: 0.8162 (mt0) cc_final: 0.7774 (tm-30) REVERT: A 466 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: A 631 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.6761 (m90) REVERT: A 632 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6899 (m-80) REVERT: A 648 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7741 (tp30) outliers start: 28 outliers final: 12 residues processed: 77 average time/residue: 0.4290 time to fit residues: 34.3824 Evaluate side-chains 74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 361 LEU 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 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 631 HIS 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 21 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 22 optimal weight: 0.0000 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.157943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.135451 restraints weight = 6336.603| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 3.05 r_work: 0.3891 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4075 Z= 0.135 Angle : 0.656 10.831 5521 Z= 0.323 Chirality : 0.040 0.183 626 Planarity : 0.004 0.052 705 Dihedral : 7.078 57.609 542 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.45 % Favored : 93.35 % Rotamer: Outliers : 6.22 % Allowed : 31.34 % Favored : 62.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.39), residues: 496 helix: 2.32 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.29 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 688 TYR 0.008 0.001 TYR A 323 PHE 0.013 0.001 PHE A 629 TRP 0.009 0.001 TRP A 577 HIS 0.004 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4075) covalent geometry : angle 0.65552 ( 5521) hydrogen bonds : bond 0.03966 ( 235) hydrogen bonds : angle 3.40741 ( 705) *********************** 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 86 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.5609 (mmm) REVERT: A 233 LEU cc_start: 0.4544 (OUTLIER) cc_final: 0.4021 (mp) REVERT: A 466 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: A 520 LYS cc_start: 0.7254 (ttmm) cc_final: 0.6960 (tttp) REVERT: A 557 ASP cc_start: 0.6884 (m-30) cc_final: 0.6260 (m-30) REVERT: A 600 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6805 (mmt90) REVERT: A 632 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: A 648 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7582 (tp30) outliers start: 27 outliers final: 13 residues processed: 79 average time/residue: 0.4535 time to fit residues: 37.1053 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 : 0.089 ------------------------------------------------------------------------------- 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 427 LEU Chi-restraints excluded: chain A residue 447 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.156485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.133860 restraints weight = 6548.494| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 3.10 r_work: 0.3870 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4075 Z= 0.142 Angle : 0.649 10.516 5521 Z= 0.324 Chirality : 0.040 0.180 626 Planarity : 0.004 0.050 705 Dihedral : 7.092 58.851 541 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.26 % Favored : 92.54 % Rotamer: Outliers : 5.76 % Allowed : 32.72 % Favored : 61.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.39), residues: 496 helix: 2.33 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.28 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 688 TYR 0.011 0.001 TYR A 323 PHE 0.014 0.001 PHE A 629 TRP 0.011 0.001 TRP A 577 HIS 0.004 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4075) covalent geometry : angle 0.64930 ( 5521) hydrogen bonds : bond 0.04089 ( 235) hydrogen bonds : angle 3.42242 ( 705) *********************** 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 84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5586 (mmm) REVERT: A 233 LEU cc_start: 0.4590 (OUTLIER) cc_final: 0.4018 (mp) REVERT: A 285 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7188 (mmt) REVERT: A 393 ASN cc_start: 0.7919 (t0) cc_final: 0.7675 (t0) REVERT: A 410 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7742 (mm-30) REVERT: A 520 LYS cc_start: 0.7279 (ttmm) cc_final: 0.6993 (tttp) REVERT: A 600 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6841 (mmt90) REVERT: A 648 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7554 (tp30) REVERT: A 707 GLN cc_start: 0.7592 (mp10) cc_final: 0.7349 (mt0) outliers start: 25 outliers final: 15 residues processed: 76 average time/residue: 0.4873 time to fit residues: 38.2837 Evaluate side-chains 76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 361 LEU Chi-restraints excluded: chain A residue 363 HIS 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 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 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 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.156349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.133486 restraints weight = 6517.667| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.10 r_work: 0.3873 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4075 Z= 0.147 Angle : 0.675 10.395 5521 Z= 0.339 Chirality : 0.040 0.197 626 Planarity : 0.004 0.048 705 Dihedral : 5.964 56.485 536 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.85 % Favored : 92.94 % Rotamer: Outliers : 6.45 % Allowed : 32.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.39), residues: 496 helix: 2.37 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.29 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 463 TYR 0.011 0.001 TYR A 323 PHE 0.011 0.001 PHE A 629 TRP 0.009 0.001 TRP A 577 HIS 0.003 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4075) covalent geometry : angle 0.67491 ( 5521) hydrogen bonds : bond 0.04070 ( 235) hydrogen bonds : angle 3.37366 ( 705) *********************** 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 84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5630 (mmm) REVERT: A 233 LEU cc_start: 0.4607 (OUTLIER) cc_final: 0.4079 (mp) REVERT: A 285 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7256 (mmt) REVERT: A 410 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7617 (mm-30) REVERT: A 520 LYS cc_start: 0.7322 (ttmm) cc_final: 0.7050 (tttm) REVERT: A 557 ASP cc_start: 0.6781 (m-30) cc_final: 0.6221 (m-30) REVERT: A 600 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6835 (mmt90) REVERT: A 648 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7659 (tp30) REVERT: A 707 GLN cc_start: 0.7592 (mp10) cc_final: 0.7356 (mt0) outliers start: 28 outliers final: 20 residues processed: 75 average time/residue: 0.4923 time to fit residues: 38.2129 Evaluate side-chains 77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 228 ILE 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 361 LEU Chi-restraints excluded: chain A residue 401 MET 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 479 ILE 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 609 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 629 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 0.0020 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 0.0040 chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.0470 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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 = 0.4311 r_free = 0.4311 target = 0.154852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.131554 restraints weight = 6782.584| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 3.15 r_work: 0.3910 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4075 Z= 0.133 Angle : 0.669 10.095 5521 Z= 0.334 Chirality : 0.039 0.204 626 Planarity : 0.004 0.050 705 Dihedral : 5.812 56.902 536 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 5.07 % Allowed : 34.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.39), residues: 496 helix: 2.62 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.21 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 528 TYR 0.008 0.001 TYR A 323 PHE 0.009 0.001 PHE A 629 TRP 0.008 0.001 TRP A 577 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 4075) covalent geometry : angle 0.66925 ( 5521) hydrogen bonds : bond 0.03611 ( 235) hydrogen bonds : angle 3.22854 ( 705) *********************** 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 80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.6116 (OUTLIER) cc_final: 0.5798 (mmm) REVERT: A 233 LEU cc_start: 0.4699 (OUTLIER) cc_final: 0.4195 (mp) REVERT: A 385 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7765 (tm) REVERT: A 410 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 520 LYS cc_start: 0.7333 (ttmm) cc_final: 0.6846 (mppt) REVERT: A 557 ASP cc_start: 0.6626 (m-30) cc_final: 0.6003 (m-30) REVERT: A 600 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7013 (mmt90) REVERT: A 648 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7699 (tp30) REVERT: A 707 GLN cc_start: 0.7513 (mp10) cc_final: 0.7295 (mt0) outliers start: 22 outliers final: 14 residues processed: 76 average time/residue: 0.4780 time to fit residues: 37.6096 Evaluate side-chains 74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 361 LEU Chi-restraints excluded: chain A residue 385 LEU 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 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 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 33 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 0.0040 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.157362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.134557 restraints weight = 6429.598| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 3.08 r_work: 0.3891 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3936 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= 0.139 Angle : 0.681 9.793 5521 Z= 0.338 Chirality : 0.040 0.200 626 Planarity : 0.004 0.050 705 Dihedral : 5.909 56.706 536 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.06 % Favored : 92.74 % Rotamer: Outliers : 4.61 % Allowed : 34.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.39), residues: 496 helix: 2.55 (0.27), residues: 324 sheet: None (None), residues: 0 loop : -2.16 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 528 TYR 0.009 0.001 TYR A 323 PHE 0.008 0.001 PHE A 629 TRP 0.008 0.001 TRP A 530 HIS 0.003 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4075) covalent geometry : angle 0.68068 ( 5521) hydrogen bonds : bond 0.03764 ( 235) hydrogen bonds : angle 3.24977 ( 705) *********************** 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 82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6396 (OUTLIER) cc_final: 0.5853 (mmm) REVERT: A 233 LEU cc_start: 0.4760 (OUTLIER) cc_final: 0.4295 (mp) REVERT: A 285 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7783 (mmt) REVERT: A 385 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7622 (tm) REVERT: A 393 ASN cc_start: 0.7928 (t0) cc_final: 0.7700 (t0) REVERT: A 410 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7521 (mm-30) REVERT: A 520 LYS cc_start: 0.7349 (ttmm) cc_final: 0.6849 (mppt) REVERT: A 557 ASP cc_start: 0.6600 (m-30) cc_final: 0.6130 (m-30) REVERT: A 600 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.6889 (mmt90) REVERT: A 648 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7737 (tp30) outliers start: 20 outliers final: 14 residues processed: 77 average time/residue: 0.5119 time to fit residues: 40.6590 Evaluate side-chains 75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 361 LEU Chi-restraints excluded: chain A residue 385 LEU 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 609 LEU Chi-restraints excluded: chain A residue 621 ILE 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 32 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.0000 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.0370 chunk 15 optimal weight: 0.0070 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.2880 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.158864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.136234 restraints weight = 6406.736| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 3.06 r_work: 0.3923 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4075 Z= 0.136 Angle : 0.718 9.899 5521 Z= 0.356 Chirality : 0.040 0.207 626 Planarity : 0.004 0.050 705 Dihedral : 5.850 57.003 536 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.85 % Favored : 92.94 % Rotamer: Outliers : 4.15 % Allowed : 35.71 % Favored : 60.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.39), residues: 496 helix: 2.66 (0.27), residues: 326 sheet: None (None), residues: 0 loop : -2.11 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 463 TYR 0.008 0.001 TYR A 323 PHE 0.009 0.001 PHE A 629 TRP 0.008 0.001 TRP A 530 HIS 0.002 0.000 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4075) covalent geometry : angle 0.71824 ( 5521) hydrogen bonds : bond 0.03489 ( 235) hydrogen bonds : angle 3.17875 ( 705) ********************** 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 80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5842 (mmm) REVERT: A 233 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.4355 (mp) REVERT: A 285 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7496 (mpp) REVERT: A 385 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7516 (tm) REVERT: A 410 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 520 LYS cc_start: 0.7376 (ttmm) cc_final: 0.6907 (mppt) REVERT: A 557 ASP cc_start: 0.6517 (m-30) cc_final: 0.5858 (m-30) REVERT: A 595 LYS cc_start: 0.7423 (tmmm) cc_final: 0.7106 (tmmm) REVERT: A 600 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6866 (mmt90) REVERT: A 648 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7689 (tp30) outliers start: 18 outliers final: 13 residues processed: 75 average time/residue: 0.5024 time to fit residues: 38.9516 Evaluate side-chains 76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 361 LEU Chi-restraints excluded: chain A residue 385 LEU 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 629 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 28 optimal weight: 0.4980 chunk 22 optimal weight: 0.0270 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 = 0.4337 r_free = 0.4337 target = 0.156799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.133987 restraints weight = 6493.790| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 3.09 r_work: 0.3914 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4075 Z= 0.134 Angle : 0.691 9.549 5521 Z= 0.341 Chirality : 0.040 0.206 626 Planarity : 0.004 0.050 705 Dihedral : 5.818 57.120 536 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.38 % Allowed : 35.48 % Favored : 60.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.39), residues: 496 helix: 2.73 (0.27), residues: 326 sheet: None (None), residues: 0 loop : -1.96 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 528 TYR 0.007 0.001 TYR A 323 PHE 0.008 0.001 PHE A 629 TRP 0.008 0.001 TRP A 530 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4075) covalent geometry : angle 0.69068 ( 5521) hydrogen bonds : bond 0.03544 ( 235) hydrogen bonds : angle 3.19630 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1481.35 seconds wall clock time: 26 minutes 1.55 seconds (1561.55 seconds total)