Starting phenix.real_space_refine on Thu Jul 24 17:16:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dvu_27745/07_2025/8dvu_27745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvu_27745/07_2025/8dvu_27745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dvu_27745/07_2025/8dvu_27745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvu_27745/07_2025/8dvu_27745.map" model { file = "/net/cci-nas-00/data/ceres_data/8dvu_27745/07_2025/8dvu_27745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvu_27745/07_2025/8dvu_27745.cif" } resolution = 2.9 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= 0.015 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 38 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3784 2.51 5 N 1059 2.21 5 O 1254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6170 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5375 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 25, 'TRANS': 643} Chain breaks: 1 Chain: "B" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 766 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 18} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4570 SG CYS A 810 36.881 19.714 31.150 1.00 7.69 S ATOM 4596 SG CYS A 813 34.935 16.553 31.282 1.00 10.45 S ATOM 4899 SG CYS A 864 36.768 16.868 27.740 1.00 13.54 S ATOM 4938 SG CYS A 869 33.961 19.186 29.142 1.00 16.27 S Time building chain proxies: 4.44, per 1000 atoms: 0.72 Number of scatterers: 6170 At special positions: 0 Unit cell: (94.218, 94.218, 71.238, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 38 15.00 Mg 1 11.99 O 1254 8.00 N 1059 7.00 C 3784 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: 1.68 Conformation dependent library (CDL) restraints added in 736.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 813 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " Number of angles added : 6 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1274 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 49.2% alpha, 9.1% beta 18 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.673A pdb=" N GLU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.629A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.792A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 469 through 491 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 506 through 522 removed outlier: 3.705A pdb=" N VAL A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 558 removed outlier: 3.650A pdb=" N GLU A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 578 removed outlier: 3.632A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 removed outlier: 3.929A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 746 through 769 Processing helix chain 'A' and resid 772 through 792 Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.750A pdb=" N THR A 260 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 294 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASP A 372 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE A 296 " --> pdb=" O ASP A 372 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A 322 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 462 Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 661 removed outlier: 6.381A pdb=" N GLY A 659 " --> pdb=" O ILE A 695 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 6.821A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 832 through 833 removed outlier: 4.532A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 844 removed outlier: 6.277A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.81 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: 1358 1.33 - 1.45: 1471 1.45 - 1.57: 3416 1.57 - 1.69: 73 1.69 - 1.81: 46 Bond restraints: 6364 Sorted by residual: bond pdb=" C GLU A 716 " pdb=" O GLU A 716 " ideal model delta sigma weight residual 1.233 1.212 0.021 1.30e-02 5.92e+03 2.59e+00 bond pdb=" C ASN A 625 " pdb=" O ASN A 625 " ideal model delta sigma weight residual 1.249 1.239 0.010 8.50e-03 1.38e+04 1.26e+00 bond pdb=" C4 ADP A1003 " pdb=" C5 ADP A1003 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.69e-01 bond pdb=" N GLU A 716 " pdb=" CA GLU A 716 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.46e-02 4.69e+03 7.81e-01 bond pdb=" CB PRO A 797 " pdb=" CG PRO A 797 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.35e-01 ... (remaining 6359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 8539 1.35 - 2.70: 176 2.70 - 4.06: 30 4.06 - 5.41: 12 5.41 - 6.76: 3 Bond angle restraints: 8760 Sorted by residual: angle pdb=" C GLY A 689 " pdb=" N ASP A 690 " pdb=" CA ASP A 690 " ideal model delta sigma weight residual 121.54 128.30 -6.76 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C GLU A 716 " pdb=" CA GLU A 716 " pdb=" CB GLU A 716 " ideal model delta sigma weight residual 111.86 108.41 3.45 1.34e+00 5.57e-01 6.62e+00 angle pdb=" N ALA A 440 " pdb=" CA ALA A 440 " pdb=" C ALA A 440 " ideal model delta sigma weight residual 110.64 114.09 -3.45 1.48e+00 4.57e-01 5.44e+00 angle pdb=" CA PRO A 797 " pdb=" C PRO A 797 " pdb=" O PRO A 797 " ideal model delta sigma weight residual 121.38 119.63 1.75 7.70e-01 1.69e+00 5.17e+00 angle pdb=" CA VAL A 332 " pdb=" CB VAL A 332 " pdb=" CG1 VAL A 332 " ideal model delta sigma weight residual 110.40 114.15 -3.75 1.70e+00 3.46e-01 4.87e+00 ... (remaining 8755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 3497 16.62 - 33.23: 250 33.23 - 49.85: 99 49.85 - 66.46: 59 66.46 - 83.08: 21 Dihedral angle restraints: 3926 sinusoidal: 1964 harmonic: 1962 Sorted by residual: dihedral pdb=" O2A ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PA ADP A1003 " pdb=" PB ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 7.39 -67.39 1 2.00e+01 2.50e-03 1.48e+01 dihedral pdb=" CA LEU A 346 " pdb=" C LEU A 346 " pdb=" N THR A 347 " pdb=" CA THR A 347 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASP A 492 " pdb=" CB ASP A 492 " pdb=" CG ASP A 492 " pdb=" OD1 ASP A 492 " ideal model delta sinusoidal sigma weight residual -30.00 -87.59 57.59 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 3923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 683 0.032 - 0.064: 227 0.064 - 0.096: 64 0.096 - 0.128: 30 0.128 - 0.160: 4 Chirality restraints: 1008 Sorted by residual: chirality pdb=" CA GLU A 716 " pdb=" N GLU A 716 " pdb=" C GLU A 716 " pdb=" CB GLU A 716 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CB ILE A 439 " pdb=" CA ILE A 439 " pdb=" CG1 ILE A 439 " pdb=" CG2 ILE A 439 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1005 not shown) Planarity restraints: 984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 716 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C GLU A 716 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU A 716 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 717 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 381 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.14e+00 pdb=" N PRO A 382 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 8 " -0.009 2.00e-02 2.50e+03 6.30e-03 8.92e-01 pdb=" N1 U B 8 " 0.016 2.00e-02 2.50e+03 pdb=" C2 U B 8 " -0.004 2.00e-02 2.50e+03 pdb=" O2 U B 8 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C5 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 8 " 0.000 2.00e-02 2.50e+03 ... (remaining 981 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 211 2.71 - 3.26: 5844 3.26 - 3.81: 10420 3.81 - 4.35: 13704 4.35 - 4.90: 21731 Nonbonded interactions: 51910 Sorted by model distance: nonbonded pdb="MG MG A1002 " pdb=" O2B ADP A1003 " model vdw 2.164 2.170 nonbonded pdb=" O CYS A 829 " pdb=" O2' G B 10 " model vdw 2.250 3.040 nonbonded pdb=" O SER A 378 " pdb=" ND2 ASN A 384 " model vdw 2.301 3.120 nonbonded pdb=" NZ LYS A 814 " pdb=" OE1 GLN A 902 " model vdw 2.308 3.120 nonbonded pdb=" NZ LYS A 458 " pdb=" OE2 GLU A 751 " model vdw 2.342 3.120 ... (remaining 51905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.230 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.900 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.003 0.092 6368 Z= 0.130 Angle : 0.618 24.590 8766 Z= 0.297 Chirality : 0.038 0.160 1008 Planarity : 0.003 0.027 984 Dihedral : 16.456 83.078 2652 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.01 % Allowed : 10.55 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.23 (0.28), residues: 665 helix: -0.12 (0.27), residues: 316 sheet: -2.08 (0.47), residues: 92 loop : -2.99 (0.27), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 908 HIS 0.002 0.000 HIS A 876 PHE 0.008 0.001 PHE A 842 TYR 0.008 0.001 TYR A 390 ARG 0.001 0.000 ARG A 811 Details of bonding type rmsd hydrogen bonds : bond 0.13589 ( 304) hydrogen bonds : angle 5.01460 ( 842) metal coordination : bond 0.07012 ( 4) metal coordination : angle 13.08373 ( 6) covalent geometry : bond 0.00221 ( 6364) covalent geometry : angle 0.51497 ( 8760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.635 Fit side-chains REVERT: A 369 MET cc_start: 0.9111 (mtm) cc_final: 0.8792 (mtm) REVERT: A 385 MET cc_start: 0.8671 (mmm) cc_final: 0.8470 (mmp) REVERT: A 492 ASP cc_start: 0.7216 (t70) cc_final: 0.6800 (t0) REVERT: A 498 GLN cc_start: 0.7766 (mm110) cc_final: 0.7544 (mp10) REVERT: A 560 MET cc_start: 0.8845 (mtt) cc_final: 0.8369 (mtt) REVERT: A 761 MET cc_start: 0.8748 (ttp) cc_final: 0.8516 (ttm) REVERT: A 786 HIS cc_start: 0.8184 (t70) cc_final: 0.7883 (t70) outliers start: 6 outliers final: 4 residues processed: 114 average time/residue: 1.3679 time to fit residues: 162.6783 Evaluate side-chains 84 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 800 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 393 GLN A 517 GLN A 588 GLN A 708 GLN A 769 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.128529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.109350 restraints weight = 6288.644| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 0.98 r_work: 0.3000 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6368 Z= 0.128 Angle : 0.524 6.474 8766 Z= 0.264 Chirality : 0.040 0.159 1008 Planarity : 0.003 0.030 984 Dihedral : 15.131 74.034 1292 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.35 % Allowed : 13.07 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.30), residues: 665 helix: 0.97 (0.28), residues: 321 sheet: -1.68 (0.48), residues: 93 loop : -2.53 (0.30), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 771 HIS 0.003 0.001 HIS A 623 PHE 0.009 0.001 PHE A 842 TYR 0.013 0.001 TYR A 390 ARG 0.002 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 304) hydrogen bonds : angle 3.66218 ( 842) metal coordination : bond 0.00850 ( 4) metal coordination : angle 3.83926 ( 6) covalent geometry : bond 0.00295 ( 6364) covalent geometry : angle 0.51484 ( 8760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.604 Fit side-chains REVERT: A 369 MET cc_start: 0.9239 (mtm) cc_final: 0.8957 (mtm) REVERT: A 425 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7941 (m-30) REVERT: A 479 MET cc_start: 0.9265 (mtp) cc_final: 0.8901 (mtp) REVERT: A 492 ASP cc_start: 0.7248 (t70) cc_final: 0.6712 (t0) REVERT: A 498 GLN cc_start: 0.7904 (mm110) cc_final: 0.7472 (mp10) REVERT: A 560 MET cc_start: 0.9006 (mtt) cc_final: 0.8492 (mtt) REVERT: A 761 MET cc_start: 0.8813 (ttp) cc_final: 0.8419 (ttm) REVERT: A 786 HIS cc_start: 0.8368 (t70) cc_final: 0.8051 (t70) REVERT: A 883 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.6411 (tm-30) REVERT: A 914 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7455 (tm-30) outliers start: 20 outliers final: 8 residues processed: 90 average time/residue: 1.2703 time to fit residues: 119.9842 Evaluate side-chains 89 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.122982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.101909 restraints weight = 6424.463| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.15 r_work: 0.2906 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6368 Z= 0.217 Angle : 0.617 6.571 8766 Z= 0.310 Chirality : 0.044 0.140 1008 Planarity : 0.004 0.033 984 Dihedral : 15.183 89.014 1286 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.36 % Allowed : 13.40 % Favored : 82.24 % 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: -0.84 (0.31), residues: 665 helix: 1.15 (0.29), residues: 321 sheet: -1.48 (0.48), residues: 89 loop : -2.51 (0.31), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 908 HIS 0.004 0.001 HIS A 317 PHE 0.011 0.002 PHE A 842 TYR 0.017 0.002 TYR A 390 ARG 0.003 0.000 ARG A 791 Details of bonding type rmsd hydrogen bonds : bond 0.04802 ( 304) hydrogen bonds : angle 3.81433 ( 842) metal coordination : bond 0.00795 ( 4) metal coordination : angle 3.65563 ( 6) covalent geometry : bond 0.00524 ( 6364) covalent geometry : angle 0.61014 ( 8760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.592 Fit side-chains REVERT: A 425 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: A 492 ASP cc_start: 0.7362 (t70) cc_final: 0.6796 (t70) REVERT: A 498 GLN cc_start: 0.7989 (mm110) cc_final: 0.7576 (mp10) REVERT: A 560 MET cc_start: 0.9076 (mtt) cc_final: 0.8671 (mtt) REVERT: A 761 MET cc_start: 0.9056 (ttp) cc_final: 0.8655 (ttm) REVERT: A 786 HIS cc_start: 0.8396 (t70) cc_final: 0.8089 (t70) REVERT: A 883 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.6505 (tm-30) REVERT: A 906 SER cc_start: 0.9151 (OUTLIER) cc_final: 0.8797 (p) REVERT: A 914 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7486 (tm-30) outliers start: 26 outliers final: 9 residues processed: 88 average time/residue: 1.2370 time to fit residues: 114.2364 Evaluate side-chains 89 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.127167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.106532 restraints weight = 6456.638| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.13 r_work: 0.2962 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6368 Z= 0.114 Angle : 0.513 5.946 8766 Z= 0.259 Chirality : 0.039 0.137 1008 Planarity : 0.003 0.036 984 Dihedral : 15.116 82.588 1286 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.18 % Allowed : 14.57 % Favored : 82.24 % 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: -0.20 (0.32), residues: 665 helix: 1.68 (0.29), residues: 321 sheet: -1.15 (0.49), residues: 101 loop : -2.24 (0.33), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 771 HIS 0.002 0.001 HIS A 317 PHE 0.009 0.001 PHE A 842 TYR 0.011 0.001 TYR A 390 ARG 0.001 0.000 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 304) hydrogen bonds : angle 3.55114 ( 842) metal coordination : bond 0.00541 ( 4) metal coordination : angle 3.08657 ( 6) covalent geometry : bond 0.00260 ( 6364) covalent geometry : angle 0.50708 ( 8760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.574 Fit side-chains REVERT: A 425 ASP cc_start: 0.8234 (m-30) cc_final: 0.7933 (m-30) REVERT: A 479 MET cc_start: 0.9224 (mtp) cc_final: 0.8835 (mtp) REVERT: A 492 ASP cc_start: 0.7266 (t70) cc_final: 0.6662 (t70) REVERT: A 498 GLN cc_start: 0.7913 (mm110) cc_final: 0.7455 (mp10) REVERT: A 560 MET cc_start: 0.9045 (mtt) cc_final: 0.8580 (mtt) REVERT: A 679 LYS cc_start: 0.8481 (tttt) cc_final: 0.7517 (mttp) REVERT: A 761 MET cc_start: 0.8894 (ttp) cc_final: 0.8499 (ttm) REVERT: A 786 HIS cc_start: 0.8329 (t70) cc_final: 0.8025 (t70) REVERT: A 906 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8777 (p) REVERT: A 914 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7540 (tm-30) outliers start: 19 outliers final: 8 residues processed: 91 average time/residue: 1.2247 time to fit residues: 116.9929 Evaluate side-chains 88 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 0.0020 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.127841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.107896 restraints weight = 6415.171| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.09 r_work: 0.2967 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6368 Z= 0.108 Angle : 0.503 6.585 8766 Z= 0.252 Chirality : 0.039 0.136 1008 Planarity : 0.003 0.035 984 Dihedral : 15.102 78.980 1286 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.52 % Allowed : 15.08 % Favored : 81.41 % 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: 0.16 (0.32), residues: 665 helix: 1.94 (0.29), residues: 321 sheet: -0.86 (0.51), residues: 96 loop : -2.05 (0.33), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 771 HIS 0.002 0.001 HIS A 876 PHE 0.009 0.001 PHE A 842 TYR 0.011 0.001 TYR A 717 ARG 0.004 0.000 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 304) hydrogen bonds : angle 3.45053 ( 842) metal coordination : bond 0.00480 ( 4) metal coordination : angle 2.94979 ( 6) covalent geometry : bond 0.00246 ( 6364) covalent geometry : angle 0.49754 ( 8760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.614 Fit side-chains REVERT: A 425 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: A 479 MET cc_start: 0.9243 (mtp) cc_final: 0.8865 (mtp) REVERT: A 492 ASP cc_start: 0.7185 (t70) cc_final: 0.6314 (t0) REVERT: A 560 MET cc_start: 0.9070 (mtt) cc_final: 0.8650 (mtt) REVERT: A 679 LYS cc_start: 0.8507 (tttt) cc_final: 0.7492 (mttp) REVERT: A 761 MET cc_start: 0.8866 (ttp) cc_final: 0.8497 (ttm) REVERT: A 786 HIS cc_start: 0.8372 (t70) cc_final: 0.8044 (t70) REVERT: A 906 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8776 (p) REVERT: A 914 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7576 (tm-30) outliers start: 21 outliers final: 10 residues processed: 87 average time/residue: 1.2777 time to fit residues: 116.5319 Evaluate side-chains 87 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 68 optimal weight: 6.9990 chunk 1 optimal weight: 0.0370 chunk 44 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 56 optimal weight: 0.0000 chunk 46 optimal weight: 4.9990 overall best weight: 0.2620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.132780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.114400 restraints weight = 6414.663| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.06 r_work: 0.3053 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6368 Z= 0.087 Angle : 0.471 6.894 8766 Z= 0.236 Chirality : 0.038 0.138 1008 Planarity : 0.003 0.035 984 Dihedral : 15.054 73.824 1286 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.18 % Allowed : 16.25 % Favored : 80.57 % 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: 0.55 (0.32), residues: 665 helix: 2.26 (0.29), residues: 321 sheet: -0.56 (0.55), residues: 88 loop : -1.89 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 771 HIS 0.002 0.000 HIS A 876 PHE 0.009 0.001 PHE A 842 TYR 0.013 0.001 TYR A 717 ARG 0.004 0.000 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 304) hydrogen bonds : angle 3.30694 ( 842) metal coordination : bond 0.00382 ( 4) metal coordination : angle 2.54678 ( 6) covalent geometry : bond 0.00186 ( 6364) covalent geometry : angle 0.46688 ( 8760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.686 Fit side-chains REVERT: A 312 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7629 (mtmm) REVERT: A 425 ASP cc_start: 0.8224 (m-30) cc_final: 0.7936 (m-30) REVERT: A 479 MET cc_start: 0.9250 (mtp) cc_final: 0.8843 (mtp) REVERT: A 491 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6931 (tppt) REVERT: A 492 ASP cc_start: 0.6994 (t70) cc_final: 0.6106 (t0) REVERT: A 560 MET cc_start: 0.9043 (mtt) cc_final: 0.8652 (mtt) REVERT: A 607 GLU cc_start: 0.7723 (tt0) cc_final: 0.7467 (tp30) REVERT: A 679 LYS cc_start: 0.8508 (tttt) cc_final: 0.7538 (mttp) REVERT: A 690 ASP cc_start: 0.8235 (t70) cc_final: 0.7721 (t0) REVERT: A 761 MET cc_start: 0.8799 (ttp) cc_final: 0.8425 (ttm) REVERT: A 767 ARG cc_start: 0.8267 (ttp-110) cc_final: 0.7893 (ttp-110) REVERT: A 786 HIS cc_start: 0.8344 (t70) cc_final: 0.8006 (t70) REVERT: A 906 SER cc_start: 0.9043 (t) cc_final: 0.8712 (p) REVERT: A 914 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7297 (tt0) outliers start: 19 outliers final: 8 residues processed: 91 average time/residue: 1.3267 time to fit residues: 126.4089 Evaluate side-chains 85 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.125131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.104254 restraints weight = 6465.911| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.14 r_work: 0.2934 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6368 Z= 0.179 Angle : 0.580 7.657 8766 Z= 0.288 Chirality : 0.042 0.196 1008 Planarity : 0.004 0.032 984 Dihedral : 15.114 82.066 1285 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.35 % Allowed : 16.58 % Favored : 80.07 % 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: 0.24 (0.32), residues: 665 helix: 1.99 (0.29), residues: 321 sheet: -0.74 (0.53), residues: 84 loop : -1.98 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.003 0.001 HIS A 317 PHE 0.011 0.001 PHE A 842 TYR 0.020 0.002 TYR A 717 ARG 0.004 0.000 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 304) hydrogen bonds : angle 3.55297 ( 842) metal coordination : bond 0.00643 ( 4) metal coordination : angle 2.98418 ( 6) covalent geometry : bond 0.00434 ( 6364) covalent geometry : angle 0.57524 ( 8760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.786 Fit side-chains REVERT: A 312 LYS cc_start: 0.8000 (mtmm) cc_final: 0.7591 (mtmm) REVERT: A 425 ASP cc_start: 0.8313 (m-30) cc_final: 0.8033 (m-30) REVERT: A 491 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6838 (mppt) REVERT: A 492 ASP cc_start: 0.7192 (t70) cc_final: 0.6265 (t0) REVERT: A 560 MET cc_start: 0.9095 (mtt) cc_final: 0.8583 (mtt) REVERT: A 761 MET cc_start: 0.8974 (ttp) cc_final: 0.8483 (ttm) REVERT: A 786 HIS cc_start: 0.8401 (t70) cc_final: 0.8073 (t70) REVERT: A 843 VAL cc_start: 0.8747 (t) cc_final: 0.8504 (m) REVERT: A 906 SER cc_start: 0.9115 (OUTLIER) cc_final: 0.8804 (p) REVERT: A 914 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7401 (tm-30) outliers start: 20 outliers final: 8 residues processed: 87 average time/residue: 1.1428 time to fit residues: 104.6513 Evaluate side-chains 83 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 12 optimal weight: 0.0370 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 588 GLN A 595 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.127122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.107386 restraints weight = 6366.793| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.14 r_work: 0.2961 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6368 Z= 0.116 Angle : 0.524 7.953 8766 Z= 0.261 Chirality : 0.040 0.181 1008 Planarity : 0.003 0.034 984 Dihedral : 15.099 78.193 1285 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.85 % Allowed : 17.25 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.46 (0.32), residues: 665 helix: 2.17 (0.29), residues: 321 sheet: -0.61 (0.52), residues: 96 loop : -1.91 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 512 HIS 0.003 0.001 HIS A 830 PHE 0.009 0.001 PHE A 842 TYR 0.016 0.001 TYR A 717 ARG 0.004 0.000 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 304) hydrogen bonds : angle 3.46032 ( 842) metal coordination : bond 0.00505 ( 4) metal coordination : angle 2.73092 ( 6) covalent geometry : bond 0.00266 ( 6364) covalent geometry : angle 0.51921 ( 8760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.580 Fit side-chains REVERT: A 312 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7593 (mtmm) REVERT: A 425 ASP cc_start: 0.8297 (m-30) cc_final: 0.8022 (m-30) REVERT: A 479 MET cc_start: 0.9230 (mtp) cc_final: 0.8816 (mtp) REVERT: A 491 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6717 (mppt) REVERT: A 492 ASP cc_start: 0.7072 (t70) cc_final: 0.6151 (t0) REVERT: A 560 MET cc_start: 0.9087 (mtt) cc_final: 0.8578 (mtt) REVERT: A 679 LYS cc_start: 0.8570 (tttt) cc_final: 0.7574 (mttp) REVERT: A 761 MET cc_start: 0.8929 (ttp) cc_final: 0.8545 (ttm) REVERT: A 786 HIS cc_start: 0.8393 (t70) cc_final: 0.8074 (t70) REVERT: A 843 VAL cc_start: 0.8687 (t) cc_final: 0.8458 (m) REVERT: A 906 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8786 (p) REVERT: A 914 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7212 (tt0) outliers start: 17 outliers final: 10 residues processed: 83 average time/residue: 1.1847 time to fit residues: 103.7530 Evaluate side-chains 87 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.0000 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.125606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.105490 restraints weight = 6442.478| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.10 r_work: 0.2958 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6368 Z= 0.132 Angle : 0.538 8.116 8766 Z= 0.268 Chirality : 0.040 0.179 1008 Planarity : 0.003 0.033 984 Dihedral : 15.108 80.356 1285 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.02 % Allowed : 17.25 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.32), residues: 665 helix: 2.14 (0.29), residues: 321 sheet: -0.61 (0.52), residues: 96 loop : -1.91 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 512 HIS 0.002 0.001 HIS A 830 PHE 0.010 0.001 PHE A 842 TYR 0.017 0.002 TYR A 717 ARG 0.003 0.000 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 304) hydrogen bonds : angle 3.46671 ( 842) metal coordination : bond 0.00518 ( 4) metal coordination : angle 2.62305 ( 6) covalent geometry : bond 0.00310 ( 6364) covalent geometry : angle 0.53415 ( 8760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.552 Fit side-chains REVERT: A 312 LYS cc_start: 0.7963 (mtmm) cc_final: 0.7519 (mtmm) REVERT: A 425 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: A 491 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6759 (mppt) REVERT: A 492 ASP cc_start: 0.7135 (t70) cc_final: 0.6184 (OUTLIER) REVERT: A 560 MET cc_start: 0.9060 (mtt) cc_final: 0.8560 (mtt) REVERT: A 679 LYS cc_start: 0.8515 (tttt) cc_final: 0.7496 (mttp) REVERT: A 761 MET cc_start: 0.8908 (ttp) cc_final: 0.8494 (ttm) REVERT: A 786 HIS cc_start: 0.8350 (t70) cc_final: 0.8022 (t70) REVERT: A 843 VAL cc_start: 0.8718 (t) cc_final: 0.8479 (m) REVERT: A 906 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8774 (p) REVERT: A 914 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7142 (tt0) outliers start: 18 outliers final: 11 residues processed: 86 average time/residue: 1.3739 time to fit residues: 124.5598 Evaluate side-chains 89 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 0.0030 chunk 1 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.128664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.109747 restraints weight = 6493.623| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.10 r_work: 0.2998 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6368 Z= 0.096 Angle : 0.503 8.161 8766 Z= 0.251 Chirality : 0.039 0.173 1008 Planarity : 0.003 0.035 984 Dihedral : 15.073 73.901 1285 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.51 % Allowed : 17.76 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.32), residues: 665 helix: 2.34 (0.29), residues: 322 sheet: -0.40 (0.56), residues: 88 loop : -1.81 (0.33), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 771 HIS 0.003 0.001 HIS A 830 PHE 0.009 0.001 PHE A 842 TYR 0.018 0.001 TYR A 717 ARG 0.004 0.000 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 304) hydrogen bonds : angle 3.36813 ( 842) metal coordination : bond 0.00405 ( 4) metal coordination : angle 2.32170 ( 6) covalent geometry : bond 0.00211 ( 6364) covalent geometry : angle 0.49997 ( 8760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.715 Fit side-chains REVERT: A 312 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7597 (mtmm) REVERT: A 425 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: A 479 MET cc_start: 0.9229 (mtp) cc_final: 0.8798 (mtp) REVERT: A 491 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6941 (tppt) REVERT: A 492 ASP cc_start: 0.6970 (t70) cc_final: 0.6022 (OUTLIER) REVERT: A 560 MET cc_start: 0.9089 (mtt) cc_final: 0.8653 (mtt) REVERT: A 679 LYS cc_start: 0.8535 (tttt) cc_final: 0.7521 (mttp) REVERT: A 761 MET cc_start: 0.8860 (ttp) cc_final: 0.8538 (ttm) REVERT: A 786 HIS cc_start: 0.8363 (t70) cc_final: 0.8039 (t70) REVERT: A 843 VAL cc_start: 0.8669 (t) cc_final: 0.8445 (m) REVERT: A 906 SER cc_start: 0.9062 (t) cc_final: 0.8762 (p) REVERT: A 914 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7172 (tt0) outliers start: 15 outliers final: 10 residues processed: 84 average time/residue: 2.0899 time to fit residues: 185.5699 Evaluate side-chains 87 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 67 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.128014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.107844 restraints weight = 6568.030| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.12 r_work: 0.2964 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6368 Z= 0.113 Angle : 0.521 8.492 8766 Z= 0.258 Chirality : 0.039 0.171 1008 Planarity : 0.003 0.035 984 Dihedral : 15.062 73.947 1285 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.35 % Allowed : 17.76 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.32), residues: 665 helix: 2.30 (0.28), residues: 322 sheet: -0.51 (0.53), residues: 96 loop : -1.81 (0.34), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 512 HIS 0.002 0.001 HIS A 830 PHE 0.009 0.001 PHE A 842 TYR 0.021 0.001 TYR A 717 ARG 0.005 0.000 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 304) hydrogen bonds : angle 3.38093 ( 842) metal coordination : bond 0.00423 ( 4) metal coordination : angle 2.38996 ( 6) covalent geometry : bond 0.00261 ( 6364) covalent geometry : angle 0.51724 ( 8760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4939.91 seconds wall clock time: 87 minutes 26.92 seconds (5246.92 seconds total)