Starting phenix.real_space_refine on Thu Jul 2 02:20:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nvh_12604/07_2026/7nvh_12604.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvh_12604/07_2026/7nvh_12604.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/7nvh_12604/07_2026/7nvh_12604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvh_12604/07_2026/7nvh_12604.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nvh_12604/07_2026/7nvh_12604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvh_12604/07_2026/7nvh_12604.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nvh_12604/07_2026/7nvh_12604.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nvh_12604/07_2026/7nvh_12604.cif" } 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= 0.067 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 27 5.16 5 C 3605 2.51 5 N 913 2.21 5 O 983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5528 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5459 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 717, 5440 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 35, 'TRANS': 681} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 717, 5440 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 35, 'TRANS': 681} Chain breaks: 1 bond proxies already assigned to first conformer: 5532 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.71, per 1000 atoms: 0.31 Number of scatterers: 5528 At special positions: 0 Unit cell: (82.368, 72.384, 106.496, 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 27 16.00 O 983 8.00 N 913 7.00 C 3605 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: 0.43 Conformation dependent library (CDL) restraints added in 349.6 milliseconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1308 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 3 sheets defined 71.1% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 4.100A pdb=" N ARG A 7 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR A 10 " --> pdb=" O GLY A 6 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 12 " --> pdb=" O THR A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.752A pdb=" N HIS A 37 " --> pdb=" O SER A 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 33 through 37' Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.699A pdb=" N ALA A 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 175 Processing helix chain 'A' and resid 175 through 201 removed outlier: 3.821A pdb=" N THR A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 202 through 228 Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 247 through 266 removed outlier: 3.707A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 298 removed outlier: 4.167A pdb=" N ARG A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 302 Processing helix chain 'A' and resid 304 through 337 removed outlier: 3.667A pdb=" N TYR A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Proline residue: A 330 - end of helix Processing helix chain 'A' and resid 338 through 341 removed outlier: 4.187A pdb=" N ASP A 341 " --> pdb=" O LYS A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 341' Processing helix chain 'A' and resid 384 through 392 removed outlier: 3.669A pdb=" N VAL A 389 " --> pdb=" O TRP A 385 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 409 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.633A pdb=" N LEU A 427 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.904A pdb=" N ASN A 491 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.708A pdb=" N THR A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 557 removed outlier: 3.510A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 578 removed outlier: 3.876A pdb=" N VAL A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 607 removed outlier: 3.691A pdb=" N ILE A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 Processing helix chain 'A' and resid 623 through 655 removed outlier: 4.205A pdb=" N ARG A 648 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 670 removed outlier: 3.780A pdb=" N THR A 670 " --> pdb=" O GLY A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 690 removed outlier: 3.620A pdb=" N PHE A 688 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 713 Processing helix chain 'A' and resid 713 through 727 removed outlier: 4.629A pdb=" N VAL A 719 " --> pdb=" O ARG A 715 " (cutoff:3.500A) Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 728 through 732 removed outlier: 3.735A pdb=" N TRP A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP A 732 " --> pdb=" O ASP A 729 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 728 through 732' Processing helix chain 'A' and resid 734 through 744 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 494 through 495 341 hydrogen bonds defined for protein. 979 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: 0.84 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 868 1.32 - 1.44: 1423 1.44 - 1.56: 3298 1.56 - 1.68: 11 1.68 - 1.81: 50 Bond restraints: 5650 Sorted by residual: bond pdb=" CCS AV0 A 801 " pdb=" OBZ AV0 A 801 " ideal model delta sigma weight residual 1.392 1.480 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C1 AV0 A 801 " pdb=" O5 AV0 A 801 " ideal model delta sigma weight residual 1.403 1.483 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CCR AV0 A 801 " pdb=" OBY AV0 A 801 " ideal model delta sigma weight residual 1.392 1.471 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" CBT AV0 A 801 " pdb=" CCM AV0 A 801 " ideal model delta sigma weight residual 1.528 1.606 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CCJ AV0 A 801 " pdb=" OBX AV0 A 801 " ideal model delta sigma weight residual 1.403 1.474 -0.071 2.00e-02 2.50e+03 1.28e+01 ... (remaining 5645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 7481 1.83 - 3.67: 151 3.67 - 5.50: 54 5.50 - 7.33: 5 7.33 - 9.16: 2 Bond angle restraints: 7693 Sorted by residual: angle pdb=" N ASP A 640 " pdb=" CA ASP A 640 " pdb=" C ASP A 640 " ideal model delta sigma weight residual 111.07 107.04 4.03 1.07e+00 8.73e-01 1.42e+01 angle pdb=" N ASN A 390 " pdb=" CA ASN A 390 " pdb=" C ASN A 390 " ideal model delta sigma weight residual 114.75 110.33 4.42 1.26e+00 6.30e-01 1.23e+01 angle pdb=" C4 AV0 A 801 " pdb=" O4 AV0 A 801 " pdb=" CCR AV0 A 801 " ideal model delta sigma weight residual 119.55 110.89 8.66 3.00e+00 1.11e-01 8.33e+00 angle pdb=" CA TYR A 698 " pdb=" CB TYR A 698 " pdb=" CG TYR A 698 " ideal model delta sigma weight residual 113.90 119.02 -5.12 1.80e+00 3.09e-01 8.09e+00 angle pdb=" C ASP A 710 " pdb=" CA ASP A 710 " pdb=" CB ASP A 710 " ideal model delta sigma weight residual 110.31 104.45 5.86 2.09e+00 2.29e-01 7.85e+00 ... (remaining 7688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 3105 22.47 - 44.93: 198 44.93 - 67.40: 20 67.40 - 89.87: 2 89.87 - 112.34: 1 Dihedral angle restraints: 3326 sinusoidal: 1281 harmonic: 2045 Sorted by residual: dihedral pdb=" CA LEU A 94 " pdb=" C LEU A 94 " pdb=" N ASN A 95 " pdb=" CA ASN A 95 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA VAL A 389 " pdb=" C VAL A 389 " pdb=" N ASN A 390 " pdb=" CA ASN A 390 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ARG A 96 " pdb=" C ARG A 96 " pdb=" N PHE A 97 " pdb=" CA PHE A 97 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 3323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 650 0.044 - 0.088: 215 0.088 - 0.132: 53 0.132 - 0.176: 10 0.176 - 0.220: 2 Chirality restraints: 930 Sorted by residual: chirality pdb=" CCS AV0 A 801 " pdb=" CCW AV0 A 801 " pdb=" OBZ AV0 A 801 " pdb=" OCB AV0 A 801 " both_signs ideal model delta sigma weight residual False 2.24 2.46 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CCQ AV0 A 801 " pdb=" CCF AV0 A 801 " pdb=" CCH AV0 A 801 " pdb=" OCB AV0 A 801 " both_signs ideal model delta sigma weight residual False 2.54 2.34 0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA GLN A 238 " pdb=" N GLN A 238 " pdb=" C GLN A 238 " pdb=" CB GLN A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 927 not shown) Planarity restraints: 950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 83 " -0.035 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO A 84 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 84 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 84 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 75 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO A 76 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 583 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 584 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 584 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 584 " 0.027 5.00e-02 4.00e+02 ... (remaining 947 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 105 2.70 - 3.25: 5551 3.25 - 3.80: 8793 3.80 - 4.35: 11660 4.35 - 4.90: 19780 Nonbonded interactions: 45889 Sorted by model distance: nonbonded pdb=" O ILE A 323 " pdb=" OG1 THR A 327 " model vdw 2.145 3.040 nonbonded pdb=" OG1 THR A 659 " pdb=" OD1 ASP A 728 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR A 61 " pdb=" OE2 GLU A 495 " model vdw 2.252 3.040 nonbonded pdb=" O SER A 66 " pdb=" OG SER A 131 " model vdw 2.298 3.040 nonbonded pdb=" NH2 ARG A 65 " pdb=" O GLY A 136 " model vdw 2.327 3.120 ... (remaining 45884 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=0.50 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.320 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 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 : 0.006 0.088 5650 Z= 0.300 Angle : 0.726 9.163 7693 Z= 0.374 Chirality : 0.046 0.220 930 Planarity : 0.005 0.054 950 Dihedral : 14.268 112.335 2018 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.69 % Allowed : 0.17 % Favored : 99.13 % 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: -0.42 (0.33), residues: 716 helix: 0.17 (0.25), residues: 479 sheet: -0.78 (0.86), residues: 38 loop : -0.98 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 96 TYR 0.022 0.001 TYR A 698 PHE 0.011 0.001 PHE A 306 TRP 0.012 0.001 TRP A 736 HIS 0.002 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.30 ( 5650) covalent geometry : angle 0.72610 / 0.37 ( 7693) hydrogen bonds : bond 0.15882 / 9.58 ( 341) hydrogen bonds : angle 6.22003 / 4.61 ( 979) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.198 Fit side-chains REVERT: A 406 ILE cc_start: 0.8401 (tp) cc_final: 0.8018 (pp) REVERT: A 562 MET cc_start: 0.7830 (tmm) cc_final: 0.7599 (tmt) REVERT: A 710 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7737 (t70) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.4058 time to fit residues: 28.4043 Evaluate side-chains 59 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109391 restraints weight = 19808.283| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.87 r_work: 0.3149 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5650 Z= 0.145 Angle : 0.617 8.490 7693 Z= 0.315 Chirality : 0.042 0.166 930 Planarity : 0.005 0.047 950 Dihedral : 7.953 118.968 793 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.90 % Allowed : 5.02 % Favored : 93.08 % 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: -0.05 (0.33), residues: 716 helix: 0.46 (0.25), residues: 483 sheet: -0.58 (0.88), residues: 38 loop : -0.92 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.024 0.001 TYR A 698 PHE 0.009 0.001 PHE A 306 TRP 0.010 0.001 TRP A 736 HIS 0.002 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 5650) covalent geometry : angle 0.61681 / 0.31 ( 7693) hydrogen bonds : bond 0.04011 / 2.58 ( 341) hydrogen bonds : angle 4.70999 / 3.40 ( 979) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.145 Fit side-chains REVERT: A 406 ILE cc_start: 0.8575 (tp) cc_final: 0.8206 (pp) REVERT: A 710 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8182 (t70) outliers start: 8 outliers final: 3 residues processed: 63 average time/residue: 0.4560 time to fit residues: 30.2060 Evaluate side-chains 62 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 710 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114223 restraints weight = 12048.297| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.17 r_work: 0.3192 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5650 Z= 0.120 Angle : 0.570 9.130 7693 Z= 0.287 Chirality : 0.041 0.162 930 Planarity : 0.005 0.045 950 Dihedral : 7.823 121.970 793 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.73 % Allowed : 6.92 % Favored : 91.35 % 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: 0.27 (0.33), residues: 716 helix: 0.72 (0.25), residues: 490 sheet: -0.34 (0.86), residues: 38 loop : -0.93 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 113 TYR 0.025 0.001 TYR A 698 PHE 0.009 0.001 PHE A 306 TRP 0.010 0.001 TRP A 736 HIS 0.001 0.000 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 5650) covalent geometry : angle 0.56987 / 0.29 ( 7693) hydrogen bonds : bond 0.03493 / 2.25 ( 341) hydrogen bonds : angle 4.43084 / 3.18 ( 979) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.230 Fit side-chains REVERT: A 406 ILE cc_start: 0.8591 (tp) cc_final: 0.8234 (pp) outliers start: 8 outliers final: 2 residues processed: 70 average time/residue: 0.5035 time to fit residues: 37.1158 Evaluate side-chains 62 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 116 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.110190 restraints weight = 14944.662| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.44 r_work: 0.3127 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5650 Z= 0.200 Angle : 0.617 9.104 7693 Z= 0.312 Chirality : 0.043 0.176 930 Planarity : 0.005 0.045 950 Dihedral : 7.671 122.562 791 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.91 % Favored : 94.95 % Rotamer: Outliers : 1.73 % Allowed : 9.52 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.28 (0.33), residues: 716 helix: 0.64 (0.24), residues: 494 sheet: -0.13 (0.79), residues: 44 loop : -0.74 (0.51), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 473 TYR 0.024 0.001 TYR A 698 PHE 0.023 0.001 PHE A 575 TRP 0.007 0.001 TRP A 493 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 ( 5650) covalent geometry : angle 0.61738 / 0.31 ( 7693) hydrogen bonds : bond 0.03760 / 2.42 ( 341) hydrogen bonds : angle 4.50792 / 3.23 ( 979) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.213 Fit side-chains REVERT: A 406 ILE cc_start: 0.8531 (tp) cc_final: 0.8168 (pp) outliers start: 8 outliers final: 3 residues processed: 66 average time/residue: 0.5413 time to fit residues: 37.6009 Evaluate side-chains 64 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 491 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 49 optimal weight: 0.0270 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111406 restraints weight = 17217.209| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.60 r_work: 0.3169 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5650 Z= 0.119 Angle : 0.571 10.774 7693 Z= 0.284 Chirality : 0.040 0.162 930 Planarity : 0.005 0.044 950 Dihedral : 7.464 122.511 791 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.04 % Allowed : 10.90 % Favored : 88.06 % 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: 0.51 (0.33), residues: 716 helix: 0.91 (0.25), residues: 485 sheet: -0.00 (0.86), residues: 38 loop : -0.90 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 738 TYR 0.026 0.001 TYR A 698 PHE 0.017 0.001 PHE A 575 TRP 0.010 0.001 TRP A 736 HIS 0.001 0.000 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5650) covalent geometry : angle 0.57064 / 0.28 ( 7693) hydrogen bonds : bond 0.03292 / 2.13 ( 341) hydrogen bonds : angle 4.37185 / 3.13 ( 979) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.203 Fit side-chains REVERT: A 406 ILE cc_start: 0.8532 (tp) cc_final: 0.8195 (pp) outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.5020 time to fit residues: 35.3974 Evaluate side-chains 66 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 704 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.0060 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS A 181 GLN A 616 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112644 restraints weight = 12147.247| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.15 r_work: 0.3187 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5650 Z= 0.123 Angle : 0.581 13.340 7693 Z= 0.283 Chirality : 0.040 0.157 930 Planarity : 0.005 0.045 950 Dihedral : 7.341 122.010 791 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.90 % Allowed : 11.76 % Favored : 86.33 % 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: 0.67 (0.33), residues: 716 helix: 1.03 (0.25), residues: 485 sheet: 0.14 (0.87), residues: 38 loop : -0.85 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 738 TYR 0.021 0.001 TYR A 698 PHE 0.015 0.001 PHE A 575 TRP 0.008 0.001 TRP A 736 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 5650) covalent geometry : angle 0.58075 / 0.28 ( 7693) hydrogen bonds : bond 0.03222 / 2.09 ( 341) hydrogen bonds : angle 4.35769 / 3.12 ( 979) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.201 Fit side-chains REVERT: A 36 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8190 (ptpp) REVERT: A 406 ILE cc_start: 0.8607 (tp) cc_final: 0.8270 (pp) REVERT: A 696 MET cc_start: 0.8925 (tpp) cc_final: 0.8648 (mmm) outliers start: 9 outliers final: 3 residues processed: 67 average time/residue: 0.5278 time to fit residues: 37.2382 Evaluate side-chains 64 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 391 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.112440 restraints weight = 14689.867| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.44 r_work: 0.3190 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5650 Z= 0.138 Angle : 0.581 11.599 7693 Z= 0.287 Chirality : 0.041 0.165 930 Planarity : 0.005 0.045 950 Dihedral : 7.315 121.997 791 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.38 % Allowed : 12.46 % Favored : 86.16 % 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: 0.62 (0.33), residues: 716 helix: 0.97 (0.24), residues: 493 sheet: 0.22 (0.87), residues: 38 loop : -0.89 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 738 TYR 0.023 0.001 TYR A 698 PHE 0.013 0.001 PHE A 575 TRP 0.007 0.001 TRP A 736 HIS 0.001 0.000 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 5650) covalent geometry : angle 0.58135 / 0.29 ( 7693) hydrogen bonds : bond 0.03308 / 2.15 ( 341) hydrogen bonds : angle 4.35665 / 3.12 ( 979) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.199 Fit side-chains REVERT: A 36 LYS cc_start: 0.8381 (ptmt) cc_final: 0.8129 (ptpp) REVERT: A 406 ILE cc_start: 0.8512 (tp) cc_final: 0.8176 (pp) REVERT: A 696 MET cc_start: 0.8715 (tpp) cc_final: 0.8469 (mmm) REVERT: A 738 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7430 (tpp-160) outliers start: 6 outliers final: 3 residues processed: 65 average time/residue: 0.5512 time to fit residues: 37.6158 Evaluate side-chains 63 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 391 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 61 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111132 restraints weight = 14670.986| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.41 r_work: 0.3156 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5650 Z= 0.140 Angle : 0.590 11.508 7693 Z= 0.288 Chirality : 0.041 0.165 930 Planarity : 0.005 0.044 950 Dihedral : 7.275 121.889 791 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.04 % Allowed : 12.98 % Favored : 85.99 % 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: 0.63 (0.33), residues: 716 helix: 0.95 (0.24), residues: 494 sheet: 0.26 (0.88), residues: 38 loop : -0.83 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 738 TYR 0.024 0.001 TYR A 698 PHE 0.011 0.001 PHE A 575 TRP 0.007 0.001 TRP A 736 HIS 0.001 0.000 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 5650) covalent geometry : angle 0.58973 / 0.29 ( 7693) hydrogen bonds : bond 0.03308 / 2.14 ( 341) hydrogen bonds : angle 4.34439 / 3.11 ( 979) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.205 Fit side-chains REVERT: A 36 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8150 (ptpp) REVERT: A 406 ILE cc_start: 0.8502 (tp) cc_final: 0.8151 (pp) REVERT: A 738 ARG cc_start: 0.7661 (ttm-80) cc_final: 0.7357 (tpp-160) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.5554 time to fit residues: 37.3078 Evaluate side-chains 64 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 391 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.110018 restraints weight = 22902.466| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.05 r_work: 0.3118 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5650 Z= 0.133 Angle : 0.585 14.050 7693 Z= 0.285 Chirality : 0.041 0.166 930 Planarity : 0.005 0.044 950 Dihedral : 7.231 121.726 791 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.38 % Allowed : 12.80 % Favored : 85.81 % 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: 0.68 (0.33), residues: 716 helix: 0.99 (0.25), residues: 494 sheet: 0.25 (0.88), residues: 38 loop : -0.80 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 738 TYR 0.025 0.001 TYR A 698 PHE 0.011 0.001 PHE A 575 TRP 0.008 0.001 TRP A 736 HIS 0.001 0.000 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 5650) covalent geometry : angle 0.58505 / 0.28 ( 7693) hydrogen bonds : bond 0.03241 / 2.11 ( 341) hydrogen bonds : angle 4.31683 / 3.09 ( 979) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.209 Fit side-chains REVERT: A 36 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8180 (ptpp) REVERT: A 406 ILE cc_start: 0.8507 (tp) cc_final: 0.8161 (pp) REVERT: A 738 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7392 (tpp-160) outliers start: 6 outliers final: 3 residues processed: 69 average time/residue: 0.5362 time to fit residues: 38.7544 Evaluate side-chains 68 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 704 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 39 optimal weight: 0.0270 chunk 29 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.124626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.110741 restraints weight = 19565.282| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.82 r_work: 0.3169 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5650 Z= 0.127 Angle : 0.601 14.065 7693 Z= 0.288 Chirality : 0.041 0.160 930 Planarity : 0.005 0.044 950 Dihedral : 7.198 121.442 791 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.04 % Allowed : 13.49 % Favored : 85.47 % 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: 0.73 (0.33), residues: 716 helix: 1.02 (0.25), residues: 494 sheet: 0.24 (0.88), residues: 38 loop : -0.76 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 738 TYR 0.022 0.001 TYR A 698 PHE 0.011 0.001 PHE A 575 TRP 0.008 0.001 TRP A 736 HIS 0.001 0.000 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 5650) covalent geometry : angle 0.60123 / 0.29 ( 7693) hydrogen bonds : bond 0.03220 / 2.10 ( 341) hydrogen bonds : angle 4.30679 / 3.07 ( 979) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.218 Fit side-chains REVERT: A 36 LYS cc_start: 0.8436 (ptmt) cc_final: 0.8192 (ptpp) REVERT: A 391 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7502 (mpp80) REVERT: A 406 ILE cc_start: 0.8510 (tp) cc_final: 0.8180 (pp) REVERT: A 696 MET cc_start: 0.8735 (tpp) cc_final: 0.8283 (tmm) REVERT: A 738 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7411 (tpp-160) outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.4445 time to fit residues: 31.3086 Evaluate side-chains 67 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 704 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 0.0270 chunk 57 optimal weight: 1.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112576 restraints weight = 14833.246| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.41 r_work: 0.3178 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5650 Z= 0.118 Angle : 0.586 14.189 7693 Z= 0.282 Chirality : 0.041 0.163 930 Planarity : 0.005 0.044 950 Dihedral : 7.156 121.170 791 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.21 % Allowed : 13.49 % Favored : 85.29 % 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: 0.86 (0.33), residues: 716 helix: 1.10 (0.25), residues: 492 sheet: 0.28 (0.88), residues: 38 loop : -0.61 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 738 TYR 0.022 0.001 TYR A 698 PHE 0.011 0.001 PHE A 575 TRP 0.009 0.001 TRP A 736 HIS 0.001 0.000 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 5650) covalent geometry : angle 0.58644 / 0.28 ( 7693) hydrogen bonds : bond 0.03157 / 2.06 ( 341) hydrogen bonds : angle 4.29811 / 3.06 ( 979) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1723.02 seconds wall clock time: 30 minutes 14.49 seconds (1814.49 seconds total)