Starting phenix.real_space_refine on Thu Jul 2 02:28:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7slq_25198/07_2026/7slq_25198.cif Found real_map, /net/cci-nas-00/data/ceres_data/7slq_25198/07_2026/7slq_25198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7slq_25198/07_2026/7slq_25198.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7slq_25198/07_2026/7slq_25198.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7slq_25198/07_2026/7slq_25198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7slq_25198/07_2026/7slq_25198.map" model { file = "/net/cci-nas-00/data/ceres_data/7slq_25198/07_2026/7slq_25198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7slq_25198/07_2026/7slq_25198.cif" } resolution = 3.7 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= 0.005 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: 5 Type Number sf(0) Gaussians P 53 5.49 5 S 14 5.16 5 C 3269 2.51 5 N 958 2.21 5 O 1157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 5451 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1862 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2473 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 10, 'TRANS': 310} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 72 Chain: "R" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1090 Unusual residues: {'G5J': 1} Classifications: {'RNA': 50, 'undetermined': 1} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 16, 'rna3p_pyr': 21} Link IDs: {'rna2p': 12, 'rna3p': 37, None: 1} Not linked: pdbres="G5J R 1 " pdbres=" G R 2 " Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 1.29, per 1000 atoms: 0.24 Number of scatterers: 5451 At special positions: 0 Unit cell: (82.39, 92.02, 103.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 53 15.00 O 1157 8.00 N 958 7.00 C 3269 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 164.6 milliseconds 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1054 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 48.9% alpha, 12.7% beta 13 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 432 through 436 removed outlier: 3.502A pdb=" N ARG A 435 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 removed outlier: 4.131A pdb=" N TRP A 441 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 removed outlier: 4.008A pdb=" N LYS A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 removed outlier: 3.852A pdb=" N HIS A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 3.793A pdb=" N SER A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.533A pdb=" N ALA A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 606 removed outlier: 7.969A pdb=" N ASP A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N GLU A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 627 removed outlier: 3.757A pdb=" N LYS A 627 " --> pdb=" O GLY A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 638 removed outlier: 3.628A pdb=" N TYR A 634 " --> pdb=" O THR A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 55 through 63 Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.526A pdb=" N SER B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 removed outlier: 4.069A pdb=" N LYS B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 137 through 147 removed outlier: 3.580A pdb=" N ILE B 141 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.923A pdb=" N ALA B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 413 Processing helix chain 'B' and resid 467 through 477 removed outlier: 3.673A pdb=" N ALA B 477 " --> pdb=" O ASP B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 508 Processing helix chain 'B' and resid 526 through 546 Processing helix chain 'B' and resid 552 through 571 Processing sheet with id=AA1, first strand: chain 'A' and resid 554 through 557 removed outlier: 6.288A pdb=" N MET A 470 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL A 556 " --> pdb=" O MET A 470 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY A 472 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 447 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU A 473 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP A 449 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP A 446 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL A 578 " --> pdb=" O ASP A 446 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 448 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N CYS A 580 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU A 450 " --> pdb=" O CYS A 580 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP A 576 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL A 614 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 578 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLU A 616 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N CYS A 580 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 660 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 70 removed outlier: 3.673A pdb=" N VAL B 69 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 151 through 155 removed outlier: 3.755A pdb=" N TYR B 153 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 377 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 481 through 485 191 hydrogen bonds defined for protein. 555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.65 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: 1016 1.33 - 1.45: 1622 1.45 - 1.57: 2902 1.57 - 1.69: 106 1.69 - 1.81: 22 Bond restraints: 5668 Sorted by residual: bond pdb=" C3' G5J R 1 " pdb=" O3' G5J R 1 " ideal model delta sigma weight residual 1.404 1.737 -0.333 2.00e-02 2.50e+03 2.78e+02 bond pdb=" C3' G5J R 1 " pdb=" C4' G5J R 1 " ideal model delta sigma weight residual 1.526 1.248 0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C1' G5J R 1 " pdb=" C2' G5J R 1 " ideal model delta sigma weight residual 1.524 1.254 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C6 G5J R 1 " pdb=" O6 G5J R 1 " ideal model delta sigma weight residual 1.226 1.433 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C2' G5J R 1 " pdb=" C3' G5J R 1 " ideal model delta sigma weight residual 1.531 1.722 -0.191 2.00e-02 2.50e+03 9.15e+01 ... (remaining 5663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 7782 3.39 - 6.78: 108 6.78 - 10.17: 21 10.17 - 13.56: 9 13.56 - 16.95: 4 Bond angle restraints: 7924 Sorted by residual: angle pdb=" C VAL B 99 " pdb=" N VAL B 100 " pdb=" CA VAL B 100 " ideal model delta sigma weight residual 121.97 128.13 -6.16 1.00e+00 1.00e+00 3.80e+01 angle pdb=" O3' A R 298 " pdb=" C3' A R 298 " pdb=" C2' A R 298 " ideal model delta sigma weight residual 109.50 118.39 -8.89 1.50e+00 4.44e-01 3.51e+01 angle pdb=" N TYR B 68 " pdb=" CA TYR B 68 " pdb=" CB TYR B 68 " ideal model delta sigma weight residual 111.05 102.42 8.63 1.50e+00 4.44e-01 3.31e+01 angle pdb=" O3A G5J R 1 " pdb=" PB G5J R 1 " pdb=" O3B G5J R 1 " ideal model delta sigma weight residual 92.82 109.77 -16.95 3.00e+00 1.11e-01 3.19e+01 angle pdb=" C4' G R 300 " pdb=" C3' G R 300 " pdb=" O3' G R 300 " ideal model delta sigma weight residual 109.40 117.58 -8.18 1.50e+00 4.44e-01 2.98e+01 ... (remaining 7919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 3168 34.50 - 69.00: 79 69.00 - 103.50: 7 103.50 - 138.00: 1 138.00 - 172.50: 2 Dihedral angle restraints: 3257 sinusoidal: 1628 harmonic: 1629 Sorted by residual: dihedral pdb=" C5' A R 298 " pdb=" C4' A R 298 " pdb=" C3' A R 298 " pdb=" O3' A R 298 " ideal model delta sinusoidal sigma weight residual 147.00 105.99 41.01 1 8.00e+00 1.56e-02 3.68e+01 dihedral pdb=" CA ASN B 135 " pdb=" C ASN B 135 " pdb=" N VAL B 136 " pdb=" CA VAL B 136 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" O4' A R 296 " pdb=" C1' A R 296 " pdb=" N9 A R 296 " pdb=" C4 A R 296 " ideal model delta sinusoidal sigma weight residual -106.00 -171.42 65.42 1 1.70e+01 3.46e-03 1.94e+01 ... (remaining 3254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 875 0.118 - 0.237: 54 0.237 - 0.355: 2 0.355 - 0.473: 2 0.473 - 0.591: 1 Chirality restraints: 934 Sorted by residual: chirality pdb=" C3' A R 298 " pdb=" C4' A R 298 " pdb=" O3' A R 298 " pdb=" C2' A R 298 " both_signs ideal model delta sigma weight residual False -2.74 -2.15 -0.59 2.00e-01 2.50e+01 8.75e+00 chirality pdb=" CA PRO A 427 " pdb=" N PRO A 427 " pdb=" C PRO A 427 " pdb=" CB PRO A 427 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C3' G5J R 1 " pdb=" C2' G5J R 1 " pdb=" C4' G5J R 1 " pdb=" O3' G5J R 1 " both_signs ideal model delta sigma weight residual False -2.71 -3.10 0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 931 not shown) Planarity restraints: 815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 549 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO A 550 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 550 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 550 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G5J R 1 " -0.031 2.00e-02 2.50e+03 1.47e-02 6.50e+00 pdb=" C2 G5J R 1 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G5J R 1 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G5J R 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G5J R 1 " -0.000 2.00e-02 2.50e+03 pdb=" C8 G5J R 1 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G5J R 1 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G5J R 1 " 0.010 2.00e-02 2.50e+03 pdb=" N3 G5J R 1 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G5J R 1 " 0.026 2.00e-02 2.50e+03 pdb=" N9 G5J R 1 " 0.011 2.00e-02 2.50e+03 pdb=" O6 G5J R 1 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 132 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO B 133 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " -0.032 5.00e-02 4.00e+02 ... (remaining 812 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 184 2.69 - 3.25: 4857 3.25 - 3.80: 8758 3.80 - 4.35: 10821 4.35 - 4.90: 17235 Nonbonded interactions: 41855 Sorted by model distance: nonbonded pdb=" O2' A R 297 " pdb=" OP1 A R 298 " model vdw 2.144 3.040 nonbonded pdb=" O GLY A 532 " pdb=" OH TYR B 391 " model vdw 2.239 3.040 nonbonded pdb=" O SER B 461 " pdb=" OG1 THR B 491 " model vdw 2.331 3.040 nonbonded pdb=" O TYR A 650 " pdb=" OG SER A 653 " model vdw 2.337 3.040 nonbonded pdb=" OD1 ASP A 474 " pdb=" O2' SAH A 701 " model vdw 2.341 3.040 ... (remaining 41850 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 group one per residue 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: 0.660 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 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 : 0.011 0.333 5669 Z= 0.560 Angle : 1.161 16.945 7924 Z= 0.628 Chirality : 0.062 0.591 934 Planarity : 0.007 0.069 815 Dihedral : 14.972 172.502 2203 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.35 % Allowed : 4.94 % Favored : 93.71 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.00 % 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: -2.83 (0.30), residues: 546 helix: -2.16 (0.25), residues: 252 sheet: -0.52 (0.63), residues: 64 loop : -1.76 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 484 TYR 0.022 0.003 TYR B 68 PHE 0.022 0.003 PHE B 168 TRP 0.018 0.002 TRP A 620 HIS 0.005 0.002 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.01068 / 0.56 ( 5668) covalent geometry : angle 1.16097 / 0.63 ( 7924) hydrogen bonds : bond 0.13755 / 8.69 ( 225) hydrogen bonds : angle 5.95426 / 4.19 ( 623) Misc. bond : bond 0.03531 / 1.86 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6972 (ptpt) REVERT: A 601 ARG cc_start: 0.7168 (ttm110) cc_final: 0.6913 (ttp-110) outliers start: 6 outliers final: 1 residues processed: 109 average time/residue: 0.0998 time to fit residues: 13.3525 Evaluate side-chains 55 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain B residue 557 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.0270 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.167390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.126462 restraints weight = 9164.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.124951 restraints weight = 10702.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.126797 restraints weight = 9103.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.130348 restraints weight = 6261.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.129043 restraints weight = 5882.761| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5669 Z= 0.143 Angle : 0.616 7.678 7924 Z= 0.321 Chirality : 0.041 0.169 934 Planarity : 0.005 0.075 815 Dihedral : 14.899 160.726 1215 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.47 % Allowed : 9.21 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.33), residues: 546 helix: -0.50 (0.30), residues: 258 sheet: 0.36 (0.75), residues: 52 loop : -1.43 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 488 TYR 0.007 0.001 TYR A 575 PHE 0.024 0.002 PHE B 46 TRP 0.020 0.002 TRP B 140 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 5668) covalent geometry : angle 0.61636 / 0.32 ( 7924) hydrogen bonds : bond 0.04237 / 2.57 ( 225) hydrogen bonds : angle 4.23033 / 2.89 ( 623) Misc. bond : bond 0.00139 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 625 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8123 (ptmm) REVERT: A 636 ASN cc_start: 0.8930 (m-40) cc_final: 0.8718 (m-40) outliers start: 11 outliers final: 6 residues processed: 71 average time/residue: 0.0877 time to fit residues: 8.0208 Evaluate side-chains 57 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 161 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 682 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.170011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.129912 restraints weight = 9635.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.129022 restraints weight = 10995.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.131826 restraints weight = 9232.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.132216 restraints weight = 6576.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.133035 restraints weight = 6943.890| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5669 Z= 0.182 Angle : 0.629 6.171 7924 Z= 0.327 Chirality : 0.041 0.188 934 Planarity : 0.005 0.075 815 Dihedral : 14.706 163.210 1209 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.04 % Allowed : 11.46 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.82 (0.35), residues: 546 helix: -0.11 (0.31), residues: 261 sheet: 0.69 (0.73), residues: 57 loop : -1.30 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 484 TYR 0.012 0.002 TYR A 560 PHE 0.026 0.002 PHE B 56 TRP 0.023 0.002 TRP A 465 HIS 0.005 0.002 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 5668) covalent geometry : angle 0.62893 / 0.33 ( 7924) hydrogen bonds : bond 0.04593 / 2.76 ( 225) hydrogen bonds : angle 4.20742 / 2.84 ( 623) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7782 (t0) cc_final: 0.7446 (t0) REVERT: A 625 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8321 (ptmm) REVERT: B 33 GLN cc_start: 0.7451 (pp30) cc_final: 0.7178 (pp30) REVERT: B 40 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7491 (ptpp) REVERT: B 545 ASN cc_start: 0.7927 (m110) cc_final: 0.7222 (t0) outliers start: 18 outliers final: 8 residues processed: 71 average time/residue: 0.0692 time to fit residues: 6.4628 Evaluate side-chains 57 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 379 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.0030 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 530 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.171358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.132504 restraints weight = 9552.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.133175 restraints weight = 10578.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.135065 restraints weight = 9276.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.135519 restraints weight = 6120.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.135811 restraints weight = 6310.554| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5669 Z= 0.137 Angle : 0.580 6.495 7924 Z= 0.299 Chirality : 0.039 0.163 934 Planarity : 0.005 0.075 815 Dihedral : 14.405 162.502 1209 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.60 % Allowed : 14.38 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.57 (0.35), residues: 546 helix: 0.36 (0.33), residues: 254 sheet: 0.09 (0.78), residues: 51 loop : -1.25 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.011 0.001 TYR B 391 PHE 0.026 0.002 PHE B 56 TRP 0.023 0.002 TRP A 465 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 5668) covalent geometry : angle 0.58019 / 0.30 ( 7924) hydrogen bonds : bond 0.03935 / 2.36 ( 225) hydrogen bonds : angle 4.05149 / 2.71 ( 623) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7700 (t0) cc_final: 0.7403 (t0) REVERT: B 40 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7467 (ptpp) REVERT: B 545 ASN cc_start: 0.7998 (m110) cc_final: 0.7232 (t0) outliers start: 16 outliers final: 8 residues processed: 60 average time/residue: 0.0497 time to fit residues: 4.0485 Evaluate side-chains 52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 379 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.165162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.126261 restraints weight = 10004.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.125977 restraints weight = 11625.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.127349 restraints weight = 10251.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.127713 restraints weight = 6786.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.128203 restraints weight = 6771.338| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 5669 Z= 0.299 Angle : 0.753 7.953 7924 Z= 0.382 Chirality : 0.045 0.171 934 Planarity : 0.006 0.078 815 Dihedral : 14.755 162.917 1209 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.94 % Allowed : 13.48 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.34), residues: 546 helix: -0.05 (0.31), residues: 261 sheet: -0.02 (0.72), residues: 59 loop : -1.63 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 108 TYR 0.013 0.002 TYR A 490 PHE 0.016 0.002 PHE B 56 TRP 0.051 0.003 TRP A 465 HIS 0.007 0.002 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.30 ( 5668) covalent geometry : angle 0.75294 / 0.38 ( 7924) hydrogen bonds : bond 0.05802 / 3.50 ( 225) hydrogen bonds : angle 4.60702 / 3.08 ( 623) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7721 (t0) cc_final: 0.7417 (t0) REVERT: A 625 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8368 (ptmm) REVERT: B 33 GLN cc_start: 0.7758 (pp30) cc_final: 0.7444 (pp30) outliers start: 22 outliers final: 13 residues processed: 63 average time/residue: 0.0591 time to fit residues: 5.2154 Evaluate side-chains 56 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 606 HIS Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 554 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 18 optimal weight: 0.0770 chunk 47 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.169264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.130137 restraints weight = 9772.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.129295 restraints weight = 11883.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.132088 restraints weight = 9176.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.132609 restraints weight = 6636.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.133123 restraints weight = 6787.513| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5669 Z= 0.143 Angle : 0.582 7.488 7924 Z= 0.298 Chirality : 0.039 0.151 934 Planarity : 0.005 0.079 815 Dihedral : 14.360 163.315 1209 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.92 % Allowed : 15.96 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.58 (0.35), residues: 546 helix: 0.51 (0.33), residues: 253 sheet: -0.33 (0.77), residues: 51 loop : -1.34 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 108 TYR 0.015 0.001 TYR B 391 PHE 0.019 0.001 PHE B 56 TRP 0.029 0.002 TRP A 465 HIS 0.006 0.001 HIS B 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 5668) covalent geometry : angle 0.58173 / 0.30 ( 7924) hydrogen bonds : bond 0.04096 / 2.47 ( 225) hydrogen bonds : angle 4.18984 / 2.79 ( 623) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7790 (t0) cc_final: 0.7495 (t0) REVERT: B 33 GLN cc_start: 0.7657 (pp30) cc_final: 0.7378 (pp30) REVERT: B 100 VAL cc_start: 0.7545 (OUTLIER) cc_final: 0.7105 (p) REVERT: B 545 ASN cc_start: 0.7777 (p0) cc_final: 0.7071 (p0) outliers start: 13 outliers final: 11 residues processed: 54 average time/residue: 0.0596 time to fit residues: 4.4100 Evaluate side-chains 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 554 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.169764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.131725 restraints weight = 9777.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.131892 restraints weight = 10957.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.133837 restraints weight = 9448.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.134087 restraints weight = 6615.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.134969 restraints weight = 6503.800| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5669 Z= 0.137 Angle : 0.561 6.852 7924 Z= 0.288 Chirality : 0.038 0.142 934 Planarity : 0.005 0.085 815 Dihedral : 14.219 161.828 1209 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.15 % Allowed : 15.96 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.43 (0.35), residues: 546 helix: 0.67 (0.33), residues: 260 sheet: -0.35 (0.79), residues: 49 loop : -1.34 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 484 TYR 0.015 0.001 TYR B 391 PHE 0.021 0.001 PHE B 56 TRP 0.035 0.002 TRP A 465 HIS 0.006 0.001 HIS B 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 5668) covalent geometry : angle 0.56102 / 0.29 ( 7924) hydrogen bonds : bond 0.04031 / 2.44 ( 225) hydrogen bonds : angle 4.15076 / 2.74 ( 623) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7648 (t0) cc_final: 0.7350 (t0) REVERT: B 33 GLN cc_start: 0.7615 (pp30) cc_final: 0.7373 (pp30) REVERT: B 137 ASN cc_start: 0.7092 (t0) cc_final: 0.6877 (t0) REVERT: B 545 ASN cc_start: 0.7736 (p0) cc_final: 0.7074 (p0) outliers start: 14 outliers final: 10 residues processed: 57 average time/residue: 0.0467 time to fit residues: 3.8752 Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 554 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 0.0030 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.170549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.132562 restraints weight = 9775.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.132004 restraints weight = 10931.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.134221 restraints weight = 9466.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.134262 restraints weight = 6741.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.134762 restraints weight = 6524.947| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5669 Z= 0.126 Angle : 0.570 10.757 7924 Z= 0.291 Chirality : 0.038 0.148 934 Planarity : 0.005 0.086 815 Dihedral : 14.200 161.808 1209 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.92 % Allowed : 17.75 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.33 (0.36), residues: 546 helix: 0.81 (0.34), residues: 259 sheet: -0.29 (0.76), residues: 51 loop : -1.35 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 58 TYR 0.015 0.001 TYR B 391 PHE 0.021 0.001 PHE B 56 TRP 0.038 0.002 TRP A 465 HIS 0.007 0.001 HIS B 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 5668) covalent geometry : angle 0.57041 / 0.29 ( 7924) hydrogen bonds : bond 0.03831 / 2.32 ( 225) hydrogen bonds : angle 4.19562 / 2.79 ( 623) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7679 (t0) cc_final: 0.7380 (t0) REVERT: B 33 GLN cc_start: 0.7632 (pp30) cc_final: 0.7338 (pp30) REVERT: B 40 LYS cc_start: 0.7496 (ptpp) cc_final: 0.7219 (ptpp) REVERT: B 545 ASN cc_start: 0.7762 (p0) cc_final: 0.7052 (p0) outliers start: 13 outliers final: 9 residues processed: 52 average time/residue: 0.0460 time to fit residues: 3.4396 Evaluate side-chains 47 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 554 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.169141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.130356 restraints weight = 9751.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.130761 restraints weight = 10458.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.132768 restraints weight = 9502.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.133534 restraints weight = 6649.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.133985 restraints weight = 6956.687| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5669 Z= 0.161 Angle : 0.589 6.571 7924 Z= 0.304 Chirality : 0.039 0.155 934 Planarity : 0.005 0.090 815 Dihedral : 14.215 161.404 1209 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.37 % Allowed : 17.08 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.40 (0.36), residues: 546 helix: 0.76 (0.33), residues: 259 sheet: -0.11 (0.75), residues: 54 loop : -1.49 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 58 TYR 0.014 0.001 TYR B 391 PHE 0.016 0.001 PHE B 56 TRP 0.034 0.002 TRP A 465 HIS 0.007 0.001 HIS B 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 5668) covalent geometry : angle 0.58922 / 0.30 ( 7924) hydrogen bonds : bond 0.04225 / 2.55 ( 225) hydrogen bonds : angle 4.25168 / 2.81 ( 623) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7827 (t0) cc_final: 0.7471 (t0) REVERT: B 40 LYS cc_start: 0.7520 (ptpp) cc_final: 0.7239 (ptpp) REVERT: B 545 ASN cc_start: 0.7922 (p0) cc_final: 0.7237 (p0) outliers start: 15 outliers final: 13 residues processed: 57 average time/residue: 0.0612 time to fit residues: 4.7712 Evaluate side-chains 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 606 HIS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 554 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.171187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.133023 restraints weight = 9665.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.132412 restraints weight = 10472.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.135318 restraints weight = 9053.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.134897 restraints weight = 6685.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.135893 restraints weight = 6567.015| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5669 Z= 0.120 Angle : 0.550 6.738 7924 Z= 0.283 Chirality : 0.037 0.154 934 Planarity : 0.005 0.086 815 Dihedral : 14.095 161.468 1209 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.92 % Allowed : 17.75 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.36), residues: 546 helix: 0.91 (0.34), residues: 259 sheet: -0.42 (0.75), residues: 51 loop : -1.34 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 58 TYR 0.016 0.001 TYR B 391 PHE 0.012 0.001 PHE B 56 TRP 0.029 0.002 TRP A 465 HIS 0.007 0.001 HIS B 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 5668) covalent geometry : angle 0.55001 / 0.28 ( 7924) hydrogen bonds : bond 0.03720 / 2.25 ( 225) hydrogen bonds : angle 4.15618 / 2.74 ( 623) Misc. bond : bond 0.00007 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7638 (t0) cc_final: 0.7390 (t0) REVERT: B 40 LYS cc_start: 0.7522 (ptpp) cc_final: 0.7227 (ptpp) outliers start: 13 outliers final: 12 residues processed: 53 average time/residue: 0.0574 time to fit residues: 4.4452 Evaluate side-chains 50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 606 HIS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 554 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN ** B 517 HIS ** 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 = 0.4374 r_free = 0.4374 target = 0.168656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130212 restraints weight = 9787.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.129906 restraints weight = 11906.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.132236 restraints weight = 9653.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.132140 restraints weight = 6471.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.132750 restraints weight = 6846.288| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5669 Z= 0.194 Angle : 0.628 6.970 7924 Z= 0.324 Chirality : 0.040 0.156 934 Planarity : 0.006 0.089 815 Dihedral : 14.187 161.111 1209 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.37 % Allowed : 17.75 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.35 (0.36), residues: 546 helix: 0.83 (0.34), residues: 254 sheet: -0.31 (0.75), residues: 54 loop : -1.37 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 108 TYR 0.014 0.001 TYR B 391 PHE 0.013 0.001 PHE B 44 TRP 0.043 0.002 TRP A 465 HIS 0.007 0.002 HIS B 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 5668) covalent geometry : angle 0.62827 / 0.32 ( 7924) hydrogen bonds : bond 0.04537 / 2.73 ( 225) hydrogen bonds : angle 4.29469 / 2.83 ( 623) Misc. bond : bond 0.00012 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 844.82 seconds wall clock time: 15 minutes 17.30 seconds (917.30 seconds total)