Starting phenix.real_space_refine on Fri Sep 11 00:13:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7slq_25198/09_2026/7slq_25198.cif Found real_map, /net/cci-nas-00/data/ceres_data/7slq_25198/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7slq_25198/09_2026/7slq_25198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7slq_25198/09_2026/7slq_25198.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7slq_25198/09_2026/7slq_25198.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7slq_25198/09_2026/7slq_25198.cif" model { file = "/net/cci-nas-00/data/ceres_data/7slq_25198/09_2026/7slq_25198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7slq_25198/09_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-2.2.1-6174/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: {'RNAv2': 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: 1.16, per 1000 atoms: 0.21 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: 0.46 Conformation dependent library (CDL) restraints added in 359.6 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: 0.48 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: 0.91 Time building geometry restraints manager: 0.61 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: 7739 3.39 - 6.78: 152 6.78 - 10.17: 20 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=" 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=" N TYR B 68 " pdb=" CA TYR B 68 " pdb=" C TYR B 68 " ideal model delta sigma weight residual 109.81 118.02 -8.21 1.53e+00 4.27e-01 2.88e+01 angle pdb=" C1' G5J R 1 " pdb=" C2' G5J R 1 " pdb=" C3' G5J R 1 " ideal model delta sigma weight residual 100.24 115.93 -15.69 3.00e+00 1.11e-01 2.73e+01 ... (remaining 7919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 3086 34.50 - 69.00: 154 69.00 - 103.50: 15 103.50 - 138.00: 0 138.00 - 172.50: 2 Dihedral angle restraints: 3257 sinusoidal: 1628 harmonic: 1629 Sorted by residual: dihedral pdb=" C4' A R 301 " pdb=" C3' A R 301 " pdb=" C2' A R 301 " pdb=" C1' A R 301 " ideal model delta sinusoidal sigma weight residual 36.34 -40.24 76.58 1 3.10e+00 1.04e-01 7.67e+02 dihedral pdb=" C4' G R 300 " pdb=" C3' G R 300 " pdb=" C2' G R 300 " pdb=" C1' G R 300 " ideal model delta sinusoidal sigma weight residual 36.34 -40.15 76.49 1 3.10e+00 1.04e-01 7.66e+02 dihedral pdb=" C4' U R 327 " pdb=" C3' U R 327 " pdb=" C2' U R 327 " pdb=" C1' U R 327 " ideal model delta sinusoidal sigma weight residual 36.35 -40.04 76.38 1 3.10e+00 1.04e-01 7.64e+02 ... (remaining 3254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 753 0.082 - 0.165: 91 0.165 - 0.247: 61 0.247 - 0.329: 24 0.329 - 0.412: 5 Chirality restraints: 934 Sorted by residual: 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 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 -2.50 -2.15 -0.35 2.00e-01 2.50e+01 2.98e+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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.650 Find NCS groups from input model: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.670 ------------------------------------------------------------------------------- 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= 0.561 Angle : 1.242 16.945 7924 Z= 0.631 Chirality : 0.089 0.412 934 Planarity : 0.007 0.069 815 Dihedral : 18.130 172.502 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 0.01075 / 0.56 ( 5668) covalent geometry : angle 1.24173 / 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 : 0.206 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: 0.0950 time to fit residues: 12.7666 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 : 0.133 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.167957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.126475 restraints weight = 9350.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.126480 restraints weight = 10866.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.128309 restraints weight = 9266.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.128919 restraints weight = 6215.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.129668 restraints weight = 5907.445| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5669 Z= 0.185 Angle : 1.107 20.203 7924 Z= 0.456 Chirality : 0.102 1.297 934 Planarity : 0.005 0.076 815 Dihedral : 16.695 153.518 1215 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.47 % Allowed : 9.66 % Favored : 87.87 % 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: -1.38 (0.33), residues: 546 helix: -0.63 (0.30), residues: 260 sheet: 0.36 (0.75), residues: 52 loop : -1.44 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 488 TYR 0.008 0.001 TYR B 391 PHE 0.024 0.002 PHE B 46 TRP 0.020 0.002 TRP B 140 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 ( 5668) covalent geometry : angle 1.10744 / 0.46 ( 7924) hydrogen bonds : bond 0.04579 / 2.83 ( 225) hydrogen bonds : angle 4.32795 / 2.95 ( 623) Misc. bond : bond 0.00154 / 0.08 ( 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 : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ILE cc_start: 0.8574 (mm) cc_final: 0.8359 (mm) REVERT: A 601 ARG cc_start: 0.7271 (ttm110) cc_final: 0.7060 (ttp-170) REVERT: A 625 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8093 (ptmm) REVERT: A 636 ASN cc_start: 0.8987 (m-40) cc_final: 0.8752 (m-40) outliers start: 11 outliers final: 6 residues processed: 71 average time/residue: 0.0815 time to fit residues: 7.4400 Evaluate side-chains 56 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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: 0.0570 chunk 45 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.5704 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.168803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.130748 restraints weight = 9665.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.130458 restraints weight = 10986.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.131945 restraints weight = 10219.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.132263 restraints weight = 6757.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.132534 restraints weight = 6609.981| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5669 Z= 0.242 Angle : 0.931 12.790 7924 Z= 0.411 Chirality : 0.074 0.735 934 Planarity : 0.006 0.072 815 Dihedral : 17.238 169.210 1209 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.72 % Allowed : 10.34 % Favored : 84.94 % 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: -0.94 (0.34), residues: 546 helix: -0.14 (0.32), residues: 260 sheet: 0.37 (0.71), residues: 57 loop : -1.37 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 484 TYR 0.017 0.002 TYR A 560 PHE 0.023 0.002 PHE B 44 TRP 0.032 0.002 TRP A 465 HIS 0.007 0.002 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 ( 5668) covalent geometry : angle 0.93150 / 0.41 ( 7924) hydrogen bonds : bond 0.05183 / 3.13 ( 225) hydrogen bonds : angle 4.43094 / 2.99 ( 623) Misc. bond : bond 0.00054 / 0.03 ( 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: 21 poor density : 54 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 ILE cc_start: 0.8682 (mm) cc_final: 0.8458 (mm) REVERT: A 576 ASP cc_start: 0.7748 (t0) cc_final: 0.7366 (t0) REVERT: B 33 GLN cc_start: 0.7576 (pp30) cc_final: 0.7256 (pp30) REVERT: B 40 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7373 (ptpp) REVERT: B 545 ASN cc_start: 0.7784 (m110) cc_final: 0.7160 (t0) outliers start: 21 outliers final: 9 residues processed: 69 average time/residue: 0.0699 time to fit residues: 6.4953 Evaluate side-chains 53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 661 TYR Chi-restraints excluded: chain A residue 678 VAL 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 Chi-restraints excluded: chain B residue 554 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4420 r_free = 0.4420 target = 0.173223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.135548 restraints weight = 9533.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135427 restraints weight = 10262.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.137197 restraints weight = 9504.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.137710 restraints weight = 6329.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.138084 restraints weight = 6238.115| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5669 Z= 0.131 Angle : 0.780 10.610 7924 Z= 0.342 Chirality : 0.066 0.506 934 Planarity : 0.005 0.075 815 Dihedral : 16.904 167.733 1209 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.15 % Allowed : 14.38 % Favored : 82.47 % 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: -0.59 (0.35), residues: 546 helix: 0.39 (0.33), residues: 260 sheet: 0.28 (0.74), residues: 56 loop : -1.44 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 108 TYR 0.012 0.001 TYR B 391 PHE 0.013 0.001 PHE B 497 TRP 0.026 0.002 TRP A 465 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 5668) covalent geometry : angle 0.78044 / 0.34 ( 7924) hydrogen bonds : bond 0.03821 / 2.30 ( 225) hydrogen bonds : angle 3.98315 / 2.68 ( 623) Misc. bond : bond 0.00020 / 0.01 ( 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 62 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 461 ILE cc_start: 0.8572 (mm) cc_final: 0.8315 (mm) REVERT: B 40 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7462 (ptpp) outliers start: 14 outliers final: 8 residues processed: 59 average time/residue: 0.0729 time to fit residues: 5.8141 Evaluate side-chains 53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 661 TYR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 159 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4388 r_free = 0.4388 target = 0.170062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.131600 restraints weight = 9844.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.131979 restraints weight = 11229.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.133389 restraints weight = 9483.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.133935 restraints weight = 6251.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.134419 restraints weight = 6169.142| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5669 Z= 0.189 Angle : 0.825 10.833 7924 Z= 0.364 Chirality : 0.066 0.520 934 Planarity : 0.005 0.079 815 Dihedral : 16.897 166.318 1209 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.92 % Allowed : 15.73 % Favored : 81.35 % 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: 0.39 (0.33), residues: 260 sheet: 0.22 (0.76), residues: 54 loop : -1.41 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 108 TYR 0.012 0.001 TYR B 391 PHE 0.012 0.001 PHE B 44 TRP 0.037 0.002 TRP A 465 HIS 0.005 0.002 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 5668) covalent geometry : angle 0.82498 / 0.36 ( 7924) hydrogen bonds : bond 0.04417 / 2.64 ( 225) hydrogen bonds : angle 4.22565 / 2.85 ( 623) Misc. bond : bond 0.00009 / 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 57 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 461 ILE cc_start: 0.8576 (mm) cc_final: 0.8364 (mm) REVERT: A 576 ASP cc_start: 0.7812 (t0) cc_final: 0.7447 (t0) REVERT: B 40 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7541 (ptpp) REVERT: B 79 LYS cc_start: 0.7505 (mtmt) cc_final: 0.7127 (ptpt) REVERT: B 545 ASN cc_start: 0.7677 (p0) cc_final: 0.7049 (p0) outliers start: 13 outliers final: 8 residues processed: 55 average time/residue: 0.0629 time to fit residues: 4.8829 Evaluate side-chains 50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 47 optimal weight: 0.0070 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN B 530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.170529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.133060 restraints weight = 9696.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.131159 restraints weight = 12706.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.133088 restraints weight = 10649.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.136585 restraints weight = 7199.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.135429 restraints weight = 6694.270| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4357 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= 0.175 Angle : 0.796 10.226 7924 Z= 0.350 Chirality : 0.063 0.456 934 Planarity : 0.005 0.079 815 Dihedral : 16.623 165.396 1209 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.72 % Allowed : 15.73 % 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: -0.64 (0.35), residues: 546 helix: 0.34 (0.32), residues: 267 sheet: 0.08 (0.75), residues: 56 loop : -1.45 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 484 TYR 0.012 0.001 TYR B 391 PHE 0.010 0.001 PHE B 44 TRP 0.030 0.002 TRP A 465 HIS 0.007 0.001 HIS B 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 ( 5668) covalent geometry : angle 0.79562 / 0.35 ( 7924) hydrogen bonds : bond 0.04214 / 2.53 ( 225) hydrogen bonds : angle 4.14437 / 2.81 ( 623) Misc. bond : bond 0.00001 / 0.00 ( 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 64 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 ILE cc_start: 0.8614 (mm) cc_final: 0.8384 (mm) REVERT: A 576 ASP cc_start: 0.7746 (t0) cc_final: 0.7427 (t0) REVERT: B 532 TYR cc_start: 0.7006 (t80) cc_final: 0.6675 (t80) REVERT: B 545 ASN cc_start: 0.7706 (p0) cc_final: 0.7126 (p0) outliers start: 21 outliers final: 14 residues processed: 60 average time/residue: 0.0576 time to fit residues: 4.9610 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 446 ASP Chi-restraints excluded: chain A residue 450 LEU 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 33 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 409 ILE 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: 4.9990 chunk 2 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 0.0470 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 0.0570 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.173775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.134638 restraints weight = 9774.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.133802 restraints weight = 11254.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.136802 restraints weight = 9007.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.137531 restraints weight = 5946.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.138335 restraints weight = 6543.459| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5669 Z= 0.118 Angle : 0.732 8.965 7924 Z= 0.321 Chirality : 0.060 0.365 934 Planarity : 0.005 0.085 815 Dihedral : 16.428 165.129 1209 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.15 % Allowed : 17.08 % Favored : 79.78 % 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: -0.39 (0.35), residues: 546 helix: 0.57 (0.33), residues: 266 sheet: 0.24 (0.75), residues: 56 loop : -1.37 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 488 TYR 0.015 0.001 TYR B 391 PHE 0.020 0.001 PHE B 46 TRP 0.026 0.001 TRP A 465 HIS 0.007 0.001 HIS B 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 5668) covalent geometry : angle 0.73220 / 0.32 ( 7924) hydrogen bonds : bond 0.03596 / 2.14 ( 225) hydrogen bonds : angle 4.04241 / 2.71 ( 623) Misc. bond : bond 0.00000 / 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 58 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 TRP cc_start: 0.8226 (m-10) cc_final: 0.7833 (m-90) REVERT: B 545 ASN cc_start: 0.7855 (p0) cc_final: 0.7320 (p0) outliers start: 14 outliers final: 11 residues processed: 56 average time/residue: 0.0577 time to fit residues: 4.6584 Evaluate side-chains 53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 554 VAL Chi-restraints excluded: chain A residue 606 HIS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 159 TYR 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: 10.0000 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.171492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.133763 restraints weight = 9781.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.132969 restraints weight = 11492.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.135125 restraints weight = 10102.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.135360 restraints weight = 6566.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135618 restraints weight = 6735.591| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5669 Z= 0.158 Angle : 0.760 9.193 7924 Z= 0.338 Chirality : 0.061 0.418 934 Planarity : 0.005 0.087 815 Dihedral : 16.425 164.171 1209 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.37 % Allowed : 17.53 % Favored : 79.10 % 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: -0.39 (0.36), residues: 546 helix: 0.59 (0.33), residues: 266 sheet: 0.07 (0.75), residues: 56 loop : -1.35 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.013 0.001 TYR B 391 PHE 0.013 0.001 PHE B 56 TRP 0.045 0.002 TRP A 465 HIS 0.007 0.001 HIS B 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 5668) covalent geometry : angle 0.75991 / 0.34 ( 7924) hydrogen bonds : bond 0.03992 / 2.36 ( 225) hydrogen bonds : angle 4.06635 / 2.73 ( 623) Misc. bond : bond 0.00009 / 0.00 ( 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 59 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7719 (t0) cc_final: 0.7335 (t0) REVERT: B 33 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7571 (pp30) REVERT: B 137 ASN cc_start: 0.7111 (t0) cc_final: 0.6871 (t0) REVERT: B 545 ASN cc_start: 0.7882 (p0) cc_final: 0.7288 (p0) outliers start: 15 outliers final: 12 residues processed: 58 average time/residue: 0.0612 time to fit residues: 5.1261 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 : 0.175 ------------------------------------------------------------------------------- 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 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 661 TYR Chi-restraints excluded: chain B residue 33 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 409 ILE 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: 0.8980 chunk 52 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.169920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.131953 restraints weight = 9772.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.130575 restraints weight = 12000.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.132953 restraints weight = 10453.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.133155 restraints weight = 6844.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.133786 restraints weight = 6899.656| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5669 Z= 0.194 Angle : 0.800 9.643 7924 Z= 0.355 Chirality : 0.062 0.467 934 Planarity : 0.005 0.090 815 Dihedral : 16.464 163.771 1209 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.60 % Allowed : 17.53 % 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: -0.47 (0.35), residues: 546 helix: 0.59 (0.33), residues: 260 sheet: -0.12 (0.75), residues: 56 loop : -1.38 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 552 TYR 0.017 0.002 TYR B 532 PHE 0.020 0.002 PHE B 56 TRP 0.050 0.002 TRP A 465 HIS 0.007 0.002 HIS B 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 5668) covalent geometry : angle 0.79950 / 0.36 ( 7924) hydrogen bonds : bond 0.04396 / 2.60 ( 225) hydrogen bonds : angle 4.24435 / 2.83 ( 623) Misc. bond : bond 0.00012 / 0.01 ( 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: 16 poor density : 43 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7770 (t0) cc_final: 0.7388 (t0) outliers start: 16 outliers final: 15 residues processed: 58 average time/residue: 0.0589 time to fit residues: 4.9063 Evaluate side-chains 57 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 476 ASP Chi-restraints excluded: chain A residue 487 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 661 TYR Chi-restraints excluded: chain B residue 33 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 409 ILE 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: 0.8980 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 30 optimal weight: 0.0060 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.173707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.136660 restraints weight = 9667.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.137567 restraints weight = 10351.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.139477 restraints weight = 9272.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.139280 restraints weight = 6286.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.140027 restraints weight = 6014.533| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5669 Z= 0.122 Angle : 0.734 9.705 7924 Z= 0.328 Chirality : 0.059 0.367 934 Planarity : 0.005 0.090 815 Dihedral : 16.330 164.083 1209 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.15 % Allowed : 17.75 % Favored : 79.10 % 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: -0.28 (0.36), residues: 546 helix: 0.69 (0.34), residues: 266 sheet: 0.15 (0.75), residues: 56 loop : -1.30 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 30 TYR 0.015 0.001 TYR B 391 PHE 0.025 0.001 PHE B 56 TRP 0.025 0.002 TRP A 465 HIS 0.007 0.001 HIS B 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 5668) covalent geometry : angle 0.73384 / 0.33 ( 7924) hydrogen bonds : bond 0.03688 / 2.21 ( 225) hydrogen bonds : angle 4.15502 / 2.75 ( 623) Misc. bond : bond 0.00004 / 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 56 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 TRP cc_start: 0.8161 (m-10) cc_final: 0.7876 (m-90) REVERT: B 545 ASN cc_start: 0.7941 (p0) cc_final: 0.7238 (p0) outliers start: 14 outliers final: 12 residues processed: 55 average time/residue: 0.0559 time to fit residues: 4.4585 Evaluate side-chains 54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 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 661 TYR Chi-restraints excluded: chain B residue 33 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 554 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.172028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.134182 restraints weight = 9798.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.133329 restraints weight = 11115.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.135535 restraints weight = 9562.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.136459 restraints weight = 6685.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.136843 restraints weight = 6934.844| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4991 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= 0.153 Angle : 0.758 9.261 7924 Z= 0.339 Chirality : 0.060 0.404 934 Planarity : 0.005 0.092 815 Dihedral : 16.334 163.627 1209 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.15 % Allowed : 17.98 % 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: -0.27 (0.36), residues: 546 helix: 0.79 (0.34), residues: 260 sheet: 0.00 (0.75), residues: 56 loop : -1.34 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 488 TYR 0.018 0.001 TYR B 532 PHE 0.025 0.002 PHE B 56 TRP 0.035 0.002 TRP A 465 HIS 0.007 0.001 HIS B 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 5668) covalent geometry : angle 0.75767 / 0.34 ( 7924) hydrogen bonds : bond 0.04018 / 2.37 ( 225) hydrogen bonds : angle 4.26472 / 2.83 ( 623) Misc. bond : bond 0.00013 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 953.87 seconds wall clock time: 17 minutes 11.56 seconds (1031.56 seconds total)