Starting phenix.real_space_refine on Tue Feb 11 13:58:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7slq_25198/02_2025/7slq_25198.cif Found real_map, /net/cci-nas-00/data/ceres_data/7slq_25198/02_2025/7slq_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_25198/02_2025/7slq_25198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7slq_25198/02_2025/7slq_25198.map" model { file = "/net/cci-nas-00/data/ceres_data/7slq_25198/02_2025/7slq_25198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7slq_25198/02_2025/7slq_25198.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP: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: {'GLN:plan1': 5, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 2} 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: 3.81, per 1000 atoms: 0.70 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: 1.52 Conformation dependent library (CDL) restraints added in 689.1 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 48.8% alpha, 12.7% beta 13 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.84 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: 1.74 Time building geometry restraints manager: 1.70 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 - 35.50: 3273 35.50 - 71.00: 184 71.00 - 106.51: 23 106.51 - 142.01: 1 142.01 - 177.51: 3 Dihedral angle restraints: 3484 sinusoidal: 1855 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=" C3' G5J R 1 " pdb=" C4' G5J R 1 " pdb=" C5' G5J R 1 " pdb=" O5' G5J R 1 " ideal model delta sinusoidal sigma weight residual 176.65 -0.86 177.51 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 3481 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: 1.580 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 17.660 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.040 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 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 5668 Z= 0.625 Angle : 1.161 16.945 7924 Z= 0.628 Chirality : 0.062 0.591 934 Planarity : 0.007 0.069 815 Dihedral : 19.871 177.509 2430 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (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 TRP 0.018 0.002 TRP A 620 HIS 0.005 0.002 HIS B 158 PHE 0.022 0.003 PHE B 168 TYR 0.022 0.003 TYR B 68 ARG 0.009 0.001 ARG A 484 *********************** 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 : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 ARG cc_start: 0.7168 (ttm110) cc_final: 0.6914 (ttp-110) outliers start: 6 outliers final: 2 residues processed: 109 average time/residue: 0.2503 time to fit residues: 33.3272 Evaluate side-chains 56 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 50 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 528 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.167629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.125672 restraints weight = 9085.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.125908 restraints weight = 10324.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.127878 restraints weight = 8969.555| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5668 Z= 0.197 Angle : 0.616 8.791 7924 Z= 0.319 Chirality : 0.041 0.196 934 Planarity : 0.005 0.076 815 Dihedral : 21.448 161.864 1442 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.70 % Allowed : 9.66 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.33), residues: 546 helix: -0.51 (0.30), residues: 258 sheet: 0.38 (0.74), residues: 52 loop : -1.44 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 140 HIS 0.004 0.001 HIS B 528 PHE 0.023 0.002 PHE B 46 TYR 0.008 0.001 TYR B 483 ARG 0.006 0.001 ARG A 488 *********************** 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 70 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 ILE cc_start: 0.8601 (mm) cc_final: 0.8395 (mm) REVERT: A 601 ARG cc_start: 0.7265 (ttm110) cc_final: 0.7059 (ttp-170) REVERT: A 625 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8112 (ptmm) REVERT: A 636 ASN cc_start: 0.8979 (m-40) cc_final: 0.8754 (m-40) outliers start: 12 outliers final: 7 residues processed: 67 average time/residue: 0.2044 time to fit residues: 17.4433 Evaluate side-chains 54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 185 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.0670 chunk 10 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 51 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.0570 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 530 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.174891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.136040 restraints weight = 9594.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135022 restraints weight = 10273.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.137566 restraints weight = 8492.856| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5668 Z= 0.135 Angle : 0.550 6.938 7924 Z= 0.286 Chirality : 0.038 0.178 934 Planarity : 0.005 0.078 815 Dihedral : 20.771 162.175 1436 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.92 % Allowed : 10.34 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.35), residues: 546 helix: 0.23 (0.32), residues: 263 sheet: 0.16 (0.69), residues: 56 loop : -1.10 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 533 HIS 0.003 0.001 HIS B 52 PHE 0.029 0.001 PHE B 56 TYR 0.010 0.001 TYR B 391 ARG 0.004 0.000 ARG A 488 *********************** 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 74 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 625 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7936 (ptmm) REVERT: B 40 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7382 (ptpp) outliers start: 13 outliers final: 5 residues processed: 69 average time/residue: 0.1823 time to fit residues: 16.5531 Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 159 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 0.0980 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 HIS B 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.171706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.133956 restraints weight = 9761.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.132892 restraints weight = 11595.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.135086 restraints weight = 10204.920| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5668 Z= 0.238 Angle : 0.612 8.947 7924 Z= 0.312 Chirality : 0.040 0.186 934 Planarity : 0.005 0.078 815 Dihedral : 20.346 161.861 1436 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.04 % Allowed : 14.16 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.35), residues: 546 helix: 0.42 (0.33), residues: 258 sheet: 0.69 (0.70), residues: 59 loop : -1.39 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 465 HIS 0.005 0.001 HIS B 52 PHE 0.026 0.002 PHE B 56 TYR 0.016 0.002 TYR A 560 ARG 0.005 0.001 ARG A 484 *********************** 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 61 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 625 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8029 (ptmm) REVERT: B 40 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7467 (ptpp) REVERT: B 545 ASN cc_start: 0.7834 (m110) cc_final: 0.7144 (t0) outliers start: 18 outliers final: 11 residues processed: 57 average time/residue: 0.1698 time to fit residues: 13.0478 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 : 0.539 ------------------------------------------------------------------------------- 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 603 ILE Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 159 TYR 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 36 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.171166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.133256 restraints weight = 9663.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.131123 restraints weight = 11230.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.133343 restraints weight = 10424.189| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5668 Z= 0.234 Angle : 0.594 8.846 7924 Z= 0.304 Chirality : 0.040 0.185 934 Planarity : 0.005 0.078 815 Dihedral : 20.272 162.289 1436 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.60 % Allowed : 15.73 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.35), residues: 546 helix: 0.67 (0.33), residues: 252 sheet: 0.22 (0.72), residues: 56 loop : -1.29 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 465 HIS 0.004 0.001 HIS B 52 PHE 0.023 0.001 PHE B 56 TYR 0.014 0.001 TYR A 560 ARG 0.004 0.000 ARG A 484 *********************** 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 55 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7760 (t0) cc_final: 0.7387 (t0) REVERT: A 625 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8158 (ptmm) REVERT: B 40 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7497 (ptpp) REVERT: B 545 ASN cc_start: 0.8095 (m110) cc_final: 0.7295 (t0) outliers start: 16 outliers final: 9 residues processed: 52 average time/residue: 0.1532 time to fit residues: 11.0963 Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TRP Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 379 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.0030 chunk 52 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.168091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.129103 restraints weight = 9445.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.128724 restraints weight = 12276.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.130753 restraints weight = 10363.097| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5668 Z= 0.169 Angle : 0.550 9.997 7924 Z= 0.277 Chirality : 0.038 0.177 934 Planarity : 0.005 0.081 815 Dihedral : 20.137 162.247 1436 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.60 % Allowed : 16.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.35), residues: 546 helix: 0.69 (0.33), residues: 260 sheet: 0.35 (0.70), residues: 58 loop : -1.40 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 465 HIS 0.003 0.001 HIS B 52 PHE 0.022 0.001 PHE B 56 TYR 0.011 0.001 TYR A 560 ARG 0.003 0.000 ARG A 488 *********************** 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 57 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7518 (ptpp) REVERT: B 79 LYS cc_start: 0.7359 (mtpt) cc_final: 0.6620 (mtpt) REVERT: B 545 ASN cc_start: 0.8197 (m110) cc_final: 0.7437 (t0) outliers start: 16 outliers final: 11 residues processed: 54 average time/residue: 0.1468 time to fit residues: 11.2726 Evaluate side-chains 52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 603 ILE Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 129 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 57 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.0030 chunk 52 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.167712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.127446 restraints weight = 9349.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.126188 restraints weight = 9983.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.128668 restraints weight = 9245.765| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5668 Z= 0.171 Angle : 0.537 7.723 7924 Z= 0.274 Chirality : 0.038 0.176 934 Planarity : 0.005 0.085 815 Dihedral : 20.036 161.886 1436 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.60 % Allowed : 16.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.36), residues: 546 helix: 0.80 (0.33), residues: 260 sheet: 0.43 (0.71), residues: 58 loop : -1.40 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 465 HIS 0.003 0.001 HIS B 52 PHE 0.020 0.001 PHE B 56 TYR 0.011 0.001 TYR B 391 ARG 0.002 0.000 ARG A 488 *********************** 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 55 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7598 (ptpp) REVERT: B 79 LYS cc_start: 0.7432 (mtpt) cc_final: 0.6605 (mtpt) outliers start: 16 outliers final: 12 residues processed: 53 average time/residue: 0.1492 time to fit residues: 11.1676 Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 603 ILE Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 129 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.168789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.128661 restraints weight = 9587.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.127760 restraints weight = 9866.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.130074 restraints weight = 9425.216| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 5668 Z= 0.153 Angle : 0.542 10.308 7924 Z= 0.274 Chirality : 0.038 0.173 934 Planarity : 0.005 0.087 815 Dihedral : 19.908 161.690 1436 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.60 % Allowed : 17.75 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.36), residues: 546 helix: 0.89 (0.34), residues: 260 sheet: 0.56 (0.71), residues: 58 loop : -1.32 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 465 HIS 0.003 0.001 HIS B 52 PHE 0.019 0.001 PHE B 46 TYR 0.011 0.001 TYR B 391 ARG 0.003 0.000 ARG B 58 *********************** 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: 16 poor density : 37 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7463 (mtpp) REVERT: B 79 LYS cc_start: 0.7550 (mtpt) cc_final: 0.6686 (mtpt) REVERT: B 545 ASN cc_start: 0.7877 (p0) cc_final: 0.7262 (p0) outliers start: 16 outliers final: 12 residues processed: 51 average time/residue: 0.1541 time to fit residues: 11.1294 Evaluate side-chains 47 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 33 GLN Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 129 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 0.0270 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.0060 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.168055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.128589 restraints weight = 9556.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.129281 restraints weight = 9713.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.131031 restraints weight = 9148.547| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5668 Z= 0.170 Angle : 0.542 7.463 7924 Z= 0.281 Chirality : 0.038 0.176 934 Planarity : 0.005 0.090 815 Dihedral : 19.835 161.455 1436 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.15 % Allowed : 18.65 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.36), residues: 546 helix: 0.96 (0.34), residues: 260 sheet: 0.55 (0.71), residues: 58 loop : -1.31 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 465 HIS 0.003 0.001 HIS B 52 PHE 0.021 0.001 PHE B 46 TYR 0.011 0.001 TYR B 391 ARG 0.002 0.000 ARG A 531 *********************** 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 50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7384 (mtpp) REVERT: B 79 LYS cc_start: 0.7532 (mtpt) cc_final: 0.6977 (mtpp) REVERT: B 545 ASN cc_start: 0.7788 (p0) cc_final: 0.7154 (p0) outliers start: 14 outliers final: 10 residues processed: 47 average time/residue: 0.1501 time to fit residues: 9.9727 Evaluate side-chains 47 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 33 GLN Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 129 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 0.0170 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.169411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.129047 restraints weight = 9459.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.128835 restraints weight = 9378.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.131139 restraints weight = 8944.843| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5668 Z= 0.151 Angle : 0.534 8.633 7924 Z= 0.273 Chirality : 0.037 0.172 934 Planarity : 0.005 0.087 815 Dihedral : 19.779 161.369 1436 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.70 % Allowed : 19.33 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.36), residues: 546 helix: 1.08 (0.34), residues: 260 sheet: 0.71 (0.71), residues: 58 loop : -1.27 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 465 HIS 0.003 0.001 HIS B 52 PHE 0.019 0.001 PHE B 46 TYR 0.011 0.001 TYR B 391 ARG 0.002 0.000 ARG B 58 ********************** 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 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7266 (mtpp) REVERT: B 79 LYS cc_start: 0.7533 (mtpt) cc_final: 0.6966 (mtpp) REVERT: B 545 ASN cc_start: 0.7882 (p0) cc_final: 0.7244 (p0) outliers start: 12 outliers final: 10 residues processed: 49 average time/residue: 0.1480 time to fit residues: 10.2222 Evaluate side-chains 48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 33 GLN Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 129 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 51 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.0060 chunk 49 optimal weight: 0.0000 chunk 19 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.172581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.133269 restraints weight = 9657.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.133631 restraints weight = 8799.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.135401 restraints weight = 9139.433| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5668 Z= 0.133 Angle : 0.511 6.551 7924 Z= 0.264 Chirality : 0.037 0.165 934 Planarity : 0.005 0.087 815 Dihedral : 19.704 161.154 1436 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.25 % Allowed : 20.45 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.37), residues: 546 helix: 1.11 (0.34), residues: 267 sheet: 0.86 (0.71), residues: 58 loop : -1.30 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 465 HIS 0.002 0.000 HIS B 52 PHE 0.019 0.001 PHE B 46 TYR 0.010 0.001 TYR B 391 ARG 0.002 0.000 ARG A 443 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1688.02 seconds wall clock time: 31 minutes 5.46 seconds (1865.46 seconds total)