Starting phenix.real_space_refine on Sun Apr 5 02:08:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lk2_63161/04_2026/9lk2_63161.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lk2_63161/04_2026/9lk2_63161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lk2_63161/04_2026/9lk2_63161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lk2_63161/04_2026/9lk2_63161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lk2_63161/04_2026/9lk2_63161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lk2_63161/04_2026/9lk2_63161.map" } resolution = 3.37 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4519 2.51 5 N 1231 2.21 5 O 1321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7117 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5711 Classifications: {'peptide': 720} Link IDs: {'PTRANS': 22, 'TRANS': 697} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "C" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 90} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Time building chain proxies: 1.63, per 1000 atoms: 0.23 Number of scatterers: 7117 At special positions: 0 Unit cell: (76.8, 98.4, 127.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1321 8.00 N 1231 7.00 C 4519 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 234.9 milliseconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1726 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 4 sheets defined 55.0% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.716A pdb=" N PHE A 33 " --> pdb=" O HIS A 29 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 29 through 34' Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 51 through 66 Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.594A pdb=" N ILE A 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 removed outlier: 3.845A pdb=" N CYS A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.569A pdb=" N SER A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.707A pdb=" N GLU A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.569A pdb=" N GLN A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.664A pdb=" N HIS A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 removed outlier: 3.612A pdb=" N LYS A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 Processing helix chain 'A' and resid 400 through 418 removed outlier: 4.138A pdb=" N ASP A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 433 removed outlier: 3.516A pdb=" N ASN A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 440 Processing helix chain 'A' and resid 444 through 459 removed outlier: 4.015A pdb=" N ALA A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.505A pdb=" N ALA A 468 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 removed outlier: 3.930A pdb=" N GLN A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 525 removed outlier: 3.583A pdb=" N LYS A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 538 Processing helix chain 'A' and resid 540 through 551 Processing helix chain 'A' and resid 554 through 570 removed outlier: 4.013A pdb=" N LYS A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 570 " --> pdb=" O ASN A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 575 Processing helix chain 'A' and resid 580 through 592 removed outlier: 4.172A pdb=" N HIS A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 611 Processing helix chain 'A' and resid 620 through 636 removed outlier: 4.115A pdb=" N ARG A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 625 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 659 Proline residue: A 656 - end of helix Processing helix chain 'A' and resid 663 through 681 removed outlier: 3.845A pdb=" N GLN A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 691 removed outlier: 3.756A pdb=" N TYR A 685 " --> pdb=" O ASN A 681 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 704 removed outlier: 4.187A pdb=" N HIS A 697 " --> pdb=" O GLY A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 729 Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.658A pdb=" N LEU B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 34 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.872A pdb=" N GLY B 61 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 47 removed outlier: 3.517A pdb=" N LYS C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 84 removed outlier: 3.920A pdb=" N LYS C 72 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 110 removed outlier: 3.779A pdb=" N MET C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87 removed outlier: 6.684A pdb=" N ALA A 86 " --> pdb=" O ASP A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 142 removed outlier: 7.216A pdb=" N LEU A 141 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 167 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU A 242 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU A 271 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 319 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.669A pdb=" N VAL B 75 " --> pdb=" O MET B 6 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS C 32 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 10.907A pdb=" N ASP B 17 " --> pdb=" O LYS C 32 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2355 1.34 - 1.46: 1301 1.46 - 1.58: 3524 1.58 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 7251 Sorted by residual: bond pdb=" N PHE A 544 " pdb=" CA PHE A 544 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.28e-02 6.10e+03 6.65e+00 bond pdb=" N GLU A 12 " pdb=" CA GLU A 12 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.31e-02 5.83e+03 5.53e+00 bond pdb=" CA SER A 14 " pdb=" CB SER A 14 " ideal model delta sigma weight residual 1.530 1.495 0.035 1.58e-02 4.01e+03 4.95e+00 bond pdb=" N MET A 545 " pdb=" CA MET A 545 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.20e-02 6.94e+03 3.92e+00 bond pdb=" N GLU A 11 " pdb=" CA GLU A 11 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 3.78e+00 ... (remaining 7246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 9710 2.49 - 4.97: 97 4.97 - 7.46: 7 7.46 - 9.95: 1 9.95 - 12.44: 1 Bond angle restraints: 9816 Sorted by residual: angle pdb=" N GLU A 11 " pdb=" CA GLU A 11 " pdb=" C GLU A 11 " ideal model delta sigma weight residual 111.28 106.43 4.85 1.09e+00 8.42e-01 1.98e+01 angle pdb=" CA GLU A 12 " pdb=" C GLU A 12 " pdb=" O GLU A 12 " ideal model delta sigma weight residual 121.94 118.01 3.93 1.15e+00 7.56e-01 1.17e+01 angle pdb=" N GLU A 12 " pdb=" CA GLU A 12 " pdb=" C GLU A 12 " ideal model delta sigma weight residual 110.53 106.26 4.27 1.29e+00 6.01e-01 1.10e+01 angle pdb=" CA PHE A 544 " pdb=" CB PHE A 544 " pdb=" CG PHE A 544 " ideal model delta sigma weight residual 113.80 110.55 3.25 1.00e+00 1.00e+00 1.06e+01 angle pdb=" N GLY B 76 " pdb=" CA GLY B 76 " pdb=" C GLY B 76 " ideal model delta sigma weight residual 111.14 115.57 -4.43 1.46e+00 4.69e-01 9.22e+00 ... (remaining 9811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3768 17.95 - 35.90: 483 35.90 - 53.85: 129 53.85 - 71.79: 24 71.79 - 89.74: 7 Dihedral angle restraints: 4411 sinusoidal: 1774 harmonic: 2637 Sorted by residual: dihedral pdb=" CA TRP A 638 " pdb=" C TRP A 638 " pdb=" N PRO A 639 " pdb=" CA PRO A 639 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA HIS A 704 " pdb=" C HIS A 704 " pdb=" N GLU A 705 " pdb=" CA GLU A 705 " ideal model delta harmonic sigma weight residual 180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA HIS B 10 " pdb=" C HIS B 10 " pdb=" N LYS B 11 " pdb=" CA LYS B 11 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 4408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 627 0.027 - 0.054: 340 0.054 - 0.081: 108 0.081 - 0.108: 58 0.108 - 0.135: 14 Chirality restraints: 1147 Sorted by residual: chirality pdb=" CA ILE B 14 " pdb=" N ILE B 14 " pdb=" C ILE B 14 " pdb=" CB ILE B 14 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA MET A 545 " pdb=" N MET A 545 " pdb=" C MET A 545 " pdb=" CB MET A 545 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA GLU A 12 " pdb=" N GLU A 12 " pdb=" C GLU A 12 " pdb=" CB GLU A 12 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1144 not shown) Planarity restraints: 1253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 359 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO A 360 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 346 " 0.004 2.00e-02 2.50e+03 9.09e-03 1.45e+00 pdb=" CG PHE A 346 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 346 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 346 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 346 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 346 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 346 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 637 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C LYS A 637 " -0.020 2.00e-02 2.50e+03 pdb=" O LYS A 637 " 0.008 2.00e-02 2.50e+03 pdb=" N TRP A 638 " 0.007 2.00e-02 2.50e+03 ... (remaining 1250 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 3005 2.93 - 3.42: 7066 3.42 - 3.92: 10678 3.92 - 4.41: 12087 4.41 - 4.90: 20276 Nonbonded interactions: 53112 Sorted by model distance: nonbonded pdb=" O ALA A 13 " pdb=" OG SER A 14 " model vdw 2.440 3.040 nonbonded pdb=" O LYS A 637 " pdb=" CA TRP A 638 " model vdw 2.481 2.776 nonbonded pdb=" O THR A 358 " pdb=" OG1 THR A 358 " model vdw 2.498 3.040 nonbonded pdb=" O ASN G 482 " pdb=" OD1 ASP G 483 " model vdw 2.515 3.040 nonbonded pdb=" O THR A 618 " pdb=" OG1 THR A 618 " model vdw 2.531 3.040 ... (remaining 53107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 0.004 0.039 7251 Z= 0.172 Angle : 0.622 12.435 9816 Z= 0.339 Chirality : 0.040 0.135 1147 Planarity : 0.003 0.034 1253 Dihedral : 17.487 89.743 2685 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.76 % Allowed : 26.07 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.28), residues: 892 helix: 0.36 (0.24), residues: 470 sheet: -2.71 (0.71), residues: 55 loop : -1.77 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.015 0.002 TYR A 600 PHE 0.020 0.002 PHE A 346 TRP 0.015 0.002 TRP A 580 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 7251) covalent geometry : angle 0.62224 ( 9816) hydrogen bonds : bond 0.18835 ( 324) hydrogen bonds : angle 5.43835 ( 918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.6502 (t80) REVERT: A 199 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8327 (p) REVERT: A 728 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7514 (ttp-170) REVERT: B 28 LYS cc_start: 0.8256 (mttp) cc_final: 0.7659 (mmmt) REVERT: B 34 ILE cc_start: 0.7971 (mm) cc_final: 0.7737 (mt) outliers start: 14 outliers final: 9 residues processed: 102 average time/residue: 0.0885 time to fit residues: 12.1721 Evaluate side-chains 89 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 638 TRP Chi-restraints excluded: chain A residue 728 ARG Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 84 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.0370 chunk 74 optimal weight: 0.8980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 249 GLN ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.158926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.129368 restraints weight = 10753.470| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.03 r_work: 0.3618 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7251 Z= 0.112 Angle : 0.520 11.209 9816 Z= 0.267 Chirality : 0.039 0.162 1147 Planarity : 0.003 0.042 1253 Dihedral : 5.531 64.940 975 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.16 % Allowed : 23.80 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.28), residues: 892 helix: 0.62 (0.24), residues: 477 sheet: -2.29 (0.74), residues: 49 loop : -1.77 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.012 0.001 TYR A 600 PHE 0.011 0.001 PHE A 544 TRP 0.015 0.002 TRP A 580 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7251) covalent geometry : angle 0.51984 ( 9816) hydrogen bonds : bond 0.04303 ( 324) hydrogen bonds : angle 3.90026 ( 918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.6602 (t80) REVERT: A 391 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8151 (p) REVERT: A 491 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.7038 (pp) REVERT: B 28 LYS cc_start: 0.8309 (mttp) cc_final: 0.7642 (mmmt) outliers start: 41 outliers final: 18 residues processed: 126 average time/residue: 0.0837 time to fit residues: 14.3268 Evaluate side-chains 100 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 60 optimal weight: 0.0020 chunk 8 optimal weight: 0.7980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 249 GLN ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.155865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.126314 restraints weight = 10604.225| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.01 r_work: 0.3587 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7251 Z= 0.131 Angle : 0.531 12.222 9816 Z= 0.271 Chirality : 0.039 0.166 1147 Planarity : 0.003 0.034 1253 Dihedral : 4.560 57.376 961 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.29 % Allowed : 23.55 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.28), residues: 892 helix: 0.69 (0.24), residues: 482 sheet: -2.15 (0.74), residues: 49 loop : -1.82 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.016 0.002 TYR A 600 PHE 0.012 0.001 PHE A 309 TRP 0.011 0.001 TRP A 580 HIS 0.003 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7251) covalent geometry : angle 0.53074 ( 9816) hydrogen bonds : bond 0.04278 ( 324) hydrogen bonds : angle 3.75353 ( 918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7097 (pm20) REVERT: A 158 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.6544 (t80) REVERT: A 391 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8242 (p) REVERT: A 491 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6988 (pp) REVERT: A 528 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8009 (p) REVERT: B 28 LYS cc_start: 0.8348 (mttp) cc_final: 0.7652 (mmmt) outliers start: 42 outliers final: 25 residues processed: 115 average time/residue: 0.0791 time to fit residues: 12.6841 Evaluate side-chains 112 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 84 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.155567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125834 restraints weight = 10783.807| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.04 r_work: 0.3574 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7251 Z= 0.132 Angle : 0.521 12.878 9816 Z= 0.267 Chirality : 0.039 0.167 1147 Planarity : 0.003 0.033 1253 Dihedral : 4.549 57.722 959 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 6.05 % Allowed : 23.55 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.28), residues: 892 helix: 0.76 (0.24), residues: 483 sheet: -2.21 (0.73), residues: 49 loop : -1.84 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.017 0.002 TYR A 600 PHE 0.013 0.001 PHE A 346 TRP 0.011 0.001 TRP A 580 HIS 0.002 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7251) covalent geometry : angle 0.52072 ( 9816) hydrogen bonds : bond 0.04095 ( 324) hydrogen bonds : angle 3.65810 ( 918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 82 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7111 (pm20) REVERT: A 158 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.6655 (t80) REVERT: A 391 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8218 (p) REVERT: A 491 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7044 (pp) REVERT: A 528 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8028 (p) REVERT: B 28 LYS cc_start: 0.8340 (mttp) cc_final: 0.7648 (mmmt) outliers start: 48 outliers final: 30 residues processed: 121 average time/residue: 0.0781 time to fit residues: 13.1678 Evaluate side-chains 117 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 84 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 0.0020 chunk 9 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.4766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.157960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.128200 restraints weight = 10770.374| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.05 r_work: 0.3605 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7251 Z= 0.106 Angle : 0.491 11.403 9816 Z= 0.253 Chirality : 0.038 0.159 1147 Planarity : 0.003 0.033 1253 Dihedral : 4.405 58.197 959 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.91 % Allowed : 23.93 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.29), residues: 892 helix: 0.98 (0.25), residues: 477 sheet: -1.85 (0.70), residues: 56 loop : -1.77 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.011 0.001 TYR A 600 PHE 0.010 0.001 PHE A 544 TRP 0.010 0.001 TRP A 580 HIS 0.002 0.000 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7251) covalent geometry : angle 0.49147 ( 9816) hydrogen bonds : bond 0.03646 ( 324) hydrogen bonds : angle 3.53076 ( 918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: A 158 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.6623 (t80) REVERT: A 391 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8131 (p) REVERT: A 491 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6990 (pp) REVERT: A 528 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.7963 (p) REVERT: B 28 LYS cc_start: 0.8311 (mttp) cc_final: 0.7629 (mmmt) REVERT: B 45 TYR cc_start: 0.6616 (m-80) cc_final: 0.6380 (m-10) outliers start: 39 outliers final: 28 residues processed: 121 average time/residue: 0.0762 time to fit residues: 12.8794 Evaluate side-chains 116 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 84 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 3 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 82 optimal weight: 0.0870 chunk 4 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.156963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127258 restraints weight = 10765.106| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.03 r_work: 0.3592 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7251 Z= 0.119 Angle : 0.519 12.715 9816 Z= 0.260 Chirality : 0.038 0.162 1147 Planarity : 0.003 0.032 1253 Dihedral : 4.415 58.327 959 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 6.05 % Allowed : 23.43 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.29), residues: 892 helix: 1.00 (0.25), residues: 478 sheet: -1.88 (0.70), residues: 56 loop : -1.74 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.014 0.001 TYR A 600 PHE 0.015 0.001 PHE A 346 TRP 0.008 0.001 TRP A 580 HIS 0.002 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7251) covalent geometry : angle 0.51894 ( 9816) hydrogen bonds : bond 0.03786 ( 324) hydrogen bonds : angle 3.54325 ( 918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 85 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: A 158 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.6640 (t80) REVERT: A 391 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8197 (p) REVERT: A 491 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.7002 (pp) REVERT: A 528 SER cc_start: 0.8430 (OUTLIER) cc_final: 0.7968 (p) REVERT: B 28 LYS cc_start: 0.8325 (mttp) cc_final: 0.7633 (mmmt) REVERT: B 45 TYR cc_start: 0.6596 (m-80) cc_final: 0.6317 (m-10) outliers start: 48 outliers final: 32 residues processed: 124 average time/residue: 0.0723 time to fit residues: 12.6461 Evaluate side-chains 117 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 80 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 84 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.155212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125623 restraints weight = 10745.442| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.04 r_work: 0.3568 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7251 Z= 0.125 Angle : 0.525 12.574 9816 Z= 0.265 Chirality : 0.039 0.162 1147 Planarity : 0.003 0.033 1253 Dihedral : 4.481 58.551 959 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.79 % Allowed : 23.80 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.28), residues: 892 helix: 0.98 (0.24), residues: 483 sheet: -1.93 (0.69), residues: 56 loop : -1.80 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.014 0.001 TYR A 600 PHE 0.010 0.001 PHE A 544 TRP 0.008 0.001 TRP A 580 HIS 0.003 0.000 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7251) covalent geometry : angle 0.52493 ( 9816) hydrogen bonds : bond 0.03863 ( 324) hydrogen bonds : angle 3.54594 ( 918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 82 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7127 (pm20) REVERT: A 158 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.6617 (t80) REVERT: A 391 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8198 (p) REVERT: A 491 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6968 (pp) REVERT: B 28 LYS cc_start: 0.8343 (mttp) cc_final: 0.7640 (mmmt) REVERT: B 45 TYR cc_start: 0.6647 (m-80) cc_final: 0.6370 (m-10) outliers start: 46 outliers final: 28 residues processed: 118 average time/residue: 0.0760 time to fit residues: 12.4786 Evaluate side-chains 113 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 84 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 0.0050 chunk 46 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.157583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.128278 restraints weight = 10803.471| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 3.02 r_work: 0.3628 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7251 Z= 0.107 Angle : 0.509 12.371 9816 Z= 0.257 Chirality : 0.038 0.156 1147 Planarity : 0.003 0.032 1253 Dihedral : 4.349 58.831 959 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.53 % Allowed : 24.69 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.29), residues: 892 helix: 1.05 (0.25), residues: 483 sheet: -1.88 (0.69), residues: 56 loop : -1.75 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.011 0.001 TYR C 76 PHE 0.018 0.001 PHE A 346 TRP 0.008 0.001 TRP A 580 HIS 0.002 0.000 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7251) covalent geometry : angle 0.50933 ( 9816) hydrogen bonds : bond 0.03553 ( 324) hydrogen bonds : angle 3.49462 ( 918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: A 158 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.6739 (t80) REVERT: A 391 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8132 (p) REVERT: A 491 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6969 (pp) REVERT: B 28 LYS cc_start: 0.8327 (mttp) cc_final: 0.7616 (mmmt) REVERT: B 45 TYR cc_start: 0.6675 (m-80) cc_final: 0.6370 (m-10) outliers start: 36 outliers final: 27 residues processed: 119 average time/residue: 0.0762 time to fit residues: 12.6911 Evaluate side-chains 112 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 84 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.156677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.127315 restraints weight = 10743.964| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.01 r_work: 0.3615 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7251 Z= 0.119 Angle : 0.532 11.998 9816 Z= 0.268 Chirality : 0.039 0.161 1147 Planarity : 0.003 0.033 1253 Dihedral : 4.398 58.909 959 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.53 % Allowed : 24.69 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.29), residues: 892 helix: 1.08 (0.25), residues: 482 sheet: -1.47 (0.64), residues: 66 loop : -1.73 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.014 0.001 TYR A 600 PHE 0.010 0.001 PHE A 544 TRP 0.007 0.001 TRP A 580 HIS 0.003 0.000 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7251) covalent geometry : angle 0.53171 ( 9816) hydrogen bonds : bond 0.03732 ( 324) hydrogen bonds : angle 3.51237 ( 918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: A 158 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.6751 (t80) REVERT: A 391 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8183 (p) REVERT: A 491 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6977 (pp) REVERT: B 28 LYS cc_start: 0.8318 (mttp) cc_final: 0.7637 (mmmt) REVERT: B 45 TYR cc_start: 0.6670 (m-80) cc_final: 0.6352 (m-10) outliers start: 36 outliers final: 29 residues processed: 113 average time/residue: 0.0775 time to fit residues: 12.2656 Evaluate side-chains 114 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 65 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 73 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 chunk 60 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.159101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.129975 restraints weight = 10697.699| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.01 r_work: 0.3630 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7251 Z= 0.100 Angle : 0.518 11.837 9816 Z= 0.260 Chirality : 0.038 0.152 1147 Planarity : 0.003 0.032 1253 Dihedral : 4.234 59.412 959 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.27 % Allowed : 25.82 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.29), residues: 892 helix: 1.19 (0.25), residues: 483 sheet: -1.49 (0.63), residues: 66 loop : -1.66 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.010 0.001 TYR C 76 PHE 0.022 0.001 PHE A 346 TRP 0.009 0.001 TRP A 669 HIS 0.003 0.000 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7251) covalent geometry : angle 0.51811 ( 9816) hydrogen bonds : bond 0.03261 ( 324) hydrogen bonds : angle 3.45525 ( 918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.6736 (t80) REVERT: A 391 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8073 (p) REVERT: A 491 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6883 (pp) REVERT: A 579 MET cc_start: 0.7989 (mmm) cc_final: 0.7758 (mmm) REVERT: B 28 LYS cc_start: 0.8249 (mttp) cc_final: 0.7567 (mmmt) REVERT: B 45 TYR cc_start: 0.6664 (m-80) cc_final: 0.6326 (m-10) outliers start: 26 outliers final: 18 residues processed: 110 average time/residue: 0.0802 time to fit residues: 12.2770 Evaluate side-chains 107 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 22 optimal weight: 0.0030 chunk 29 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.159050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129877 restraints weight = 10748.238| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 3.02 r_work: 0.3630 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7251 Z= 0.104 Angle : 0.522 10.551 9816 Z= 0.264 Chirality : 0.038 0.160 1147 Planarity : 0.003 0.044 1253 Dihedral : 4.182 59.685 958 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.02 % Allowed : 26.20 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.29), residues: 892 helix: 1.28 (0.25), residues: 477 sheet: -1.48 (0.62), residues: 66 loop : -1.70 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.010 0.001 TYR C 76 PHE 0.009 0.001 PHE A 544 TRP 0.008 0.001 TRP A 669 HIS 0.002 0.000 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7251) covalent geometry : angle 0.52243 ( 9816) hydrogen bonds : bond 0.03313 ( 324) hydrogen bonds : angle 3.41983 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1661.74 seconds wall clock time: 29 minutes 10.41 seconds (1750.41 seconds total)