Starting phenix.real_space_refine on Fri Nov 15 07:53:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2i_38856/11_2024/8y2i_38856.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2i_38856/11_2024/8y2i_38856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2i_38856/11_2024/8y2i_38856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2i_38856/11_2024/8y2i_38856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2i_38856/11_2024/8y2i_38856.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2i_38856/11_2024/8y2i_38856.cif" } resolution = 2.92 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= -0.002 sd= 0.097 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 143 5.49 5 S 20 5.16 5 C 4960 2.51 5 N 1577 2.21 5 O 1976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8676 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 587 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 5671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5671 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 35, 'TRANS': 687} Chain breaks: 4 Chain: "C" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2208 Classifications: {'RNA': 104} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 46, 'rna3p_pyr': 46} Link IDs: {'rna2p': 12, 'rna3p': 91} Chain breaks: 1 Time building chain proxies: 5.57, per 1000 atoms: 0.64 Number of scatterers: 8676 At special positions: 0 Unit cell: (109.08, 93.96, 112.32, 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 20 16.00 P 143 15.00 O 1976 8.00 N 1577 7.00 C 4960 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: 2.70 Conformation dependent library (CDL) restraints added in 705.8 milliseconds 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 4 sheets defined 48.8% alpha, 12.3% beta 43 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.667A pdb=" N HIS A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 81 removed outlier: 3.959A pdb=" N LEU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 90 removed outlier: 3.657A pdb=" N LYS A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 removed outlier: 3.888A pdb=" N TRP A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 162 removed outlier: 4.125A pdb=" N GLY A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 185 through 189 removed outlier: 4.296A pdb=" N LEU A 189 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 211 removed outlier: 3.708A pdb=" N TRP A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 removed outlier: 3.821A pdb=" N LYS A 215 " --> pdb=" O LEU A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 246 through 265 removed outlier: 3.649A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 267 No H-bonds generated for 'chain 'A' and resid 266 through 267' Processing helix chain 'A' and resid 268 through 272 removed outlier: 3.767A pdb=" N LYS A 271 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 272 " --> pdb=" O PHE A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 272' Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 300 through 316 removed outlier: 4.301A pdb=" N ALA A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 333 removed outlier: 3.651A pdb=" N LEU A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 350 through 369 Processing helix chain 'A' and resid 369 through 376 Processing helix chain 'A' and resid 379 through 399 Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.792A pdb=" N GLU A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 635 through 658 removed outlier: 3.897A pdb=" N ALA A 641 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU A 642 " --> pdb=" O ARG A 638 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 698 removed outlier: 3.556A pdb=" N MET A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 859 removed outlier: 3.552A pdb=" N GLU A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 884 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 43 removed outlier: 6.609A pdb=" N ASP A 552 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG A 541 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 554 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU A 539 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR A 556 " --> pdb=" O GLY A 537 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A 537 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR A 558 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 455 Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 455 removed outlier: 4.835A pdb=" N LEU A 428 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N SER A 475 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N GLY A 426 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 594 through 600 removed outlier: 7.262A pdb=" N LEU A 596 " --> pdb=" O ASP A 591 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP A 591 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE A 662 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 575 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ALA A 664 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N ILE A 577 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 661 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 721 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU A 663 " --> pdb=" O VAL A 721 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 804 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 115 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1077 1.29 - 1.42: 3154 1.42 - 1.55: 4606 1.55 - 1.68: 280 1.68 - 1.81: 32 Bond restraints: 9149 Sorted by residual: bond pdb=" C GLU A 370 " pdb=" O GLU A 370 " ideal model delta sigma weight residual 1.244 1.167 0.076 1.00e-02 1.00e+04 5.80e+01 bond pdb=" C LYS A 356 " pdb=" O LYS A 356 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.26e-02 6.30e+03 3.58e+01 bond pdb=" CA GLY A 413 " pdb=" C GLY A 413 " ideal model delta sigma weight residual 1.512 1.454 0.058 1.15e-02 7.56e+03 2.50e+01 bond pdb=" O3' G C 0 " pdb=" P A C 1 " ideal model delta sigma weight residual 1.607 1.548 0.059 1.50e-02 4.44e+03 1.55e+01 bond pdb=" C LYS A 356 " pdb=" N LEU A 357 " ideal model delta sigma weight residual 1.334 1.279 0.056 1.43e-02 4.89e+03 1.51e+01 ... (remaining 9144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 12606 2.01 - 4.02: 341 4.02 - 6.04: 55 6.04 - 8.05: 11 8.05 - 10.06: 6 Bond angle restraints: 13019 Sorted by residual: angle pdb=" N ARG A 334 " pdb=" CA ARG A 334 " pdb=" C ARG A 334 " ideal model delta sigma weight residual 113.16 103.10 10.06 1.24e+00 6.50e-01 6.58e+01 angle pdb=" N ASP A 156 " pdb=" CA ASP A 156 " pdb=" C ASP A 156 " ideal model delta sigma weight residual 111.14 104.53 6.61 1.08e+00 8.57e-01 3.75e+01 angle pdb=" N ASN A 45 " pdb=" CA ASN A 45 " pdb=" CB ASN A 45 " ideal model delta sigma weight residual 110.57 118.62 -8.05 1.35e+00 5.49e-01 3.56e+01 angle pdb=" C THR A 412 " pdb=" CA THR A 412 " pdb=" CB THR A 412 " ideal model delta sigma weight residual 110.79 120.66 -9.87 1.66e+00 3.63e-01 3.54e+01 angle pdb=" O4' A C -11 " pdb=" C4' A C -11 " pdb=" C3' A C -11 " ideal model delta sigma weight residual 106.10 100.44 5.66 1.00e+00 1.00e+00 3.20e+01 ... (remaining 13014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.21: 4658 21.21 - 42.42: 548 42.42 - 63.63: 257 63.63 - 84.84: 74 84.84 - 106.05: 9 Dihedral angle restraints: 5546 sinusoidal: 3475 harmonic: 2071 Sorted by residual: dihedral pdb=" C THR A 412 " pdb=" N THR A 412 " pdb=" CA THR A 412 " pdb=" CB THR A 412 " ideal model delta harmonic sigma weight residual -122.00 -137.57 15.57 0 2.50e+00 1.60e-01 3.88e+01 dihedral pdb=" N THR A 412 " pdb=" C THR A 412 " pdb=" CA THR A 412 " pdb=" CB THR A 412 " ideal model delta harmonic sigma weight residual 123.40 134.44 -11.04 0 2.50e+00 1.60e-01 1.95e+01 dihedral pdb=" O4' U C-100 " pdb=" C1' U C-100 " pdb=" N1 U C-100 " pdb=" C2 U C-100 " ideal model delta sinusoidal sigma weight residual 232.00 167.57 64.43 1 1.70e+01 3.46e-03 1.89e+01 ... (remaining 5543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1444 0.098 - 0.196: 52 0.196 - 0.294: 5 0.294 - 0.392: 0 0.392 - 0.490: 3 Chirality restraints: 1504 Sorted by residual: chirality pdb=" CA THR A 412 " pdb=" N THR A 412 " pdb=" C THR A 412 " pdb=" CB THR A 412 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" C1' DT D -4 " pdb=" O4' DT D -4 " pdb=" C2' DT D -4 " pdb=" N1 DT D -4 " both_signs ideal model delta sigma weight residual False 2.47 2.05 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" C1' DT D -5 " pdb=" O4' DT D -5 " pdb=" C2' DT D -5 " pdb=" N1 DT D -5 " both_signs ideal model delta sigma weight residual False 2.47 2.05 0.42 2.00e-01 2.50e+01 4.36e+00 ... (remaining 1501 not shown) Planarity restraints: 1162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 731 " 0.026 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C SER A 731 " -0.088 2.00e-02 2.50e+03 pdb=" O SER A 731 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA A 732 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 385 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C GLU A 385 " -0.070 2.00e-02 2.50e+03 pdb=" O GLU A 385 " 0.026 2.00e-02 2.50e+03 pdb=" N THR A 386 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 684 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C GLN A 684 " 0.065 2.00e-02 2.50e+03 pdb=" O GLN A 684 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR A 685 " -0.023 2.00e-02 2.50e+03 ... (remaining 1159 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1391 2.75 - 3.29: 8245 3.29 - 3.83: 16412 3.83 - 4.36: 19783 4.36 - 4.90: 29550 Nonbonded interactions: 75381 Sorted by model distance: nonbonded pdb=" N ARG A 240 " pdb=" OP1 G C 6 " model vdw 2.219 3.120 nonbonded pdb=" O CYS A 91 " pdb=" OG SER A 92 " model vdw 2.221 3.040 nonbonded pdb=" OP1 DA B 23 " pdb=" NZ LYS A 488 " model vdw 2.236 3.120 nonbonded pdb=" O GLU A 440 " pdb=" O4 U C-101 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLN A 878 " pdb=" NZ LYS A 882 " model vdw 2.271 3.120 ... (remaining 75376 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: 1.470 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.150 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 9149 Z= 0.372 Angle : 0.793 10.060 13019 Z= 0.494 Chirality : 0.047 0.490 1504 Planarity : 0.006 0.057 1162 Dihedral : 21.145 106.055 4214 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Rotamer: Outliers : 0.71 % Allowed : 1.07 % Favored : 98.22 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % 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: -2.35 (0.31), residues: 713 helix: -0.72 (0.28), residues: 320 sheet: -1.56 (0.48), residues: 100 loop : -2.45 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 PHE 0.036 0.002 PHE A 717 TYR 0.017 0.002 TYR A 241 ARG 0.012 0.001 ARG A 874 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.706 Fit side-chains REVERT: A 22 GLN cc_start: 0.7509 (mt0) cc_final: 0.7156 (mm110) REVERT: A 90 LYS cc_start: 0.6715 (ptpt) cc_final: 0.6354 (pptt) REVERT: A 262 TYR cc_start: 0.8103 (t80) cc_final: 0.7790 (t80) REVERT: A 384 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6363 (mt-10) REVERT: A 390 LYS cc_start: 0.6322 (mmtt) cc_final: 0.5923 (tppt) REVERT: A 410 GLN cc_start: 0.6034 (OUTLIER) cc_final: 0.5682 (tt0) REVERT: A 693 GLU cc_start: 0.7223 (mt-10) cc_final: 0.7013 (mt-10) REVERT: A 850 ARG cc_start: 0.6083 (mtt-85) cc_final: 0.4648 (mtt-85) REVERT: A 851 LYS cc_start: 0.6813 (tttp) cc_final: 0.6474 (tptp) outliers start: 4 outliers final: 2 residues processed: 108 average time/residue: 1.4849 time to fit residues: 169.2419 Evaluate side-chains 80 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 733 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.0670 chunk 77 optimal weight: 7.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 303 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9149 Z= 0.244 Angle : 0.656 6.488 13019 Z= 0.341 Chirality : 0.037 0.171 1504 Planarity : 0.006 0.088 1162 Dihedral : 22.066 102.801 2845 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 3.20 % Allowed : 11.19 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.61 (0.32), residues: 713 helix: -0.03 (0.29), residues: 320 sheet: -1.30 (0.49), residues: 104 loop : -2.12 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 520 HIS 0.006 0.001 HIS A 657 PHE 0.021 0.002 PHE A 717 TYR 0.019 0.002 TYR A 725 ARG 0.012 0.001 ARG A 855 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.724 Fit side-chains REVERT: A 22 GLN cc_start: 0.7286 (mt0) cc_final: 0.6933 (mm110) REVERT: A 90 LYS cc_start: 0.6663 (ptpt) cc_final: 0.6259 (pptt) REVERT: A 133 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6940 (mtt) REVERT: A 155 TYR cc_start: 0.7459 (t80) cc_final: 0.6907 (t80) REVERT: A 262 TYR cc_start: 0.8118 (t80) cc_final: 0.7878 (t80) REVERT: A 384 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6429 (mt-10) REVERT: A 390 LYS cc_start: 0.6249 (mmtt) cc_final: 0.5621 (ptmm) REVERT: A 410 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.6246 (tt0) REVERT: A 489 LYS cc_start: 0.7874 (ptpp) cc_final: 0.7509 (pttt) REVERT: A 636 ARG cc_start: 0.6967 (mmt180) cc_final: 0.6698 (mmm-85) REVERT: A 693 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6894 (mt-10) REVERT: A 698 GLU cc_start: 0.7310 (tt0) cc_final: 0.6732 (tt0) REVERT: A 850 ARG cc_start: 0.5780 (mtt-85) cc_final: 0.4575 (mtt-85) REVERT: A 851 LYS cc_start: 0.6558 (tttp) cc_final: 0.6191 (tptt) REVERT: A 855 ARG cc_start: 0.5143 (tpp-160) cc_final: 0.4745 (tmm160) outliers start: 18 outliers final: 5 residues processed: 86 average time/residue: 1.3930 time to fit residues: 126.8509 Evaluate side-chains 77 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9149 Z= 0.228 Angle : 0.613 6.387 13019 Z= 0.319 Chirality : 0.035 0.173 1504 Planarity : 0.005 0.060 1162 Dihedral : 21.940 101.938 2844 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 3.91 % Allowed : 13.85 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.31), residues: 713 helix: 0.17 (0.29), residues: 324 sheet: -1.33 (0.48), residues: 98 loop : -1.99 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 520 HIS 0.005 0.001 HIS A 110 PHE 0.018 0.002 PHE A 717 TYR 0.016 0.002 TYR A 241 ARG 0.007 0.001 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.716 Fit side-chains REVERT: A 22 GLN cc_start: 0.7363 (mt0) cc_final: 0.7004 (mm110) REVERT: A 90 LYS cc_start: 0.6741 (ptpt) cc_final: 0.6222 (pptt) REVERT: A 133 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6868 (mtt) REVERT: A 153 LYS cc_start: 0.7959 (tmmt) cc_final: 0.7651 (ttpp) REVERT: A 262 TYR cc_start: 0.8027 (t80) cc_final: 0.7813 (t80) REVERT: A 303 GLN cc_start: 0.7840 (mt0) cc_final: 0.7606 (mt0) REVERT: A 390 LYS cc_start: 0.6268 (mmtt) cc_final: 0.5876 (tppt) REVERT: A 410 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.6232 (tt0) REVERT: A 489 LYS cc_start: 0.7963 (ptpp) cc_final: 0.7522 (pttp) REVERT: A 572 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6035 (tp30) REVERT: A 636 ARG cc_start: 0.6982 (mmt180) cc_final: 0.6756 (mmm-85) REVERT: A 693 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6956 (mt-10) REVERT: A 698 GLU cc_start: 0.7314 (tt0) cc_final: 0.6777 (tt0) REVERT: A 851 LYS cc_start: 0.6535 (tttp) cc_final: 0.6165 (tptt) outliers start: 22 outliers final: 5 residues processed: 92 average time/residue: 1.3751 time to fit residues: 134.5148 Evaluate side-chains 83 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 501 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9149 Z= 0.204 Angle : 0.603 6.403 13019 Z= 0.312 Chirality : 0.035 0.172 1504 Planarity : 0.005 0.090 1162 Dihedral : 21.900 101.384 2844 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 4.44 % Allowed : 13.68 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.32), residues: 713 helix: 0.34 (0.29), residues: 327 sheet: -1.27 (0.49), residues: 99 loop : -2.00 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 520 HIS 0.004 0.001 HIS A 657 PHE 0.018 0.001 PHE A 717 TYR 0.016 0.002 TYR A 241 ARG 0.009 0.000 ARG A 855 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.729 Fit side-chains REVERT: A 22 GLN cc_start: 0.7371 (mt0) cc_final: 0.7004 (mm110) REVERT: A 90 LYS cc_start: 0.6736 (ptpt) cc_final: 0.6197 (pptt) REVERT: A 133 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6926 (mtt) REVERT: A 153 LYS cc_start: 0.8044 (tmmt) cc_final: 0.7708 (ttpp) REVERT: A 262 TYR cc_start: 0.8010 (t80) cc_final: 0.7793 (t80) REVERT: A 303 GLN cc_start: 0.7825 (mt0) cc_final: 0.7588 (mt0) REVERT: A 384 GLU cc_start: 0.5727 (mt-10) cc_final: 0.5519 (tt0) REVERT: A 390 LYS cc_start: 0.6313 (mmtt) cc_final: 0.5883 (tppt) REVERT: A 410 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6146 (tt0) REVERT: A 489 LYS cc_start: 0.7943 (ptpp) cc_final: 0.7492 (pttp) REVERT: A 572 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6168 (tp30) REVERT: A 636 ARG cc_start: 0.6990 (mmt180) cc_final: 0.6758 (mmm-85) REVERT: A 698 GLU cc_start: 0.7316 (tt0) cc_final: 0.6721 (tt0) REVERT: A 848 ILE cc_start: 0.5539 (OUTLIER) cc_final: 0.5291 (tt) REVERT: A 851 LYS cc_start: 0.6606 (tttp) cc_final: 0.6250 (tptt) REVERT: A 855 ARG cc_start: 0.5001 (tpp-160) cc_final: 0.4603 (tmm160) outliers start: 25 outliers final: 10 residues processed: 96 average time/residue: 1.3179 time to fit residues: 134.5465 Evaluate side-chains 86 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 848 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 chunk 70 optimal weight: 0.0470 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.1980 chunk 73 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9149 Z= 0.168 Angle : 0.569 6.405 13019 Z= 0.299 Chirality : 0.033 0.175 1504 Planarity : 0.005 0.081 1162 Dihedral : 21.871 100.938 2844 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.55 % Allowed : 15.99 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.00 (0.32), residues: 713 helix: 0.56 (0.29), residues: 328 sheet: -1.21 (0.48), residues: 113 loop : -1.89 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 520 HIS 0.007 0.001 HIS A 14 PHE 0.012 0.001 PHE A 717 TYR 0.017 0.001 TYR A 241 ARG 0.008 0.000 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.735 Fit side-chains REVERT: A 22 GLN cc_start: 0.7377 (mt0) cc_final: 0.7014 (mm110) REVERT: A 90 LYS cc_start: 0.6759 (ptpt) cc_final: 0.6217 (pptt) REVERT: A 133 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6555 (mtp) REVERT: A 149 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6483 (pt0) REVERT: A 262 TYR cc_start: 0.8012 (t80) cc_final: 0.7705 (t80) REVERT: A 303 GLN cc_start: 0.7808 (mt0) cc_final: 0.7582 (mt0) REVERT: A 333 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7483 (mm) REVERT: A 334 ARG cc_start: 0.5647 (mmt90) cc_final: 0.5026 (mpt-90) REVERT: A 384 GLU cc_start: 0.5731 (mt-10) cc_final: 0.5471 (tt0) REVERT: A 390 LYS cc_start: 0.6322 (mmtt) cc_final: 0.5872 (tppt) REVERT: A 410 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.6247 (tt0) REVERT: A 489 LYS cc_start: 0.7869 (ptpp) cc_final: 0.7429 (pttp) REVERT: A 572 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6113 (tp30) REVERT: A 636 ARG cc_start: 0.6936 (mmt180) cc_final: 0.6728 (mmm-85) REVERT: A 848 ILE cc_start: 0.5259 (OUTLIER) cc_final: 0.4990 (tt) REVERT: A 851 LYS cc_start: 0.6481 (tttp) cc_final: 0.6143 (tptt) outliers start: 20 outliers final: 4 residues processed: 94 average time/residue: 1.3711 time to fit residues: 137.0587 Evaluate side-chains 80 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 848 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.0170 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.0670 chunk 79 optimal weight: 7.9990 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 715 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9149 Z= 0.172 Angle : 0.577 8.333 13019 Z= 0.302 Chirality : 0.033 0.165 1504 Planarity : 0.005 0.085 1162 Dihedral : 21.859 100.535 2844 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 3.37 % Allowed : 18.12 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.32), residues: 713 helix: 0.68 (0.29), residues: 328 sheet: -1.06 (0.50), residues: 109 loop : -1.89 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 520 HIS 0.006 0.001 HIS A 14 PHE 0.012 0.001 PHE A 717 TYR 0.016 0.002 TYR A 241 ARG 0.011 0.000 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7369 (mt0) cc_final: 0.7024 (mm110) REVERT: A 90 LYS cc_start: 0.6705 (ptpt) cc_final: 0.5721 (mmtm) REVERT: A 133 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6557 (mtp) REVERT: A 262 TYR cc_start: 0.8021 (t80) cc_final: 0.7736 (t80) REVERT: A 303 GLN cc_start: 0.7858 (mt0) cc_final: 0.7620 (mt0) REVERT: A 334 ARG cc_start: 0.5612 (mmt90) cc_final: 0.4961 (mpt-90) REVERT: A 390 LYS cc_start: 0.6348 (mmtt) cc_final: 0.5877 (tppt) REVERT: A 410 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.6204 (tt0) REVERT: A 489 LYS cc_start: 0.7898 (ptpp) cc_final: 0.7463 (pttp) REVERT: A 557 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8422 (mp) REVERT: A 572 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6191 (tp30) REVERT: A 636 ARG cc_start: 0.6951 (mmt180) cc_final: 0.6733 (mmm-85) REVERT: A 848 ILE cc_start: 0.5234 (OUTLIER) cc_final: 0.4985 (tt) REVERT: A 851 LYS cc_start: 0.6459 (tttp) cc_final: 0.6134 (tptt) REVERT: A 855 ARG cc_start: 0.4971 (tpp-160) cc_final: 0.4424 (tmm160) outliers start: 19 outliers final: 4 residues processed: 91 average time/residue: 1.3777 time to fit residues: 133.2042 Evaluate side-chains 82 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 848 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 51 optimal weight: 0.0030 chunk 49 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 0.0570 overall best weight: 0.4708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9149 Z= 0.178 Angle : 0.576 8.306 13019 Z= 0.301 Chirality : 0.033 0.167 1504 Planarity : 0.004 0.075 1162 Dihedral : 21.833 100.028 2844 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.02 % Allowed : 18.65 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.79 (0.32), residues: 713 helix: 0.75 (0.29), residues: 328 sheet: -1.01 (0.50), residues: 109 loop : -1.86 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 520 HIS 0.003 0.001 HIS A 110 PHE 0.014 0.001 PHE A 717 TYR 0.016 0.001 TYR A 241 ARG 0.004 0.000 ARG A 855 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.640 Fit side-chains REVERT: A 22 GLN cc_start: 0.7381 (mt0) cc_final: 0.7024 (mm110) REVERT: A 90 LYS cc_start: 0.6656 (ptpt) cc_final: 0.5988 (mttm) REVERT: A 133 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6889 (mtt) REVERT: A 262 TYR cc_start: 0.7991 (t80) cc_final: 0.7688 (t80) REVERT: A 334 ARG cc_start: 0.5552 (mmt90) cc_final: 0.4983 (mpt-90) REVERT: A 390 LYS cc_start: 0.6375 (mmtt) cc_final: 0.5885 (tppt) REVERT: A 410 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6379 (tt0) REVERT: A 489 LYS cc_start: 0.7844 (ptpp) cc_final: 0.7390 (pttp) REVERT: A 557 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8447 (mp) REVERT: A 572 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6239 (tp30) REVERT: A 636 ARG cc_start: 0.6973 (mmt180) cc_final: 0.6734 (mmm-85) REVERT: A 687 ARG cc_start: 0.6714 (mtp85) cc_final: 0.6450 (mtp-110) REVERT: A 851 LYS cc_start: 0.6469 (tttp) cc_final: 0.6137 (tptt) REVERT: A 855 ARG cc_start: 0.5130 (tpp-160) cc_final: 0.4856 (tpp-160) outliers start: 17 outliers final: 5 residues processed: 89 average time/residue: 1.3254 time to fit residues: 125.5172 Evaluate side-chains 79 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 557 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9149 Z= 0.194 Angle : 0.581 8.869 13019 Z= 0.304 Chirality : 0.034 0.164 1504 Planarity : 0.005 0.079 1162 Dihedral : 21.826 99.696 2844 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 2.49 % Allowed : 21.14 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.85 (0.32), residues: 713 helix: 0.71 (0.29), residues: 327 sheet: -1.00 (0.51), residues: 108 loop : -1.91 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 PHE 0.015 0.001 PHE A 717 TYR 0.016 0.001 TYR A 241 ARG 0.004 0.000 ARG A 855 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.689 Fit side-chains REVERT: A 22 GLN cc_start: 0.7393 (mt0) cc_final: 0.7053 (mm110) REVERT: A 90 LYS cc_start: 0.6607 (ptpt) cc_final: 0.5479 (mmtm) REVERT: A 133 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6950 (mtt) REVERT: A 262 TYR cc_start: 0.8026 (t80) cc_final: 0.7782 (t80) REVERT: A 334 ARG cc_start: 0.5523 (mmt90) cc_final: 0.4784 (mpt-90) REVERT: A 410 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6368 (tt0) REVERT: A 489 LYS cc_start: 0.7860 (ptpp) cc_final: 0.7409 (pttp) REVERT: A 557 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8508 (mp) REVERT: A 572 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6267 (tp30) REVERT: A 636 ARG cc_start: 0.6949 (mmt180) cc_final: 0.6722 (mmm-85) REVERT: A 687 ARG cc_start: 0.6712 (mtp85) cc_final: 0.6452 (mtp-110) REVERT: A 698 GLU cc_start: 0.8051 (pt0) cc_final: 0.7694 (pt0) REVERT: A 851 LYS cc_start: 0.6481 (tttp) cc_final: 0.6144 (tptt) REVERT: A 855 ARG cc_start: 0.5169 (tpp-160) cc_final: 0.4887 (tpp-160) outliers start: 14 outliers final: 5 residues processed: 83 average time/residue: 1.3919 time to fit residues: 122.6643 Evaluate side-chains 81 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 557 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 0.0050 chunk 68 optimal weight: 0.3980 chunk 72 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9149 Z= 0.179 Angle : 0.577 8.281 13019 Z= 0.301 Chirality : 0.033 0.162 1504 Planarity : 0.004 0.069 1162 Dihedral : 21.818 99.023 2844 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.31 % Allowed : 21.67 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.32), residues: 713 helix: 0.83 (0.29), residues: 324 sheet: -0.87 (0.52), residues: 102 loop : -2.00 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 PHE 0.010 0.001 PHE A 717 TYR 0.016 0.001 TYR A 241 ARG 0.003 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.796 Fit side-chains REVERT: A 22 GLN cc_start: 0.7363 (mt0) cc_final: 0.7033 (mm110) REVERT: A 48 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7245 (mp) REVERT: A 90 LYS cc_start: 0.6590 (ptpt) cc_final: 0.5483 (mmtm) REVERT: A 133 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6575 (mtp) REVERT: A 255 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6467 (pt0) REVERT: A 262 TYR cc_start: 0.7956 (t80) cc_final: 0.7754 (t80) REVERT: A 332 VAL cc_start: 0.7192 (t) cc_final: 0.6976 (p) REVERT: A 334 ARG cc_start: 0.5674 (mmt90) cc_final: 0.5290 (mmt90) REVERT: A 390 LYS cc_start: 0.6317 (mmtm) cc_final: 0.5538 (ptmm) REVERT: A 410 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6371 (tt0) REVERT: A 489 LYS cc_start: 0.7834 (ptpp) cc_final: 0.7383 (pttp) REVERT: A 557 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8489 (mp) REVERT: A 572 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6198 (OUTLIER) REVERT: A 636 ARG cc_start: 0.6957 (mmt180) cc_final: 0.6736 (mmm-85) REVERT: A 687 ARG cc_start: 0.6751 (mtp85) cc_final: 0.6421 (mtp-110) REVERT: A 698 GLU cc_start: 0.8100 (pt0) cc_final: 0.7709 (pt0) REVERT: A 851 LYS cc_start: 0.6469 (tttp) cc_final: 0.6147 (tptt) REVERT: A 855 ARG cc_start: 0.5128 (tpp-160) cc_final: 0.4896 (tpp-160) outliers start: 13 outliers final: 6 residues processed: 83 average time/residue: 1.4167 time to fit residues: 124.9160 Evaluate side-chains 85 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 557 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 7 optimal weight: 0.0770 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9149 Z= 0.205 Angle : 0.595 9.242 13019 Z= 0.308 Chirality : 0.034 0.163 1504 Planarity : 0.004 0.072 1162 Dihedral : 21.810 99.014 2844 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.49 % Allowed : 21.31 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.32), residues: 713 helix: 0.86 (0.29), residues: 321 sheet: -0.93 (0.52), residues: 102 loop : -2.08 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 520 HIS 0.003 0.001 HIS A 657 PHE 0.016 0.001 PHE A 717 TYR 0.016 0.001 TYR A 241 ARG 0.003 0.000 ARG A 850 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.554 Fit side-chains REVERT: A 22 GLN cc_start: 0.7403 (mt0) cc_final: 0.7074 (mm110) REVERT: A 90 LYS cc_start: 0.6600 (ptpt) cc_final: 0.5473 (mmtm) REVERT: A 133 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6946 (mtt) REVERT: A 255 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6619 (pt0) REVERT: A 332 VAL cc_start: 0.7205 (t) cc_final: 0.6981 (p) REVERT: A 334 ARG cc_start: 0.5684 (mmt90) cc_final: 0.5311 (mmt90) REVERT: A 390 LYS cc_start: 0.6275 (mmtm) cc_final: 0.5355 (ptmm) REVERT: A 410 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6427 (tt0) REVERT: A 489 LYS cc_start: 0.7876 (ptpp) cc_final: 0.7426 (pttp) REVERT: A 557 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8532 (mp) REVERT: A 572 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6226 (OUTLIER) REVERT: A 636 ARG cc_start: 0.6973 (mmt180) cc_final: 0.6742 (mmm-85) REVERT: A 698 GLU cc_start: 0.8152 (pt0) cc_final: 0.7838 (pt0) REVERT: A 851 LYS cc_start: 0.6491 (tttp) cc_final: 0.6160 (tptt) REVERT: A 855 ARG cc_start: 0.5189 (tpp-160) cc_final: 0.4945 (tpp-160) outliers start: 14 outliers final: 6 residues processed: 83 average time/residue: 1.3078 time to fit residues: 115.3048 Evaluate side-chains 82 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 557 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 67 optimal weight: 0.0270 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 0.0670 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.0170 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 overall best weight: 0.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.256210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.224357 restraints weight = 9408.522| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 1.95 r_work: 0.4131 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9149 Z= 0.157 Angle : 0.587 8.694 13019 Z= 0.303 Chirality : 0.033 0.162 1504 Planarity : 0.004 0.064 1162 Dihedral : 21.821 98.717 2844 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 1.95 % Allowed : 22.38 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.32), residues: 713 helix: 0.98 (0.30), residues: 324 sheet: -1.06 (0.53), residues: 94 loop : -2.04 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 441 HIS 0.005 0.001 HIS A 14 PHE 0.009 0.001 PHE A 453 TYR 0.021 0.001 TYR A 262 ARG 0.004 0.000 ARG A 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2897.97 seconds wall clock time: 52 minutes 47.68 seconds (3167.68 seconds total)