Starting phenix.real_space_refine on Fri Mar 15 07:27:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/03_2024/7k8c_22726.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/03_2024/7k8c_22726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/03_2024/7k8c_22726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/03_2024/7k8c_22726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/03_2024/7k8c_22726.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/03_2024/7k8c_22726.pdb" } resolution = 4.27 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 ------------------------------------------------------------------------------- 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= 0.149 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5524 atoms to isotropic. 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 28 5.16 5 C 3579 2.51 5 N 916 2.21 5 O 1001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A ASP 119": "OD1" <-> "OD2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ASP 645": "OD1" <-> "OD2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 747": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5524 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5524 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 723, 5516 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 36, 'TRANS': 686} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Conformer: "B" Number of residues, atoms: 723, 5516 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 36, 'TRANS': 686} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 bond proxies already assigned to first conformer: 5616 Time building chain proxies: 5.96, per 1000 atoms: 1.08 Number of scatterers: 5524 At special positions: 0 Unit cell: (75.92, 82.16, 109.2, 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 28 16.00 O 1001 8.00 N 916 7.00 C 3579 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 - 3.50 Amino acid : False - 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: 2.13 Conformation dependent library (CDL) restraints added in 2.2 seconds 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 73.6% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 removed outlier: 3.524A pdb=" N TRP A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 13 " --> pdb=" O VAL A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 32 removed outlier: 4.003A pdb=" N GLY A 18 " --> pdb=" O TYR A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 62 removed outlier: 3.583A pdb=" N ALA A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 101 removed outlier: 4.202A pdb=" N LYS A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 90 " --> pdb=" O TRP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 removed outlier: 3.816A pdb=" N LYS A 113 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 143 through 165 removed outlier: 3.778A pdb=" N ILE A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 4.066A pdb=" N VAL A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY A 163 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 205 removed outlier: 3.569A pdb=" N LEU A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 207 through 234 Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 245 through 272 removed outlier: 3.564A pdb=" N ASP A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 302 removed outlier: 4.102A pdb=" N VAL A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 309 through 342 Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.717A pdb=" N ARG A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.551A pdb=" N ILE A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 428 through 432 removed outlier: 3.842A pdb=" N TYR A 431 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 470 through 483 Processing helix chain 'A' and resid 525 through 536 Processing helix chain 'A' and resid 548 through 583 removed outlier: 3.548A pdb=" N GLU A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Proline residue: A 565 - end of helix Processing helix chain 'A' and resid 586 through 614 removed outlier: 4.077A pdb=" N PHE A 611 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.891A pdb=" N MET A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 661 removed outlier: 3.749A pdb=" N ILE A 632 " --> pdb=" O MET A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 695 removed outlier: 3.569A pdb=" N THR A 675 " --> pdb=" O GLY A 671 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ARG A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 686 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 722 Processing helix chain 'A' and resid 722 through 728 Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'A' and resid 732 through 737 removed outlier: 4.154A pdb=" N TRP A 736 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP A 737 " --> pdb=" O ASP A 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 732 through 737' Processing helix chain 'A' and resid 739 through 748 removed outlier: 3.687A pdb=" N VAL A 745 " --> pdb=" O TRP A 741 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN A 746 " --> pdb=" O MET A 742 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 136 Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 500 removed outlier: 3.646A pdb=" N ILE A 516 " --> pdb=" O LEU A 459 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1122 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: 1.54 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1106 1.33 - 1.45: 1218 1.45 - 1.57: 3258 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 5636 Sorted by residual: bond pdb=" N VAL A 279 " pdb=" CA VAL A 279 " ideal model delta sigma weight residual 1.461 1.429 0.032 1.19e-02 7.06e+03 7.14e+00 bond pdb=" C ALA A 526 " pdb=" O ALA A 526 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.17e-02 7.31e+03 5.71e+00 bond pdb=" N ASP A 274 " pdb=" CA ASP A 274 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.26e+00 bond pdb=" CA ARG A 280 " pdb=" C ARG A 280 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.44e-02 4.82e+03 5.23e+00 bond pdb=" CA TYR A 273 " pdb=" C TYR A 273 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.28e-02 6.10e+03 4.92e+00 ... (remaining 5631 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.88: 188 106.88 - 113.67: 3160 113.67 - 120.46: 2293 120.46 - 127.25: 1971 127.25 - 134.03: 57 Bond angle restraints: 7669 Sorted by residual: angle pdb=" N ALA A 278 " pdb=" CA ALA A 278 " pdb=" C ALA A 278 " ideal model delta sigma weight residual 111.28 105.35 5.93 1.09e+00 8.42e-01 2.96e+01 angle pdb=" N GLU A 276 " pdb=" CA GLU A 276 " pdb=" C GLU A 276 " ideal model delta sigma weight residual 111.07 116.87 -5.80 1.07e+00 8.73e-01 2.94e+01 angle pdb=" N ALA A 270 " pdb=" CA ALA A 270 " pdb=" C ALA A 270 " ideal model delta sigma weight residual 111.36 105.56 5.80 1.09e+00 8.42e-01 2.83e+01 angle pdb=" N THR A 121 " pdb=" CA THR A 121 " pdb=" C THR A 121 " ideal model delta sigma weight residual 111.28 116.32 -5.04 1.09e+00 8.42e-01 2.14e+01 angle pdb=" N ALA A 527 " pdb=" CA ALA A 527 " pdb=" C ALA A 527 " ideal model delta sigma weight residual 111.28 106.47 4.81 1.09e+00 8.42e-01 1.95e+01 ... (remaining 7664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 3036 16.93 - 33.86: 260 33.86 - 50.79: 56 50.79 - 67.72: 9 67.72 - 84.66: 4 Dihedral angle restraints: 3365 sinusoidal: 1305 harmonic: 2060 Sorted by residual: dihedral pdb=" C TYR A 273 " pdb=" N TYR A 273 " pdb=" CA TYR A 273 " pdb=" CB TYR A 273 " ideal model delta harmonic sigma weight residual -122.60 -134.55 11.95 0 2.50e+00 1.60e-01 2.28e+01 dihedral pdb=" CA MET A 628 " pdb=" C MET A 628 " pdb=" N ALA A 629 " pdb=" CA ALA A 629 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" N TYR A 273 " pdb=" C TYR A 273 " pdb=" CA TYR A 273 " pdb=" CB TYR A 273 " ideal model delta harmonic sigma weight residual 122.80 134.08 -11.28 0 2.50e+00 1.60e-01 2.03e+01 ... (remaining 3362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 868 0.093 - 0.187: 44 0.187 - 0.280: 2 0.280 - 0.373: 0 0.373 - 0.467: 2 Chirality restraints: 916 Sorted by residual: chirality pdb=" CA TYR A 273 " pdb=" N TYR A 273 " pdb=" C TYR A 273 " pdb=" CB TYR A 273 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" CA ASP A 274 " pdb=" N ASP A 274 " pdb=" C ASP A 274 " pdb=" CB ASP A 274 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA VAL A 279 " pdb=" N VAL A 279 " pdb=" C VAL A 279 " pdb=" CB VAL A 279 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 913 not shown) Planarity restraints: 968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 417 " -0.056 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO A 418 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 418 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 418 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 406 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO A 407 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 520 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.07e+00 pdb=" C LEU A 520 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU A 520 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 521 " -0.014 2.00e-02 2.50e+03 ... (remaining 965 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 437 2.74 - 3.28: 6057 3.28 - 3.82: 9256 3.82 - 4.36: 9743 4.36 - 4.90: 16756 Nonbonded interactions: 42249 Sorted by model distance: nonbonded pdb=" OG1 THR A 599 " pdb=" OD2 ASP A 715 " model vdw 2.196 2.440 nonbonded pdb=" NH1 ARG A 65 " pdb=" O LEU A 139 " model vdw 2.300 2.520 nonbonded pdb=" OG1 THR A 74 " pdb=" ND1 HIS A 132 " model vdw 2.331 2.520 nonbonded pdb=" O LEU A 598 " pdb=" OG SER A 602 " model vdw 2.334 2.440 nonbonded pdb=" O GLY A 584 " pdb=" OG SER A 585 " model vdw 2.349 2.440 ... (remaining 42244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.430 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 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 0.040 5636 Z= 0.242 Angle : 0.838 7.716 7669 Z= 0.465 Chirality : 0.051 0.467 916 Planarity : 0.007 0.085 968 Dihedral : 13.696 84.656 2041 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.85 % Allowed : 0.68 % Favored : 98.47 % Cbeta Deviations : 0.30 % 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: 0.14 (0.31), residues: 720 helix: 0.72 (0.25), residues: 458 sheet: 0.05 (0.75), residues: 38 loop : -1.08 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 498 HIS 0.002 0.000 HIS A 239 PHE 0.036 0.002 PHE A 693 TYR 0.016 0.001 TYR A 10 ARG 0.005 0.000 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 173 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.4955 (mmp) cc_final: 0.4505 (mmp) REVERT: A 324 MET cc_start: 0.7752 (tpp) cc_final: 0.7457 (tpt) REVERT: A 555 ASP cc_start: 0.7411 (m-30) cc_final: 0.7081 (m-30) outliers start: 4 outliers final: 3 residues processed: 177 average time/residue: 0.1768 time to fit residues: 40.9488 Evaluate side-chains 155 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5636 Z= 0.262 Angle : 0.750 7.143 7669 Z= 0.381 Chirality : 0.045 0.202 916 Planarity : 0.007 0.069 968 Dihedral : 4.903 24.813 770 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.17 % Allowed : 3.05 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.31), residues: 720 helix: 1.00 (0.24), residues: 464 sheet: 0.19 (0.84), residues: 29 loop : -1.09 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 741 HIS 0.004 0.001 HIS A 68 PHE 0.029 0.002 PHE A 693 TYR 0.021 0.002 TYR A 10 ARG 0.009 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5252 (mmp) cc_final: 0.4736 (mmp) REVERT: A 43 PHE cc_start: 0.5576 (p90) cc_final: 0.5354 (p90) REVERT: A 188 ARG cc_start: 0.8320 (tpm170) cc_final: 0.8012 (tpp-160) REVERT: A 281 ARG cc_start: 0.6843 (mtt180) cc_final: 0.6354 (mtt180) REVERT: A 555 ASP cc_start: 0.7599 (m-30) cc_final: 0.7318 (m-30) REVERT: A 560 LEU cc_start: 0.8169 (tt) cc_final: 0.7711 (tt) REVERT: A 631 MET cc_start: 0.7288 (ptp) cc_final: 0.6497 (ptt) REVERT: A 653 ARG cc_start: 0.6650 (tmt170) cc_final: 0.6276 (tmm160) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1655 time to fit residues: 36.3765 Evaluate side-chains 141 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 243 GLN A 309 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5636 Z= 0.268 Angle : 0.740 7.174 7669 Z= 0.373 Chirality : 0.044 0.192 916 Planarity : 0.006 0.062 968 Dihedral : 4.977 26.406 770 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.17 % Allowed : 3.90 % Favored : 95.93 % 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: 0.44 (0.31), residues: 720 helix: 1.09 (0.24), residues: 457 sheet: -0.01 (0.79), residues: 29 loop : -1.23 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 640 HIS 0.005 0.001 HIS A 615 PHE 0.030 0.002 PHE A 693 TYR 0.020 0.002 TYR A 10 ARG 0.005 0.001 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.531 Fit side-chains REVERT: A 20 MET cc_start: 0.5016 (mmp) cc_final: 0.4479 (mmp) REVERT: A 43 PHE cc_start: 0.5456 (p90) cc_final: 0.5236 (p90) REVERT: A 188 ARG cc_start: 0.8358 (tpm170) cc_final: 0.7977 (tpp-160) REVERT: A 257 TYR cc_start: 0.8457 (m-80) cc_final: 0.8080 (m-80) REVERT: A 264 ARG cc_start: 0.6252 (ttm-80) cc_final: 0.5378 (ttp-170) REVERT: A 281 ARG cc_start: 0.6750 (mtt180) cc_final: 0.6179 (mtt180) REVERT: A 324 MET cc_start: 0.7831 (tpp) cc_final: 0.7580 (tpp) REVERT: A 402 ILE cc_start: 0.1857 (mt) cc_final: -0.0896 (tt) REVERT: A 560 LEU cc_start: 0.8404 (tt) cc_final: 0.8008 (tt) REVERT: A 640 TRP cc_start: 0.7442 (t-100) cc_final: 0.7197 (t-100) REVERT: A 662 MET cc_start: 0.5123 (mmt) cc_final: 0.4776 (ttm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1679 time to fit residues: 36.2128 Evaluate side-chains 134 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN A 309 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 5636 Z= 0.294 Angle : 0.780 7.151 7669 Z= 0.398 Chirality : 0.045 0.157 916 Planarity : 0.007 0.074 968 Dihedral : 5.208 27.701 770 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.17 % Allowed : 2.37 % Favored : 97.46 % 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: 0.19 (0.31), residues: 720 helix: 0.96 (0.24), residues: 459 sheet: -0.42 (0.75), residues: 31 loop : -1.44 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 498 HIS 0.004 0.001 HIS A 68 PHE 0.030 0.003 PHE A 693 TYR 0.014 0.002 TYR A 622 ARG 0.010 0.001 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 20 MET cc_start: 0.5003 (mmp) cc_final: 0.4312 (mmp) REVERT: A 43 PHE cc_start: 0.5671 (p90) cc_final: 0.5454 (p90) REVERT: A 188 ARG cc_start: 0.8361 (tpm170) cc_final: 0.8008 (tpp-160) REVERT: A 264 ARG cc_start: 0.6475 (ttm-80) cc_final: 0.5558 (ttp-170) REVERT: A 281 ARG cc_start: 0.6820 (mtt180) cc_final: 0.6155 (mtt180) REVERT: A 560 LEU cc_start: 0.8398 (tt) cc_final: 0.7964 (tt) REVERT: A 723 LEU cc_start: 0.6806 (tt) cc_final: 0.6424 (tp) REVERT: A 742 MET cc_start: 0.2132 (tpt) cc_final: 0.1789 (tpt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1665 time to fit residues: 36.4769 Evaluate side-chains 137 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5636 Z= 0.271 Angle : 0.774 9.506 7669 Z= 0.386 Chirality : 0.044 0.162 916 Planarity : 0.006 0.065 968 Dihedral : 5.170 28.326 770 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.17 % Allowed : 1.69 % Favored : 98.14 % 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: 0.18 (0.31), residues: 720 helix: 0.92 (0.24), residues: 465 sheet: -0.28 (0.78), residues: 31 loop : -1.46 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 640 HIS 0.003 0.001 HIS A 68 PHE 0.033 0.002 PHE A 693 TYR 0.014 0.002 TYR A 10 ARG 0.005 0.001 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.528 Fit side-chains REVERT: A 20 MET cc_start: 0.5063 (mmp) cc_final: 0.4306 (mmp) REVERT: A 188 ARG cc_start: 0.8380 (tpm170) cc_final: 0.8019 (tpp-160) REVERT: A 264 ARG cc_start: 0.6416 (ttm-80) cc_final: 0.5551 (ttp-170) REVERT: A 464 GLU cc_start: 0.6934 (tt0) cc_final: 0.6713 (tt0) REVERT: A 524 ASN cc_start: 0.8034 (p0) cc_final: 0.7833 (p0) REVERT: A 560 LEU cc_start: 0.8535 (tt) cc_final: 0.8044 (tt) REVERT: A 662 MET cc_start: 0.4992 (mmt) cc_final: 0.4437 (ttp) REVERT: A 723 LEU cc_start: 0.6888 (tt) cc_final: 0.6104 (tp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1447 time to fit residues: 31.5131 Evaluate side-chains 135 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 0.0010 chunk 17 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5636 Z= 0.263 Angle : 0.776 7.590 7669 Z= 0.386 Chirality : 0.044 0.145 916 Planarity : 0.006 0.066 968 Dihedral : 5.246 28.986 770 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.17 % Allowed : 2.03 % Favored : 97.80 % 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: 0.13 (0.31), residues: 720 helix: 0.95 (0.24), residues: 459 sheet: -0.20 (0.82), residues: 31 loop : -1.60 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 741 HIS 0.014 0.002 HIS A 239 PHE 0.033 0.002 PHE A 693 TYR 0.020 0.002 TYR A 10 ARG 0.010 0.001 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5271 (mmp) cc_final: 0.4425 (mmp) REVERT: A 43 PHE cc_start: 0.5919 (p90) cc_final: 0.5667 (p90) REVERT: A 264 ARG cc_start: 0.6411 (ttm-80) cc_final: 0.5570 (ttp-170) REVERT: A 461 MET cc_start: 0.7483 (mpp) cc_final: 0.7093 (mpp) REVERT: A 477 MET cc_start: 0.7662 (mmm) cc_final: 0.7338 (ttm) REVERT: A 611 PHE cc_start: 0.5354 (t80) cc_final: 0.5068 (t80) REVERT: A 631 MET cc_start: 0.8373 (pmm) cc_final: 0.8062 (pmm) REVERT: A 662 MET cc_start: 0.4978 (mmt) cc_final: 0.4327 (ttp) REVERT: A 723 LEU cc_start: 0.6907 (tt) cc_final: 0.6319 (tp) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1627 time to fit residues: 33.7217 Evaluate side-chains 135 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 58 optimal weight: 0.0070 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5636 Z= 0.205 Angle : 0.752 7.867 7669 Z= 0.368 Chirality : 0.044 0.143 916 Planarity : 0.006 0.061 968 Dihedral : 5.059 28.503 770 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.17 % Allowed : 1.02 % Favored : 98.81 % 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: 0.29 (0.31), residues: 720 helix: 1.02 (0.24), residues: 463 sheet: 0.19 (0.87), residues: 31 loop : -1.50 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 498 HIS 0.004 0.001 HIS A 239 PHE 0.033 0.002 PHE A 693 TYR 0.016 0.001 TYR A 10 ARG 0.012 0.001 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.4945 (mmp) cc_final: 0.4087 (mmp) REVERT: A 264 ARG cc_start: 0.6231 (ttm-80) cc_final: 0.5482 (ttp-170) REVERT: A 595 MET cc_start: 0.6642 (tpp) cc_final: 0.6372 (tpp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1554 time to fit residues: 34.0501 Evaluate side-chains 146 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 34 optimal weight: 0.0050 chunk 6 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 overall best weight: 4.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 442 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 5636 Z= 0.279 Angle : 0.790 9.150 7669 Z= 0.395 Chirality : 0.045 0.154 916 Planarity : 0.006 0.056 968 Dihedral : 5.243 30.282 770 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.07 (0.31), residues: 720 helix: 0.87 (0.24), residues: 462 sheet: -0.03 (0.88), residues: 31 loop : -1.62 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 741 HIS 0.004 0.001 HIS A 239 PHE 0.036 0.002 PHE A 693 TYR 0.021 0.002 TYR A 10 ARG 0.015 0.001 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5222 (mmp) cc_final: 0.4251 (mmp) REVERT: A 477 MET cc_start: 0.7819 (mmm) cc_final: 0.7513 (mmm) REVERT: A 595 MET cc_start: 0.6948 (tpp) cc_final: 0.6694 (tpp) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.1672 time to fit residues: 35.5710 Evaluate side-chains 145 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5636 Z= 0.227 Angle : 0.790 10.550 7669 Z= 0.390 Chirality : 0.044 0.142 916 Planarity : 0.006 0.056 968 Dihedral : 5.197 29.737 770 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.32 % 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: 0.10 (0.31), residues: 720 helix: 0.91 (0.24), residues: 460 sheet: 0.19 (0.91), residues: 31 loop : -1.66 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 640 HIS 0.004 0.001 HIS A 239 PHE 0.035 0.002 PHE A 693 TYR 0.029 0.002 TYR A 622 ARG 0.009 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5144 (mmp) cc_final: 0.4194 (mmp) REVERT: A 167 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.6543 (mmm-85) REVERT: A 430 LYS cc_start: 0.8781 (tppt) cc_final: 0.8374 (tppt) REVERT: A 442 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8135 (tp40) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.1669 time to fit residues: 35.0817 Evaluate side-chains 142 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 0.0000 chunk 45 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 162 ASN A 309 GLN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5636 Z= 0.202 Angle : 0.790 8.971 7669 Z= 0.382 Chirality : 0.044 0.145 916 Planarity : 0.006 0.065 968 Dihedral : 5.045 29.295 770 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.66 % 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: 0.29 (0.32), residues: 720 helix: 1.03 (0.24), residues: 461 sheet: 0.42 (0.91), residues: 31 loop : -1.55 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 640 HIS 0.004 0.001 HIS A 239 PHE 0.036 0.002 PHE A 693 TYR 0.019 0.001 TYR A 622 ARG 0.007 0.001 ARG A 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5085 (mmp) cc_final: 0.4189 (mmp) REVERT: A 167 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.6807 (mmm-85) REVERT: A 430 LYS cc_start: 0.8760 (tppt) cc_final: 0.8291 (tppt) REVERT: A 723 LEU cc_start: 0.6567 (tt) cc_final: 0.6104 (tp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1625 time to fit residues: 35.3137 Evaluate side-chains 140 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN A 309 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.248332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.220897 restraints weight = 13418.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.225522 restraints weight = 9427.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.228637 restraints weight = 6042.710| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4392 r_free = 0.4392 target_work(ls_wunit_k1) = 0.228 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4392 r_free = 0.4392 target_work(ls_wunit_k1) = 0.228 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5636 Z= 0.199 Angle : 0.764 8.548 7669 Z= 0.372 Chirality : 0.043 0.147 916 Planarity : 0.006 0.053 968 Dihedral : 4.862 28.784 770 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.17 % Allowed : 0.00 % Favored : 99.83 % 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: 0.49 (0.32), residues: 720 helix: 1.20 (0.24), residues: 460 sheet: 0.59 (0.92), residues: 31 loop : -1.52 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 498 HIS 0.003 0.001 HIS A 239 PHE 0.034 0.002 PHE A 693 TYR 0.017 0.001 TYR A 622 ARG 0.005 0.000 ARG A 264 =============================================================================== Job complete usr+sys time: 1391.40 seconds wall clock time: 25 minutes 37.34 seconds (1537.34 seconds total)