Starting phenix.real_space_refine on Wed Sep 25 09:18:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/09_2024/7k8c_22726.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/09_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_22726/09_2024/7k8c_22726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/09_2024/7k8c_22726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/09_2024/7k8c_22726.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/09_2024/7k8c_22726.cif" } 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. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.15, per 1000 atoms: 1.11 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 - 3.00 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: 1.43 Conformation dependent library (CDL) restraints added in 1.5 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: 0.56 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: 1.52 Time building geometry restraints manager: 1.67 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: 0.00 - 1.54: 7277 1.54 - 3.09: 280 3.09 - 4.63: 57 4.63 - 6.17: 45 6.17 - 7.72: 10 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 3.040 nonbonded pdb=" NH1 ARG A 65 " pdb=" O LEU A 139 " model vdw 2.300 3.120 nonbonded pdb=" OG1 THR A 74 " pdb=" ND1 HIS A 132 " model vdw 2.331 3.120 nonbonded pdb=" O LEU A 598 " pdb=" OG SER A 602 " model vdw 2.334 3.040 nonbonded pdb=" O GLY A 584 " pdb=" OG SER A 585 " model vdw 2.349 3.040 ... (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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.200 Find NCS groups from input model: 0.060 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.850 ------------------------------------------------------------------------------- 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 : 0.538 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: 0.1560 time to fit residues: 36.1905 Evaluate side-chains 155 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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: 6.9990 chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 chunk 42 optimal weight: 0.0070 chunk 65 optimal weight: 8.9990 overall best weight: 2.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5636 Z= 0.225 Angle : 0.724 7.068 7669 Z= 0.366 Chirality : 0.044 0.205 916 Planarity : 0.006 0.071 968 Dihedral : 4.711 23.703 770 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: 0.53 (0.31), residues: 720 helix: 1.01 (0.24), residues: 468 sheet: 1.23 (0.92), residues: 24 loop : -1.07 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 640 HIS 0.002 0.001 HIS A 68 PHE 0.027 0.002 PHE A 693 TYR 0.025 0.002 TYR A 10 ARG 0.005 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 172 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.4954 (mmp) cc_final: 0.4433 (mmp) REVERT: A 43 PHE cc_start: 0.5596 (p90) cc_final: 0.5355 (p90) REVERT: A 188 ARG cc_start: 0.8314 (tpm170) cc_final: 0.8014 (tpp-160) REVERT: A 264 ARG cc_start: 0.6011 (ttm-80) cc_final: 0.5363 (ttp-170) REVERT: A 281 ARG cc_start: 0.6686 (mtt180) cc_final: 0.6383 (mtt180) REVERT: A 455 GLU cc_start: 0.7524 (mp0) cc_final: 0.7315 (mp0) REVERT: A 555 ASP cc_start: 0.7430 (m-30) cc_final: 0.7091 (m-30) REVERT: A 560 LEU cc_start: 0.8015 (tt) cc_final: 0.7576 (tt) REVERT: A 631 MET cc_start: 0.7207 (ptp) cc_final: 0.6446 (ptt) REVERT: A 640 TRP cc_start: 0.7058 (t-100) cc_final: 0.6849 (t-100) REVERT: A 653 ARG cc_start: 0.6560 (tmt170) cc_final: 0.6267 (tmm160) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1637 time to fit residues: 36.9270 Evaluate side-chains 140 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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: 20.0000 chunk 20 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN A 309 GLN A 442 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 5636 Z= 0.304 Angle : 0.770 7.029 7669 Z= 0.398 Chirality : 0.045 0.211 916 Planarity : 0.007 0.064 968 Dihedral : 5.066 26.734 770 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.17 % Allowed : 2.71 % Favored : 97.12 % 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: 0.34 (0.31), residues: 720 helix: 1.03 (0.24), residues: 456 sheet: -0.12 (0.78), residues: 29 loop : -1.29 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 741 HIS 0.006 0.002 HIS A 615 PHE 0.029 0.002 PHE A 693 TYR 0.017 0.002 TYR A 10 ARG 0.006 0.001 ARG A 439 *********************** 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 170 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.530 Fit side-chains REVERT: A 20 MET cc_start: 0.5079 (mmp) cc_final: 0.4529 (mmp) REVERT: A 43 PHE cc_start: 0.5524 (p90) cc_final: 0.5260 (p90) REVERT: A 188 ARG cc_start: 0.8338 (tpm170) cc_final: 0.7963 (tpp-160) REVERT: A 257 TYR cc_start: 0.8433 (m-80) cc_final: 0.8119 (m-80) REVERT: A 264 ARG cc_start: 0.6231 (ttm-80) cc_final: 0.5377 (ttp-170) REVERT: A 281 ARG cc_start: 0.6898 (mtt180) cc_final: 0.6233 (mtt180) REVERT: A 324 MET cc_start: 0.7829 (tpp) cc_final: 0.7598 (tpp) REVERT: A 455 GLU cc_start: 0.7510 (mp0) cc_final: 0.7294 (mp0) REVERT: A 560 LEU cc_start: 0.8439 (tt) cc_final: 0.8079 (tt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1635 time to fit residues: 36.0935 Evaluate side-chains 137 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 0.0270 chunk 33 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 34 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.6442 ------------------------------------------------------------------------------- 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: 0.6077 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5636 Z= 0.234 Angle : 0.766 7.502 7669 Z= 0.381 Chirality : 0.045 0.178 916 Planarity : 0.006 0.072 968 Dihedral : 5.020 26.080 770 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.17 % Allowed : 2.54 % Favored : 97.29 % 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: 0.36 (0.31), residues: 720 helix: 1.01 (0.24), residues: 460 sheet: 0.08 (0.83), residues: 29 loop : -1.23 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 640 HIS 0.002 0.001 HIS A 132 PHE 0.033 0.002 PHE A 693 TYR 0.013 0.002 TYR A 10 ARG 0.005 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 169 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.578 Fit side-chains REVERT: A 20 MET cc_start: 0.4714 (mmp) cc_final: 0.4023 (mmp) REVERT: A 188 ARG cc_start: 0.8329 (tpm170) cc_final: 0.7982 (tpp-160) REVERT: A 257 TYR cc_start: 0.8412 (m-80) cc_final: 0.8207 (m-80) REVERT: A 264 ARG cc_start: 0.6185 (ttm-80) cc_final: 0.5429 (ttp-170) REVERT: A 281 ARG cc_start: 0.6803 (mtt180) cc_final: 0.6137 (mtt180) REVERT: A 560 LEU cc_start: 0.8374 (tt) cc_final: 0.7985 (tt) REVERT: A 631 MET cc_start: 0.7186 (ptp) cc_final: 0.6870 (ptp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1653 time to fit residues: 36.0483 Evaluate side-chains 142 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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: 4.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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: 0.6130 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5636 Z= 0.243 Angle : 0.761 8.078 7669 Z= 0.381 Chirality : 0.044 0.145 916 Planarity : 0.006 0.064 968 Dihedral : 5.042 26.910 770 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.17 % Allowed : 1.19 % Favored : 98.64 % 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: 0.31 (0.31), residues: 720 helix: 1.00 (0.24), residues: 461 sheet: 0.07 (0.85), residues: 31 loop : -1.36 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 640 HIS 0.003 0.001 HIS A 68 PHE 0.032 0.002 PHE A 693 TYR 0.016 0.002 TYR A 10 ARG 0.012 0.001 ARG A 653 *********************** 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 171 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 20 MET cc_start: 0.4935 (mmp) cc_final: 0.4245 (mmp) REVERT: A 167 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.6888 (mmm-85) REVERT: A 264 ARG cc_start: 0.6393 (ttm-80) cc_final: 0.5927 (ttp-170) REVERT: A 281 ARG cc_start: 0.6846 (mtt180) cc_final: 0.6213 (mtt180) REVERT: A 464 GLU cc_start: 0.6740 (tt0) cc_final: 0.6508 (tt0) REVERT: A 560 LEU cc_start: 0.8564 (tt) cc_final: 0.8182 (tt) REVERT: A 662 MET cc_start: 0.7346 (ttt) cc_final: 0.6637 (tpp) REVERT: A 723 LEU cc_start: 0.6802 (tt) cc_final: 0.6292 (tp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1674 time to fit residues: 36.8602 Evaluate side-chains 141 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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: 30.0000 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.6228 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 5636 Z= 0.304 Angle : 0.839 8.104 7669 Z= 0.423 Chirality : 0.046 0.151 916 Planarity : 0.006 0.060 968 Dihedral : 5.355 28.623 770 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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: -0.03 (0.31), residues: 720 helix: 0.71 (0.24), residues: 469 sheet: -0.18 (0.83), residues: 31 loop : -1.49 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 741 HIS 0.004 0.001 HIS A 68 PHE 0.032 0.002 PHE A 693 TYR 0.023 0.002 TYR A 10 ARG 0.013 0.001 ARG A 439 *********************** 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 165 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5219 (mmp) cc_final: 0.4384 (mmp) REVERT: A 84 LYS cc_start: 0.5423 (mmmt) cc_final: 0.5195 (mmtt) REVERT: A 167 ARG cc_start: 0.8171 (mmm-85) cc_final: 0.6723 (mmm-85) REVERT: A 181 THR cc_start: 0.8526 (t) cc_final: 0.8318 (t) REVERT: A 264 ARG cc_start: 0.6464 (ttm-80) cc_final: 0.5943 (ttp-170) REVERT: A 281 ARG cc_start: 0.7035 (mtt180) cc_final: 0.6768 (mtt180) REVERT: A 461 MET cc_start: 0.7518 (mpp) cc_final: 0.7170 (mpp) REVERT: A 477 MET cc_start: 0.7681 (mmm) cc_final: 0.7373 (ttm) REVERT: A 631 MET cc_start: 0.7209 (ptp) cc_final: 0.6979 (ptt) REVERT: A 662 MET cc_start: 0.7438 (ttt) cc_final: 0.6982 (tpp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1609 time to fit residues: 34.1500 Evaluate side-chains 139 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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: 0.9990 chunk 39 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 38 optimal weight: 0.0070 chunk 69 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.0002 ------------------------------------------------------------------------------- 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: 0.6094 moved from start: 0.3812 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= 0.203 Angle : 0.774 8.062 7669 Z= 0.379 Chirality : 0.044 0.140 916 Planarity : 0.006 0.058 968 Dihedral : 4.985 27.157 770 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.17 % Allowed : 1.36 % Favored : 98.47 % 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: 0.35 (0.31), residues: 720 helix: 1.04 (0.24), residues: 460 sheet: 0.24 (0.88), residues: 31 loop : -1.38 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 640 HIS 0.002 0.001 HIS A 132 PHE 0.037 0.002 PHE A 693 TYR 0.018 0.002 TYR A 10 ARG 0.004 0.000 ARG A 439 *********************** 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 177 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.4894 (mmp) cc_final: 0.4081 (mmp) REVERT: A 167 ARG cc_start: 0.8124 (mmm-85) cc_final: 0.6701 (mmm-85) REVERT: A 181 THR cc_start: 0.8431 (t) cc_final: 0.8158 (t) REVERT: A 662 MET cc_start: 0.7298 (ttt) cc_final: 0.6948 (tpp) REVERT: A 723 LEU cc_start: 0.6767 (tt) cc_final: 0.6220 (tp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1257 time to fit residues: 29.2734 Evaluate side-chains 149 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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: 0.9980 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 309 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.3828 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= 0.201 Angle : 0.759 8.018 7669 Z= 0.375 Chirality : 0.043 0.143 916 Planarity : 0.006 0.055 968 Dihedral : 4.910 27.768 770 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.17 % Allowed : 0.68 % Favored : 99.15 % 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: 0.38 (0.31), residues: 720 helix: 1.06 (0.24), residues: 459 sheet: 0.30 (0.90), residues: 31 loop : -1.36 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 640 HIS 0.002 0.001 HIS A 239 PHE 0.036 0.002 PHE A 693 TYR 0.018 0.001 TYR A 622 ARG 0.014 0.001 ARG A 264 *********************** 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 167 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 20 MET cc_start: 0.4914 (mmp) cc_final: 0.4083 (mmp) REVERT: A 167 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.6753 (mmm-85) REVERT: A 477 MET cc_start: 0.7713 (mmm) cc_final: 0.7245 (ttm) REVERT: A 560 LEU cc_start: 0.8097 (tt) cc_final: 0.7740 (tt) REVERT: A 662 MET cc_start: 0.7236 (ttt) cc_final: 0.6818 (tpp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1643 time to fit residues: 36.0392 Evaluate side-chains 153 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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: 9.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 0.4980 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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: 0.6122 moved from start: 0.3911 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= 0.215 Angle : 0.758 7.308 7669 Z= 0.377 Chirality : 0.044 0.157 916 Planarity : 0.006 0.056 968 Dihedral : 4.876 28.343 770 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.17 % Allowed : 0.34 % Favored : 99.49 % 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: 0.42 (0.31), residues: 720 helix: 1.08 (0.24), residues: 461 sheet: 0.38 (0.92), residues: 31 loop : -1.35 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 498 HIS 0.002 0.001 HIS A 132 PHE 0.037 0.002 PHE A 693 TYR 0.020 0.002 TYR A 10 ARG 0.005 0.001 ARG A 264 *********************** 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 168 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5062 (mmp) cc_final: 0.4190 (mmp) REVERT: A 167 ARG cc_start: 0.8097 (mmm-85) cc_final: 0.6740 (mmm-85) REVERT: A 260 PHE cc_start: 0.8030 (t80) cc_final: 0.7806 (t80) REVERT: A 461 MET cc_start: 0.7282 (mpp) cc_final: 0.6982 (mpp) REVERT: A 477 MET cc_start: 0.7738 (mmm) cc_final: 0.7534 (ttm) REVERT: A 560 LEU cc_start: 0.8111 (tt) cc_final: 0.7724 (tt) REVERT: A 662 MET cc_start: 0.7268 (ttt) cc_final: 0.6874 (tpp) REVERT: A 723 LEU cc_start: 0.6859 (tt) cc_final: 0.6333 (tp) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1590 time to fit residues: 35.0039 Evaluate side-chains 153 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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: 7.9990 chunk 47 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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: 0.6162 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5636 Z= 0.241 Angle : 0.783 8.175 7669 Z= 0.391 Chirality : 0.045 0.165 916 Planarity : 0.006 0.057 968 Dihedral : 4.995 28.694 770 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: 0.37 (0.32), residues: 720 helix: 1.05 (0.24), residues: 464 sheet: 0.10 (0.92), residues: 31 loop : -1.39 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 498 HIS 0.003 0.001 HIS A 132 PHE 0.037 0.002 PHE A 693 TYR 0.021 0.002 TYR A 10 ARG 0.010 0.001 ARG A 264 ********************** 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 169 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5161 (mmp) cc_final: 0.4288 (mmp) REVERT: A 43 PHE cc_start: 0.5930 (p90) cc_final: 0.5722 (p90) REVERT: A 167 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.6757 (mmm-85) REVERT: A 560 LEU cc_start: 0.8125 (tt) cc_final: 0.7759 (tt) REVERT: A 640 TRP cc_start: 0.7379 (t-100) cc_final: 0.7098 (t-100) REVERT: A 662 MET cc_start: 0.7184 (ttt) cc_final: 0.6889 (tpp) REVERT: A 723 LEU cc_start: 0.6904 (tt) cc_final: 0.6415 (tp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1688 time to fit residues: 36.9935 Evaluate side-chains 145 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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: 0.0970 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 0.0070 chunk 57 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 58 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.247861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.218324 restraints weight = 13646.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.222390 restraints weight = 8927.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.225518 restraints weight = 5910.543| |-----------------------------------------------------------------------------| r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4354 r_free = 0.4354 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4355 r_free = 0.4355 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5636 Z= 0.193 Angle : 0.766 9.528 7669 Z= 0.378 Chirality : 0.044 0.158 916 Planarity : 0.006 0.055 968 Dihedral : 4.838 28.127 770 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % 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: 0.52 (0.32), residues: 720 helix: 1.16 (0.24), residues: 463 sheet: 0.33 (0.93), residues: 31 loop : -1.33 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 498 HIS 0.002 0.000 HIS A 132 PHE 0.038 0.002 PHE A 693 TYR 0.017 0.001 TYR A 10 ARG 0.011 0.001 ARG A 439 =============================================================================== Job complete usr+sys time: 1403.88 seconds wall clock time: 29 minutes 30.49 seconds (1770.49 seconds total)