Starting phenix.real_space_refine (version: dev) on Tue Apr 5 04:57:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/04_2022/7k8c_22726.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/04_2022/7k8c_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_22726/04_2022/7k8c_22726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/04_2022/7k8c_22726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/04_2022/7k8c_22726.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8c_22726/04_2022/7k8c_22726.pdb" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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-4553/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: 6.19, per 1000 atoms: 1.12 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: 2.20 Conformation dependent library (CDL) restraints added in 1.6 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: 0.28 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: 1.63 Time building geometry restraints manager: 2.39 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 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. 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: 0.060 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: 0.000 Extract box with map and model: 0.820 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.040 Process input model: 22.140 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 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 % 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 *********************** 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 : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 177 average time/residue: 0.1595 time to fit residues: 37.0884 Evaluate side-chains 154 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0532 time to fit residues: 1.1740 ------------------------------------------------------------------------------- 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: 5.9990 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 0.0670 chunk 42 optimal weight: 0.0570 chunk 65 optimal weight: 6.9990 overall best weight: 3.2242 ------------------------------------------------------------------------------- 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 ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.1523 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= 0.251 Angle : 0.729 7.097 7669 Z= 0.369 Chirality : 0.044 0.199 916 Planarity : 0.006 0.070 968 Dihedral : 4.759 23.989 770 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.31), residues: 720 helix: 1.04 (0.24), residues: 468 sheet: 1.05 (0.91), residues: 24 loop : -1.06 (0.40), residues: 228 *********************** 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 : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1572 time to fit residues: 34.8434 Evaluate side-chains 140 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8723 ------------------------------------------------------------------------------- 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: 0.9980 chunk 54 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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: 0.5912 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 5636 Z= 0.237 Angle : 0.719 7.054 7669 Z= 0.361 Chirality : 0.044 0.212 916 Planarity : 0.006 0.061 968 Dihedral : 4.840 25.224 770 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.31), residues: 720 helix: 1.16 (0.24), residues: 457 sheet: 0.29 (0.84), residues: 29 loop : -1.12 (0.40), residues: 234 *********************** 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 168 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1600 time to fit residues: 35.3392 Evaluate side-chains 139 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7949 ------------------------------------------------------------------------------- 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: 6.9990 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 34 optimal weight: 0.0970 chunk 62 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- 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: 0.5975 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 5636 Z= 0.257 Angle : 0.746 8.017 7669 Z= 0.374 Chirality : 0.044 0.159 916 Planarity : 0.006 0.070 968 Dihedral : 4.992 26.171 770 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.31), residues: 720 helix: 1.06 (0.24), residues: 466 sheet: 0.24 (0.80), residues: 29 loop : -1.10 (0.41), residues: 225 *********************** 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 164 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.499 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1590 time to fit residues: 34.0779 Evaluate side-chains 135 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8769 ------------------------------------------------------------------------------- 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: 10.0000 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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: 0.6014 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 5636 Z= 0.255 Angle : 0.765 9.028 7669 Z= 0.381 Chirality : 0.044 0.194 916 Planarity : 0.006 0.069 968 Dihedral : 5.024 26.684 770 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.24), residues: 459 sheet: -0.03 (0.75), residues: 31 loop : -1.28 (0.40), residues: 230 *********************** 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 166 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.586 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1641 time to fit residues: 35.6100 Evaluate side-chains 136 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.594 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8712 ------------------------------------------------------------------------------- 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: 8.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 186 GLN A 309 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 5636 Z= 0.315 Angle : 0.829 7.943 7669 Z= 0.419 Chirality : 0.046 0.143 916 Planarity : 0.007 0.068 968 Dihedral : 5.378 28.667 770 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.00 (0.31), residues: 720 helix: 0.77 (0.24), residues: 461 sheet: -0.21 (0.79), residues: 31 loop : -1.50 (0.40), residues: 228 *********************** 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 161 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1547 time to fit residues: 32.8423 Evaluate side-chains 134 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.635 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8864 ------------------------------------------------------------------------------- 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: 10.0000 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 0.0370 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 overall best weight: 2.9864 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 5636 Z= 0.238 Angle : 0.778 7.872 7669 Z= 0.383 Chirality : 0.045 0.153 916 Planarity : 0.006 0.065 968 Dihedral : 5.202 28.334 770 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.31), residues: 720 helix: 0.97 (0.24), residues: 467 sheet: 0.18 (0.88), residues: 31 loop : -1.37 (0.42), residues: 222 *********************** 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 162 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.578 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1651 time to fit residues: 34.8918 Evaluate side-chains 140 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.629 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8428 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.6050 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 5636 Z= 0.218 Angle : 0.800 11.244 7669 Z= 0.392 Chirality : 0.044 0.149 916 Planarity : 0.006 0.087 968 Dihedral : 5.155 28.083 770 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.31), residues: 720 helix: 0.99 (0.24), residues: 468 sheet: 0.43 (0.93), residues: 31 loop : -1.29 (0.42), residues: 221 *********************** 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 161 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1684 time to fit residues: 35.4303 Evaluate side-chains 143 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8520 ------------------------------------------------------------------------------- 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: 10.0000 chunk 28 optimal weight: 8.9990 chunk 50 optimal weight: 0.0050 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 0.1980 chunk 42 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 overall best weight: 3.2400 ------------------------------------------------------------------------------- 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: 0.6087 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 5636 Z= 0.247 Angle : 0.788 9.639 7669 Z= 0.392 Chirality : 0.045 0.147 916 Planarity : 0.006 0.057 968 Dihedral : 5.169 28.825 770 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.32), residues: 720 helix: 0.97 (0.24), residues: 462 sheet: 0.04 (0.94), residues: 31 loop : -1.42 (0.42), residues: 227 *********************** 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 153 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1733 time to fit residues: 34.2558 Evaluate side-chains 138 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.610 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8732 ------------------------------------------------------------------------------- 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: 30.0000 chunk 71 optimal weight: 0.0040 chunk 66 optimal weight: 50.0000 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 35 optimal weight: 0.0470 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.7292 ------------------------------------------------------------------------------- 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: 0.5993 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 5636 Z= 0.198 Angle : 0.795 10.417 7669 Z= 0.382 Chirality : 0.044 0.155 916 Planarity : 0.006 0.055 968 Dihedral : 4.983 28.471 770 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.10 (0.24), residues: 467 sheet: 0.39 (0.97), residues: 31 loop : -1.25 (0.42), residues: 222 ********************** 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 168 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1674 time to fit residues: 37.1731 Evaluate side-chains 139 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8994 ------------------------------------------------------------------------------- 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: 0.0470 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.248905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.219857 restraints weight = 13253.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.222586 restraints weight = 9539.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.226121 restraints weight = 6365.618| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4596 r_free = 0.4596 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4597 r_free = 0.4597 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5636 Z= 0.195 Angle : 0.762 8.590 7669 Z= 0.370 Chirality : 0.044 0.162 916 Planarity : 0.006 0.053 968 Dihedral : 4.868 28.158 770 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.32), residues: 720 helix: 1.23 (0.24), residues: 466 sheet: 0.42 (0.96), residues: 31 loop : -1.18 (0.42), residues: 223 =============================================================================== Job complete usr+sys time: 1374.79 seconds wall clock time: 25 minutes 33.34 seconds (1533.34 seconds total)