Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 15:05:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/04_2023/6ny1_8994.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/04_2023/6ny1_8994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/04_2023/6ny1_8994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/04_2023/6ny1_8994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/04_2023/6ny1_8994.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/04_2023/6ny1_8994.pdb" } resolution = 4.2 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= 0.003 sd= 0.056 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 196 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: 5 Type Number sf(0) Gaussians P 154 5.49 5 S 20 5.16 5 C 5724 2.51 5 N 1805 2.21 5 O 2208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y GLU 44": "OE1" <-> "OE2" Residue "Y TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 288": "OE1" <-> "OE2" Residue "Y PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 378": "OE1" <-> "OE2" Residue "Y ARG 475": "NH1" <-> "NH2" Residue "Y TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 488": "OE1" <-> "OE2" Residue "Y ASP 513": "OD1" <-> "OD2" Residue "Y TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 591": "OD1" <-> "OD2" Residue "Y PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9911 Number of models: 1 Model: "" Number of chains: 4 Chain: "Y" Number of atoms: 6671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 6671 Classifications: {'peptide': 904} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 193} Link IDs: {'PTRANS': 29, 'TRANS': 874} Unresolved chain links: 1 Chain breaks: 9 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 512 Unresolved non-hydrogen angles: 693 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 4, 'TYR:plan': 1, 'UNK:plan-1': 121, 'ASP:plan': 16, 'GLU:plan': 26, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 316 Chain: "D" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "B" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 2300 Classifications: {'RNA': 108} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 51, 'rna3p_pyr': 43} Link IDs: {'rna2p': 14, 'rna3p': 93} Chain breaks: 2 Chain: "C" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 594 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Time building chain proxies: 6.07, per 1000 atoms: 0.61 Number of scatterers: 9911 At special positions: 0 Unit cell: (99, 138.6, 120.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 154 15.00 O 2208 8.00 N 1805 7.00 C 5724 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: 5.29 Conformation dependent library (CDL) restraints added in 976.1 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 5 sheets defined 47.1% alpha, 7.5% beta 54 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'Y' and resid 4 through 15 removed outlier: 3.541A pdb=" N ASP Y 15 " --> pdb=" O LYS Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 44 Processing helix chain 'Y' and resid 59 through 88 removed outlier: 4.457A pdb=" N ASN Y 63 " --> pdb=" O ASN Y 59 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN Y 64 " --> pdb=" O ASN Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 90 through 98 Processing helix chain 'Y' and resid 194 through 198 Processing helix chain 'Y' and resid 222 through 260 removed outlier: 3.755A pdb=" N ASP Y 245 " --> pdb=" O SER Y 241 " (cutoff:3.500A) Processing helix chain 'Y' and resid 262 through 267 Processing helix chain 'Y' and resid 287 through 309 removed outlier: 3.593A pdb=" N ASP Y 291 " --> pdb=" O LYS Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 357 Processing helix chain 'Y' and resid 361 through 366 removed outlier: 3.804A pdb=" N TRP Y 365 " --> pdb=" O GLY Y 361 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER Y 366 " --> pdb=" O ARG Y 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 361 through 366' Processing helix chain 'Y' and resid 370 through 380 Processing helix chain 'Y' and resid 403 through 418 Processing helix chain 'Y' and resid 424 through 449 removed outlier: 3.569A pdb=" N ARG Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS Y 436 " --> pdb=" O ARG Y 432 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU Y 445 " --> pdb=" O THR Y 441 " (cutoff:3.500A) Processing helix chain 'Y' and resid 456 through 473 removed outlier: 3.746A pdb=" N VAL Y 460 " --> pdb=" O GLN Y 456 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU Y 461 " --> pdb=" O SER Y 457 " (cutoff:3.500A) Processing helix chain 'Y' and resid 474 through 476 No H-bonds generated for 'chain 'Y' and resid 474 through 476' Processing helix chain 'Y' and resid 483 through 501 removed outlier: 3.840A pdb=" N CYS Y 487 " --> pdb=" O GLU Y 483 " (cutoff:3.500A) Processing helix chain 'Y' and resid 502 through 504 No H-bonds generated for 'chain 'Y' and resid 502 through 504' Processing helix chain 'Y' and resid 602 through 610 Processing helix chain 'Y' and resid 711 through 728 removed outlier: 3.541A pdb=" N ARG Y 727 " --> pdb=" O GLU Y 723 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG Y 728 " --> pdb=" O VAL Y 724 " (cutoff:3.500A) Processing helix chain 'Y' and resid 737 through 761 removed outlier: 4.173A pdb=" N ARG Y 741 " --> pdb=" O ALA Y 737 " (cutoff:3.500A) Processing helix chain 'Y' and resid 790 through 802 removed outlier: 3.769A pdb=" N TYR Y 802 " --> pdb=" O ALA Y 798 " (cutoff:3.500A) Processing helix chain 'Y' and resid 886 through 892 Processing helix chain 'Y' and resid 897 through 903 Processing helix chain 'Y' and resid 906 through 914 removed outlier: 4.825A pdb=" N UNK Y 910 " --> pdb=" O UNK Y 906 " (cutoff:3.500A) Processing helix chain 'Y' and resid 935 through 938 Processing helix chain 'Y' and resid 939 through 951 removed outlier: 3.764A pdb=" N LEU Y 947 " --> pdb=" O ALA Y 943 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN Y 950 " --> pdb=" O TRP Y 946 " (cutoff:3.500A) Processing helix chain 'Y' and resid 965 through 978 Processing sheet with id=AA1, first strand: chain 'Y' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'Y' and resid 27 through 29 removed outlier: 6.921A pdb=" N THR Y 651 " --> pdb=" O ALA Y 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 27 through 29 removed outlier: 6.921A pdb=" N THR Y 651 " --> pdb=" O ALA Y 625 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Y' and resid 530 through 532 removed outlier: 3.554A pdb=" N LEU Y 547 " --> pdb=" O LEU Y 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 680 through 682 removed outlier: 3.840A pdb=" N ALA Y 682 " --> pdb=" O GLY Y 670 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE Y 669 " --> pdb=" O VAL Y 767 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 134 hydrogen bonds 252 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 5.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1448 1.32 - 1.44: 3543 1.44 - 1.57: 5087 1.57 - 1.69: 303 1.69 - 1.81: 32 Bond restraints: 10413 Sorted by residual: bond pdb=" C ASP Y 685 " pdb=" N PRO Y 686 " ideal model delta sigma weight residual 1.330 1.377 -0.047 1.25e-02 6.40e+03 1.39e+01 bond pdb=" CA ASN Y 501 " pdb=" C ASN Y 501 " ideal model delta sigma weight residual 1.521 1.543 -0.021 1.17e-02 7.31e+03 3.27e+00 bond pdb=" CB PHE Y 544 " pdb=" CG PHE Y 544 " ideal model delta sigma weight residual 1.502 1.460 0.042 2.30e-02 1.89e+03 3.26e+00 bond pdb=" N PHE Y 736 " pdb=" CA PHE Y 736 " ideal model delta sigma weight residual 1.462 1.484 -0.023 1.31e-02 5.83e+03 3.02e+00 bond pdb=" C TYR Y 196 " pdb=" N SER Y 197 " ideal model delta sigma weight residual 1.334 1.304 0.030 1.79e-02 3.12e+03 2.74e+00 ... (remaining 10408 not shown) Histogram of bond angle deviations from ideal: 96.73 - 104.35: 673 104.35 - 111.98: 5348 111.98 - 119.60: 3806 119.60 - 127.23: 4583 127.23 - 134.86: 398 Bond angle restraints: 14808 Sorted by residual: angle pdb=" N PHE Y 736 " pdb=" CA PHE Y 736 " pdb=" C PHE Y 736 " ideal model delta sigma weight residual 110.91 124.49 -13.58 1.17e+00 7.31e-01 1.35e+02 angle pdb=" C LYS Y 735 " pdb=" N PHE Y 736 " pdb=" CA PHE Y 736 " ideal model delta sigma weight residual 122.93 132.33 -9.40 1.51e+00 4.39e-01 3.88e+01 angle pdb=" C PHE Y 609 " pdb=" N ILE Y 610 " pdb=" CA ILE Y 610 " ideal model delta sigma weight residual 123.16 117.10 6.06 1.06e+00 8.90e-01 3.26e+01 angle pdb=" C LEU Y 574 " pdb=" N TYR Y 575 " pdb=" CA TYR Y 575 " ideal model delta sigma weight residual 121.54 132.44 -10.90 1.91e+00 2.74e-01 3.26e+01 angle pdb=" CA LEU Y 574 " pdb=" CB LEU Y 574 " pdb=" CG LEU Y 574 " ideal model delta sigma weight residual 116.30 98.55 17.75 3.50e+00 8.16e-02 2.57e+01 ... (remaining 14803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 5431 35.46 - 70.92: 358 70.92 - 106.39: 29 106.39 - 141.85: 2 141.85 - 177.31: 7 Dihedral angle restraints: 5827 sinusoidal: 3204 harmonic: 2623 Sorted by residual: dihedral pdb=" CA LYS Y 735 " pdb=" C LYS Y 735 " pdb=" N PHE Y 736 " pdb=" CA PHE Y 736 " ideal model delta harmonic sigma weight residual -180.00 -47.13 -132.87 0 5.00e+00 4.00e-02 7.06e+02 dihedral pdb=" CA VAL Y 368 " pdb=" C VAL Y 368 " pdb=" N THR Y 369 " pdb=" CA THR Y 369 " ideal model delta harmonic sigma weight residual 180.00 124.13 55.87 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" C4' C B 40 " pdb=" C3' C B 40 " pdb=" C2' C B 40 " pdb=" C1' C B 40 " ideal model delta sinusoidal sigma weight residual -35.00 36.19 -71.19 1 8.00e+00 1.56e-02 1.02e+02 ... (remaining 5824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1498 0.076 - 0.152: 227 0.152 - 0.228: 30 0.228 - 0.303: 5 0.303 - 0.379: 2 Chirality restraints: 1762 Sorted by residual: chirality pdb=" C3' C B 111 " pdb=" C4' C B 111 " pdb=" O3' C B 111 " pdb=" C2' C B 111 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" C3' G B 30 " pdb=" C4' G B 30 " pdb=" O3' G B 30 " pdb=" C2' G B 30 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C3' G B 44 " pdb=" C4' G B 44 " pdb=" O3' G B 44 " pdb=" C2' G B 44 " both_signs ideal model delta sigma weight residual False -2.48 -2.18 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 1759 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 105 " 0.038 2.00e-02 2.50e+03 1.95e-02 8.53e+00 pdb=" N1 C B 105 " -0.028 2.00e-02 2.50e+03 pdb=" C2 C B 105 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C B 105 " -0.018 2.00e-02 2.50e+03 pdb=" N3 C B 105 " 0.007 2.00e-02 2.50e+03 pdb=" C4 C B 105 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C B 105 " 0.019 2.00e-02 2.50e+03 pdb=" C5 C B 105 " -0.020 2.00e-02 2.50e+03 pdb=" C6 C B 105 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 52 " -0.028 2.00e-02 2.50e+03 1.67e-02 8.39e+00 pdb=" N9 G B 52 " 0.012 2.00e-02 2.50e+03 pdb=" C8 G B 52 " 0.012 2.00e-02 2.50e+03 pdb=" N7 G B 52 " 0.006 2.00e-02 2.50e+03 pdb=" C5 G B 52 " 0.010 2.00e-02 2.50e+03 pdb=" C6 G B 52 " 0.020 2.00e-02 2.50e+03 pdb=" O6 G B 52 " -0.027 2.00e-02 2.50e+03 pdb=" N1 G B 52 " -0.022 2.00e-02 2.50e+03 pdb=" C2 G B 52 " 0.022 2.00e-02 2.50e+03 pdb=" N2 G B 52 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B 52 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G B 52 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY Y 25 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO Y 26 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO Y 26 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO Y 26 " -0.039 5.00e-02 4.00e+02 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 381 2.66 - 3.22: 8575 3.22 - 3.78: 17833 3.78 - 4.34: 20284 4.34 - 4.90: 29980 Nonbonded interactions: 77053 Sorted by model distance: nonbonded pdb=" O2' C B 40 " pdb=" OP1 U B 41 " model vdw 2.099 2.440 nonbonded pdb=" OD1 ASP Y 513 " pdb=" OG SER Y 515 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR Y 29 " pdb=" O2 U B 103 " model vdw 2.243 2.440 nonbonded pdb=" O ALA Y 816 " pdb=" OG1 THR Y 819 " model vdw 2.247 2.440 nonbonded pdb=" OH TYR Y 382 " pdb=" O SER Y 470 " model vdw 2.300 2.440 ... (remaining 77048 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=1.00 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 4.420 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 33.850 Find NCS groups from input model: 0.230 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.007 0.051 10413 Z= 0.453 Angle : 1.114 17.747 14808 Z= 0.597 Chirality : 0.058 0.379 1762 Planarity : 0.008 0.071 1335 Dihedral : 21.200 177.312 4123 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.39 % Allowed : 18.62 % Favored : 80.99 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -4.84 (0.24), residues: 768 helix: -2.46 (0.21), residues: 326 sheet: -3.42 (0.51), residues: 83 loop : -3.92 (0.27), residues: 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 94 average time/residue: 0.2598 time to fit residues: 33.3493 Evaluate side-chains 62 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0899 time to fit residues: 1.1930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 30.0000 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 0.0040 chunk 80 optimal weight: 50.0000 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 16 ASN ** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 283 GLN Y 398 ASN Y 636 ASN ** Y 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 930 HIS Y 937 GLN Y 950 ASN ** Y 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10413 Z= 0.203 Angle : 0.717 7.749 14808 Z= 0.386 Chirality : 0.041 0.266 1762 Planarity : 0.005 0.058 1335 Dihedral : 21.989 175.312 2712 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 17.06 % Favored : 82.68 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -3.47 (0.28), residues: 768 helix: -0.69 (0.26), residues: 335 sheet: -3.45 (0.49), residues: 89 loop : -3.72 (0.30), residues: 344 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.2299 time to fit residues: 31.7058 Evaluate side-chains 68 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.872 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0880 time to fit residues: 1.1912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 30.0000 chunk 63 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 85 GLN ** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 374 ASN Y 381 ASN Y 715 GLN Y 950 ASN ** Y 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.049 10413 Z= 0.478 Angle : 0.943 11.838 14808 Z= 0.491 Chirality : 0.049 0.279 1762 Planarity : 0.006 0.063 1335 Dihedral : 22.347 178.331 2712 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 25.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 20.57 % Favored : 79.30 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -3.31 (0.29), residues: 768 helix: -0.16 (0.28), residues: 326 sheet: -3.60 (0.48), residues: 90 loop : -3.95 (0.29), residues: 352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 78 average time/residue: 0.2300 time to fit residues: 25.6912 Evaluate side-chains 58 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0948 time to fit residues: 1.2793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 715 GLN Y 758 HIS Y 762 HIS ** Y 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 10413 Z= 0.330 Angle : 0.814 9.775 14808 Z= 0.428 Chirality : 0.044 0.278 1762 Planarity : 0.005 0.056 1335 Dihedral : 22.142 173.622 2712 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 19.40 % Favored : 80.47 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -3.13 (0.29), residues: 768 helix: 0.07 (0.29), residues: 322 sheet: -3.65 (0.48), residues: 89 loop : -3.85 (0.28), residues: 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 93 average time/residue: 0.2144 time to fit residues: 28.7989 Evaluate side-chains 65 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0914 time to fit residues: 1.2174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 50.0000 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 25 optimal weight: 0.0980 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 726 GLN ** Y 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 10413 Z= 0.288 Angle : 0.769 8.985 14808 Z= 0.406 Chirality : 0.043 0.288 1762 Planarity : 0.005 0.053 1335 Dihedral : 21.971 172.076 2712 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 19.40 % Favored : 80.47 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.10 (0.29), residues: 768 helix: -0.00 (0.28), residues: 330 sheet: -3.66 (0.48), residues: 89 loop : -3.80 (0.29), residues: 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.2217 time to fit residues: 29.0497 Evaluate side-chains 64 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.1980 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 82 optimal weight: 50.0000 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 10413 Z= 0.224 Angle : 0.721 8.235 14808 Z= 0.382 Chirality : 0.042 0.284 1762 Planarity : 0.004 0.050 1335 Dihedral : 21.775 170.725 2712 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 18.23 % Favored : 81.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.29), residues: 768 helix: 0.35 (0.29), residues: 325 sheet: -3.54 (0.47), residues: 89 loop : -3.66 (0.29), residues: 354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2195 time to fit residues: 29.6988 Evaluate side-chains 64 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 10413 Z= 0.268 Angle : 0.750 8.666 14808 Z= 0.395 Chirality : 0.043 0.288 1762 Planarity : 0.004 0.049 1335 Dihedral : 21.783 171.540 2712 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 19.40 % Favored : 80.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.29), residues: 768 helix: 0.33 (0.28), residues: 331 sheet: -3.60 (0.47), residues: 89 loop : -3.71 (0.29), residues: 348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2021 time to fit residues: 27.3476 Evaluate side-chains 58 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 0.0870 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 78 optimal weight: 40.0000 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 overall best weight: 3.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 933 HIS ** Y 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 10413 Z= 0.321 Angle : 0.798 8.947 14808 Z= 0.419 Chirality : 0.045 0.299 1762 Planarity : 0.005 0.050 1335 Dihedral : 21.868 171.768 2712 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 19.14 % Favored : 80.73 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.29), residues: 768 helix: 0.30 (0.28), residues: 328 sheet: -3.61 (0.47), residues: 89 loop : -3.66 (0.29), residues: 351 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 88 average time/residue: 0.2201 time to fit residues: 28.2282 Evaluate side-chains 60 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1070 time to fit residues: 1.3016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 72 optimal weight: 0.1980 chunk 28 optimal weight: 8.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 0.0050 chunk 97 optimal weight: 20.0000 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 190 GLN Y 250 HIS Y 971 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10413 Z= 0.164 Angle : 0.685 9.700 14808 Z= 0.361 Chirality : 0.040 0.241 1762 Planarity : 0.004 0.042 1335 Dihedral : 21.586 172.983 2712 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.76 % Favored : 84.11 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.31), residues: 768 helix: 0.93 (0.29), residues: 328 sheet: -3.07 (0.54), residues: 78 loop : -3.45 (0.30), residues: 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.808 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.1984 time to fit residues: 29.8230 Evaluate side-chains 68 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 30.0000 chunk 102 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 81 optimal weight: 40.0000 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 758 HIS Y 971 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 10413 Z= 0.367 Angle : 0.819 9.064 14808 Z= 0.429 Chirality : 0.045 0.280 1762 Planarity : 0.005 0.051 1335 Dihedral : 21.712 172.288 2712 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.26 % Allowed : 19.01 % Favored : 80.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.30), residues: 768 helix: 0.45 (0.29), residues: 331 sheet: -3.54 (0.47), residues: 89 loop : -3.74 (0.29), residues: 348 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.854 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1956 time to fit residues: 24.9256 Evaluate side-chains 60 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.1980 chunk 75 optimal weight: 0.5980 chunk 12 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 40.0000 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 10 optimal weight: 0.0470 chunk 15 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 250 HIS ** Y 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.102527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.078411 restraints weight = 32000.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.081128 restraints weight = 15606.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.082962 restraints weight = 9748.958| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10413 Z= 0.176 Angle : 0.685 9.681 14808 Z= 0.361 Chirality : 0.040 0.236 1762 Planarity : 0.004 0.043 1335 Dihedral : 21.530 171.245 2712 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.28 % Favored : 83.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.31), residues: 768 helix: 0.74 (0.28), residues: 338 sheet: -2.88 (0.55), residues: 78 loop : -3.56 (0.30), residues: 352 =============================================================================== Job complete usr+sys time: 1603.76 seconds wall clock time: 30 minutes 17.74 seconds (1817.74 seconds total)