Starting phenix.real_space_refine on Thu Mar 14 23:14:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/03_2024/6ny1_8994.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/03_2024/6ny1_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_8994/03_2024/6ny1_8994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/03_2024/6ny1_8994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/03_2024/6ny1_8994.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny1_8994/03_2024/6ny1_8994.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-dev-5265/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: 5.93, per 1000 atoms: 0.60 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: 4.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.77 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: 4.67 Time building geometry restraints manager: 5.21 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: 5628 35.46 - 70.92: 532 70.92 - 106.39: 54 106.39 - 141.85: 2 141.85 - 177.31: 7 Dihedral angle restraints: 6223 sinusoidal: 3600 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 6220 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: 0.720 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: 0.010 Extract box with map and model: 3.980 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 32.940 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.160 ------------------------------------------------------------------------------- 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 : 23.727 177.312 4519 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 % Allowed : 12.71 % Favored : 86.96 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP Y 534 HIS 0.009 0.002 HIS Y 250 PHE 0.033 0.003 PHE Y 609 TYR 0.020 0.003 TYR Y 418 ARG 0.007 0.001 ARG Y 753 *********************** 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 : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 8 ILE cc_start: 0.9688 (mm) cc_final: 0.9351 (tt) REVERT: Y 67 MET cc_start: 0.8116 (ttp) cc_final: 0.7737 (tpp) REVERT: Y 75 MET cc_start: 0.8495 (mtm) cc_final: 0.8245 (mtp) REVERT: Y 490 GLN cc_start: 0.9402 (tt0) cc_final: 0.9026 (tp-100) REVERT: Y 747 MET cc_start: 0.9235 (tmm) cc_final: 0.8893 (tmm) REVERT: Y 749 ARG cc_start: 0.8887 (mtm-85) cc_final: 0.8660 (ttm170) outliers start: 2 outliers final: 1 residues processed: 94 average time/residue: 0.2434 time to fit residues: 31.0818 Evaluate side-chains 63 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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: 1.9990 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.0000 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Y 398 ASN Y 636 ASN ** Y 762 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1692 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= 0.209 Angle : 0.718 7.802 14808 Z= 0.387 Chirality : 0.041 0.262 1762 Planarity : 0.005 0.058 1335 Dihedral : 25.188 173.787 3108 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 17.06 % Favored : 82.68 % Rotamer: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % 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: -3.44 (0.28), residues: 768 helix: -0.65 (0.26), residues: 335 sheet: -3.35 (0.50), residues: 86 loop : -3.76 (0.29), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Y 534 HIS 0.002 0.001 HIS Y 443 PHE 0.030 0.002 PHE Y 736 TYR 0.015 0.002 TYR Y 196 ARG 0.003 0.000 ARG Y 466 *********************** 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 97 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 44 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7991 (mm-30) REVERT: Y 75 MET cc_start: 0.8744 (mtm) cc_final: 0.8423 (mtp) REVERT: Y 490 GLN cc_start: 0.9355 (tt0) cc_final: 0.9035 (tp-100) REVERT: Y 550 TYR cc_start: 0.7537 (m-80) cc_final: 0.7216 (m-80) REVERT: Y 574 LEU cc_start: 0.9114 (tp) cc_final: 0.8889 (tp) REVERT: Y 747 MET cc_start: 0.9260 (tmm) cc_final: 0.8899 (tmm) REVERT: Y 749 ARG cc_start: 0.8866 (mtm-85) cc_final: 0.8635 (ttm170) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2167 time to fit residues: 29.3383 Evaluate side-chains 64 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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: 4.9990 chunk 29 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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 283 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10413 Z= 0.384 Angle : 0.859 10.318 14808 Z= 0.450 Chirality : 0.046 0.267 1762 Planarity : 0.006 0.060 1335 Dihedral : 25.284 178.776 3108 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 19.27 % Favored : 80.60 % Rotamer: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % 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: -3.03 (0.29), residues: 768 helix: 0.06 (0.28), residues: 326 sheet: -3.56 (0.48), residues: 90 loop : -3.74 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Y 534 HIS 0.012 0.002 HIS Y 443 PHE 0.022 0.003 PHE Y 544 TYR 0.024 0.002 TYR Y 83 ARG 0.004 0.000 ARG Y 734 *********************** 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 79 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 75 MET cc_start: 0.8661 (mtm) cc_final: 0.8370 (mtp) REVERT: Y 326 LYS cc_start: 0.8885 (tmmt) cc_final: 0.8639 (ptmm) REVERT: Y 490 GLN cc_start: 0.9380 (tt0) cc_final: 0.9046 (tp-100) REVERT: Y 550 TYR cc_start: 0.7637 (m-80) cc_final: 0.7211 (m-80) REVERT: Y 747 MET cc_start: 0.9321 (tmm) cc_final: 0.8905 (tmm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2082 time to fit residues: 23.6237 Evaluate side-chains 61 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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: 7.9990 chunk 70 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 762 HIS ** Y 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 10413 Z= 0.422 Angle : 0.882 11.127 14808 Z= 0.461 Chirality : 0.047 0.272 1762 Planarity : 0.005 0.056 1335 Dihedral : 25.260 175.617 3108 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 21.35 % Favored : 78.52 % Rotamer: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % 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: -3.20 (0.29), residues: 768 helix: 0.06 (0.29), residues: 322 sheet: -3.82 (0.46), residues: 89 loop : -3.89 (0.28), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Y 795 HIS 0.007 0.002 HIS Y 758 PHE 0.025 0.003 PHE Y 98 TYR 0.018 0.002 TYR Y 382 ARG 0.005 0.001 ARG Y 734 *********************** 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 86 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 67 MET cc_start: 0.8217 (ttp) cc_final: 0.7907 (tpp) REVERT: Y 75 MET cc_start: 0.8669 (mtm) cc_final: 0.8379 (mtp) REVERT: Y 490 GLN cc_start: 0.9389 (tt0) cc_final: 0.9021 (tp-100) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2037 time to fit residues: 25.2734 Evaluate side-chains 64 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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: 0.0770 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 25 optimal weight: 0.0270 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 190 GLN ** Y 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 726 GLN Y 950 ASN ** 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: 0.7830 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10413 Z= 0.198 Angle : 0.702 7.495 14808 Z= 0.372 Chirality : 0.041 0.263 1762 Planarity : 0.004 0.050 1335 Dihedral : 24.970 173.179 3108 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.97 % Favored : 81.90 % Rotamer: Outliers : 0.17 % Allowed : 3.18 % Favored : 96.66 % 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: -2.76 (0.30), residues: 768 helix: 0.38 (0.29), residues: 328 sheet: -3.61 (0.47), residues: 89 loop : -3.67 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 344 HIS 0.004 0.001 HIS Y 250 PHE 0.021 0.002 PHE Y 609 TYR 0.012 0.001 TYR Y 196 ARG 0.004 0.000 ARG Y 299 *********************** 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 97 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 75 MET cc_start: 0.8818 (mtm) cc_final: 0.8500 (mtp) REVERT: Y 98 PHE cc_start: 0.8692 (m-80) cc_final: 0.8478 (m-10) REVERT: Y 490 GLN cc_start: 0.9389 (tt0) cc_final: 0.9059 (tp-100) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.2178 time to fit residues: 29.9423 Evaluate side-chains 66 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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: 0.0010 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 0.0570 chunk 24 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 82 optimal weight: 50.0000 chunk 46 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 715 GLN ** 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: 0.7726 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10413 Z= 0.163 Angle : 0.657 8.117 14808 Z= 0.348 Chirality : 0.039 0.226 1762 Planarity : 0.004 0.045 1335 Dihedral : 24.683 171.538 3108 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.89 % Favored : 83.98 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: -2.42 (0.30), residues: 768 helix: 0.78 (0.29), residues: 327 sheet: -3.29 (0.48), residues: 86 loop : -3.65 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 344 HIS 0.005 0.001 HIS Y 250 PHE 0.018 0.002 PHE Y 609 TYR 0.015 0.001 TYR Y 974 ARG 0.007 0.000 ARG Y 917 *********************** 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 100 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 75 MET cc_start: 0.8766 (mtm) cc_final: 0.8428 (mtp) REVERT: Y 490 GLN cc_start: 0.9381 (tt0) cc_final: 0.9103 (tp-100) REVERT: Y 747 MET cc_start: 0.8418 (tmm) cc_final: 0.7780 (mmt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1961 time to fit residues: 28.3605 Evaluate side-chains 67 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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: 20.0000 chunk 56 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 60 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 283 GLN ** 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: 0.7736 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10413 Z= 0.178 Angle : 0.675 8.476 14808 Z= 0.355 Chirality : 0.039 0.226 1762 Planarity : 0.004 0.045 1335 Dihedral : 24.540 170.150 3108 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.28 % Favored : 83.59 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: -2.35 (0.30), residues: 768 helix: 0.81 (0.29), residues: 324 sheet: -3.17 (0.50), residues: 86 loop : -3.56 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Y 534 HIS 0.008 0.001 HIS Y 199 PHE 0.016 0.002 PHE Y 609 TYR 0.013 0.002 TYR Y 974 ARG 0.004 0.000 ARG Y 299 *********************** 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 100 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 67 MET cc_start: 0.7909 (ttp) cc_final: 0.7562 (ttm) REVERT: Y 75 MET cc_start: 0.8781 (mtm) cc_final: 0.8447 (mtp) REVERT: Y 490 GLN cc_start: 0.9375 (tt0) cc_final: 0.9065 (tp-100) REVERT: Y 747 MET cc_start: 0.8471 (tmm) cc_final: 0.7762 (mmt) REVERT: Y 749 ARG cc_start: 0.8919 (ptp-170) cc_final: 0.8573 (ptm160) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2018 time to fit residues: 29.4251 Evaluate side-chains 71 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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: 2.9990 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 30.0000 chunk 49 optimal weight: 0.0670 chunk 9 optimal weight: 6.9990 chunk 78 optimal weight: 40.0000 chunk 90 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.6122 ------------------------------------------------------------------------------- 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 Y 930 HIS Y 971 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10413 Z= 0.186 Angle : 0.670 9.433 14808 Z= 0.353 Chirality : 0.039 0.227 1762 Planarity : 0.004 0.043 1335 Dihedral : 24.431 170.527 3108 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.02 % Favored : 83.85 % Rotamer: Outliers : 0.17 % Allowed : 1.17 % Favored : 98.66 % 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: -2.31 (0.30), residues: 768 helix: 0.76 (0.28), residues: 334 sheet: -3.05 (0.50), residues: 86 loop : -3.60 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 344 HIS 0.008 0.002 HIS Y 930 PHE 0.017 0.002 PHE Y 195 TYR 0.017 0.002 TYR Y 293 ARG 0.004 0.000 ARG Y 944 *********************** 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 103 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 67 MET cc_start: 0.8009 (ttp) cc_final: 0.7653 (ttm) REVERT: Y 75 MET cc_start: 0.8786 (mtm) cc_final: 0.8466 (mtp) REVERT: Y 280 LEU cc_start: 0.8964 (mt) cc_final: 0.8660 (pt) REVERT: Y 490 GLN cc_start: 0.9392 (tt0) cc_final: 0.9082 (tp-100) REVERT: Y 747 MET cc_start: 0.8512 (tmm) cc_final: 0.7721 (tpt) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.1926 time to fit residues: 28.7113 Evaluate side-chains 71 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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: 2.9990 chunk 92 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 60 optimal weight: 0.4980 chunk 97 optimal weight: 20.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 930 HIS Y 971 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10413 Z= 0.355 Angle : 0.818 9.173 14808 Z= 0.426 Chirality : 0.044 0.244 1762 Planarity : 0.005 0.051 1335 Dihedral : 24.627 172.086 3108 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 18.36 % Favored : 81.38 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -2.67 (0.29), residues: 768 helix: 0.30 (0.28), residues: 335 sheet: -3.12 (0.50), residues: 83 loop : -3.66 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Y 795 HIS 0.010 0.003 HIS Y 930 PHE 0.017 0.002 PHE Y 609 TYR 0.016 0.002 TYR Y 382 ARG 0.009 0.001 ARG Y 191 *********************** 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 91 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 67 MET cc_start: 0.8152 (ttp) cc_final: 0.7900 (ttm) REVERT: Y 75 MET cc_start: 0.8689 (mtm) cc_final: 0.8316 (mtp) REVERT: Y 95 MET cc_start: 0.8602 (mpp) cc_final: 0.8348 (mpp) REVERT: Y 335 GLU cc_start: 0.8920 (tp30) cc_final: 0.8669 (tp30) REVERT: Y 490 GLN cc_start: 0.9443 (tt0) cc_final: 0.9061 (tp-100) REVERT: Y 550 TYR cc_start: 0.8047 (m-80) cc_final: 0.7749 (m-10) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1884 time to fit residues: 25.0165 Evaluate side-chains 63 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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: 4.9990 chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 81 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 0.0770 chunk 87 optimal weight: 5.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 250 HIS Y 930 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3180 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= 0.266 Angle : 0.745 9.723 14808 Z= 0.391 Chirality : 0.042 0.239 1762 Planarity : 0.004 0.048 1335 Dihedral : 24.595 171.217 3108 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 18.23 % Favored : 81.64 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -2.62 (0.30), residues: 768 helix: 0.39 (0.28), residues: 332 sheet: -3.21 (0.50), residues: 86 loop : -3.61 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Y 795 HIS 0.011 0.002 HIS Y 930 PHE 0.051 0.002 PHE Y 331 TYR 0.018 0.002 TYR Y 293 ARG 0.004 0.000 ARG Y 944 ********************** 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 95 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 67 MET cc_start: 0.8072 (ttp) cc_final: 0.7759 (ttm) REVERT: Y 75 MET cc_start: 0.8741 (mtm) cc_final: 0.8409 (mtp) REVERT: Y 95 MET cc_start: 0.8524 (mpp) cc_final: 0.8233 (mpp) REVERT: Y 98 PHE cc_start: 0.8769 (m-80) cc_final: 0.8365 (m-80) REVERT: Y 326 LYS cc_start: 0.8593 (ptmm) cc_final: 0.8354 (ptmm) REVERT: Y 335 GLU cc_start: 0.8846 (tp30) cc_final: 0.8607 (tp30) REVERT: Y 409 ASP cc_start: 0.8998 (m-30) cc_final: 0.8633 (m-30) REVERT: Y 490 GLN cc_start: 0.9443 (tt0) cc_final: 0.9052 (tp-100) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2036 time to fit residues: 28.2631 Evaluate side-chains 70 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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: 6.9990 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 40.0000 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 10 optimal weight: 0.0010 chunk 15 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 250 HIS Y 930 HIS ** Y 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.100819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.075838 restraints weight = 32003.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078408 restraints weight = 16170.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.080127 restraints weight = 10400.106| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10413 Z= 0.191 Angle : 0.687 9.258 14808 Z= 0.363 Chirality : 0.040 0.231 1762 Planarity : 0.004 0.043 1335 Dihedral : 24.493 170.408 3108 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.67 % Favored : 83.20 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -2.31 (0.30), residues: 768 helix: 0.56 (0.28), residues: 342 sheet: -2.65 (0.58), residues: 74 loop : -3.58 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Y 344 HIS 0.009 0.002 HIS Y 930 PHE 0.045 0.002 PHE Y 331 TYR 0.015 0.002 TYR Y 974 ARG 0.003 0.000 ARG Y 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1701.52 seconds wall clock time: 31 minutes 38.36 seconds (1898.36 seconds total)