Starting phenix.real_space_refine on Mon Mar 11 09:08:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/03_2024/6n7w_0365_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/03_2024/6n7w_0365.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/03_2024/6n7w_0365_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/03_2024/6n7w_0365_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/03_2024/6n7w_0365_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/03_2024/6n7w_0365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/03_2024/6n7w_0365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/03_2024/6n7w_0365_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/03_2024/6n7w_0365_updated.pdb" } resolution = 4.5 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 73 5.49 5 Mg 1 5.21 5 S 27 5.16 5 C 4755 2.51 5 N 1367 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 229": "NH1" <-> "NH2" Residue "H ARG 307": "NH1" <-> "NH2" Residue "H ARG 590": "NH1" <-> "NH2" 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: 7837 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5575 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 30, 'TRANS': 671} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 516 Unusual residues: {'2DA': 1} Classifications: {'DNA': 24, 'undetermined': 1} Link IDs: {'rna3p': 23, None: 1} Not linked: pdbres=" DG P 24 " pdbres="2DA P 25 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "T" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 918 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.86, per 1000 atoms: 0.62 Number of scatterers: 7837 At special positions: 0 Unit cell: (98.04, 129, 103.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 73 15.00 Mg 1 11.99 O 1614 8.00 N 1367 7.00 C 4755 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 6 sheets defined 43.7% alpha, 7.7% beta 32 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'H' and resid 39 through 51 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 91 through 98 Processing helix chain 'H' and resid 125 through 131 Processing helix chain 'H' and resid 139 through 150 Processing helix chain 'H' and resid 158 through 160 No H-bonds generated for 'chain 'H' and resid 158 through 160' Processing helix chain 'H' and resid 165 through 186 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 203 through 208 Processing helix chain 'H' and resid 212 through 230 Processing helix chain 'H' and resid 236 through 260 Processing helix chain 'H' and resid 304 through 307 No H-bonds generated for 'chain 'H' and resid 304 through 307' Processing helix chain 'H' and resid 339 through 349 Processing helix chain 'H' and resid 366 through 371 Processing helix chain 'H' and resid 377 through 399 removed outlier: 4.402A pdb=" N ASP H 384 " --> pdb=" O GLN H 380 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 409 No H-bonds generated for 'chain 'H' and resid 406 through 409' Processing helix chain 'H' and resid 437 through 439 No H-bonds generated for 'chain 'H' and resid 437 through 439' Processing helix chain 'H' and resid 448 through 453 Processing helix chain 'H' and resid 457 through 459 No H-bonds generated for 'chain 'H' and resid 457 through 459' Processing helix chain 'H' and resid 479 through 492 removed outlier: 4.980A pdb=" N ARG H 490 " --> pdb=" O HIS H 486 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N PHE H 491 " --> pdb=" O PHE H 487 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 499 Processing helix chain 'H' and resid 505 through 513 Processing helix chain 'H' and resid 518 through 529 Processing helix chain 'H' and resid 534 through 541 Processing helix chain 'H' and resid 545 through 558 Processing helix chain 'H' and resid 561 through 573 Processing helix chain 'H' and resid 609 through 635 removed outlier: 3.683A pdb=" N SER H 616 " --> pdb=" O THR H 612 " (cutoff:3.500A) Processing helix chain 'H' and resid 663 through 683 Processing helix chain 'H' and resid 700 through 703 No H-bonds generated for 'chain 'H' and resid 700 through 703' Processing helix chain 'I' and resid 9 through 15 Processing helix chain 'I' and resid 35 through 48 Proline residue: I 40 - end of helix removed outlier: 3.640A pdb=" N ASP I 47 " --> pdb=" O ASP I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 70 Processing helix chain 'I' and resid 96 through 104 Processing sheet with id= A, first strand: chain 'H' and resid 56 through 58 Processing sheet with id= B, first strand: chain 'H' and resid 264 through 266 Processing sheet with id= C, first strand: chain 'H' and resid 655 through 660 removed outlier: 3.829A pdb=" N VAL H 470 " --> pdb=" O CYS H 660 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 592 through 594 Processing sheet with id= E, first strand: chain 'H' and resid 2 through 8 removed outlier: 3.817A pdb=" N CYS H 20 " --> pdb=" O GLU H 7 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 54 through 59 removed outlier: 3.769A pdb=" N PHE I 27 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR I 77 " --> pdb=" O PHE I 27 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA I 88 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LYS I 82 " --> pdb=" O VAL I 86 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL I 86 " --> pdb=" O LYS I 82 " (cutoff:3.500A) 252 hydrogen bonds defined for protein. 747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1185 1.31 - 1.43: 2512 1.43 - 1.56: 4281 1.56 - 1.68: 141 1.68 - 1.81: 42 Bond restraints: 8161 Sorted by residual: bond pdb=" C3' 2DA P 25 " pdb=" C2' 2DA P 25 " ideal model delta sigma weight residual 1.271 1.524 -0.253 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C4' 2DA P 25 " pdb=" O4' 2DA P 25 " ideal model delta sigma weight residual 1.288 1.445 -0.157 2.00e-02 2.50e+03 6.16e+01 bond pdb=" C1' 2DA P 25 " pdb=" N9 2DA P 25 " ideal model delta sigma weight residual 1.347 1.493 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C4' 2DA P 25 " pdb=" C3' 2DA P 25 " ideal model delta sigma weight residual 1.625 1.519 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O4' 2DA P 25 " pdb=" C1' 2DA P 25 " ideal model delta sigma weight residual 1.525 1.420 0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 8156 not shown) Histogram of bond angle deviations from ideal: 98.24 - 105.44: 445 105.44 - 112.64: 4252 112.64 - 119.83: 2888 119.83 - 127.03: 3508 127.03 - 134.23: 260 Bond angle restraints: 11353 Sorted by residual: angle pdb=" C HIS H 653 " pdb=" N ASP H 654 " pdb=" CA ASP H 654 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C1' 2DA P 25 " pdb=" N9 2DA P 25 " pdb=" C8 2DA P 25 " ideal model delta sigma weight residual 128.68 115.81 12.87 3.00e+00 1.11e-01 1.84e+01 angle pdb=" PB TTP H4002 " pdb=" O3B TTP H4002 " pdb=" PG TTP H4002 " ideal model delta sigma weight residual 120.50 132.64 -12.14 3.00e+00 1.11e-01 1.64e+01 angle pdb=" PA TTP H4002 " pdb=" O3A TTP H4002 " pdb=" PB TTP H4002 " ideal model delta sigma weight residual 120.50 132.62 -12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" C1' 2DA P 25 " pdb=" N9 2DA P 25 " pdb=" C4 2DA P 25 " ideal model delta sigma weight residual 122.04 133.87 -11.83 3.00e+00 1.11e-01 1.56e+01 ... (remaining 11348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.21: 4211 30.21 - 60.42: 409 60.42 - 90.63: 14 90.63 - 120.84: 1 120.84 - 151.05: 1 Dihedral angle restraints: 4636 sinusoidal: 2324 harmonic: 2312 Sorted by residual: dihedral pdb=" C2 TTP H4002 " pdb=" C1' TTP H4002 " pdb=" N1 TTP H4002 " pdb=" O4' TTP H4002 " ideal model delta sinusoidal sigma weight residual 301.68 150.63 151.05 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" CA GLY I 33 " pdb=" C GLY I 33 " pdb=" N PRO I 34 " pdb=" CA PRO I 34 " ideal model delta harmonic sigma weight residual 180.00 150.76 29.24 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" O3B TTP H4002 " pdb=" O3A TTP H4002 " pdb=" PB TTP H4002 " pdb=" PA TTP H4002 " ideal model delta sinusoidal sigma weight residual 180.00 67.20 112.80 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 4633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 955 0.050 - 0.100: 213 0.100 - 0.150: 54 0.150 - 0.199: 3 0.199 - 0.249: 2 Chirality restraints: 1227 Sorted by residual: chirality pdb=" C3' TTP H4002 " pdb=" C2' TTP H4002 " pdb=" C4' TTP H4002 " pdb=" O3' TTP H4002 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C4' TTP H4002 " pdb=" C3' TTP H4002 " pdb=" C5' TTP H4002 " pdb=" O4' TTP H4002 " both_signs ideal model delta sigma weight residual False -2.50 -2.71 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA LEU H 690 " pdb=" N LEU H 690 " pdb=" C LEU H 690 " pdb=" CB LEU H 690 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 1224 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 52 " 0.732 9.50e-02 1.11e+02 3.28e-01 6.55e+01 pdb=" NE ARG H 52 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG H 52 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG H 52 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 52 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 307 " -0.695 9.50e-02 1.11e+02 3.11e-01 5.91e+01 pdb=" NE ARG H 307 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG H 307 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG H 307 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 307 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 96 " -0.491 9.50e-02 1.11e+02 2.20e-01 2.96e+01 pdb=" NE ARG H 96 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG H 96 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG H 96 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 96 " -0.017 2.00e-02 2.50e+03 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 156 2.68 - 3.24: 6556 3.24 - 3.79: 13196 3.79 - 4.35: 16601 4.35 - 4.90: 25354 Nonbonded interactions: 61863 Sorted by model distance: nonbonded pdb=" OD2 ASP H 654 " pdb="MG MG H4001 " model vdw 2.125 2.170 nonbonded pdb=" O SER H 568 " pdb=" OG1 THR H 572 " model vdw 2.290 2.440 nonbonded pdb=" O ALA H 476 " pdb="MG MG H4001 " model vdw 2.294 2.170 nonbonded pdb="MG MG H4001 " pdb=" O3G TTP H4002 " model vdw 2.329 2.170 nonbonded pdb=" OG SER H 4 " pdb=" OH TYR H 42 " model vdw 2.361 2.440 ... (remaining 61858 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.280 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 28.670 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.006 0.253 8161 Z= 0.314 Angle : 0.751 12.868 11353 Z= 0.414 Chirality : 0.045 0.249 1227 Planarity : 0.016 0.328 1218 Dihedral : 19.394 151.054 3156 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.36 % Favored : 95.51 % Rotamer: Outliers : 0.46 % Allowed : 3.50 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.26), residues: 802 helix: -1.57 (0.20), residues: 392 sheet: -0.88 (0.69), residues: 69 loop : -1.86 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 679 HIS 0.005 0.001 HIS H 276 PHE 0.016 0.002 PHE H 487 TYR 0.013 0.001 TYR H 326 ARG 0.004 0.000 ARG H 591 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LEU cc_start: 0.9158 (mt) cc_final: 0.8640 (mm) REVERT: H 135 MET cc_start: 0.7843 (tpp) cc_final: 0.5028 (mmm) REVERT: H 167 MET cc_start: 0.9306 (ttm) cc_final: 0.9052 (ttp) REVERT: H 488 MET cc_start: 0.8127 (ptt) cc_final: 0.7183 (ppp) REVERT: H 658 VAL cc_start: 0.9124 (t) cc_final: 0.8886 (m) REVERT: I 23 ILE cc_start: 0.9003 (mt) cc_final: 0.8768 (mm) REVERT: I 57 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8770 (mtpp) REVERT: I 70 TYR cc_start: 0.8101 (m-80) cc_final: 0.7700 (m-80) outliers start: 3 outliers final: 0 residues processed: 150 average time/residue: 0.2695 time to fit residues: 50.8788 Evaluate side-chains 70 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 GLN H 190 HIS H 230 ASN H 423 ASN H 570 GLN H 611 ASN H 615 GLN ** H 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8161 Z= 0.203 Angle : 0.546 7.690 11353 Z= 0.297 Chirality : 0.039 0.132 1227 Planarity : 0.005 0.059 1218 Dihedral : 23.515 147.702 1636 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.15 % Allowed : 1.83 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.30), residues: 802 helix: 0.71 (0.26), residues: 391 sheet: -0.23 (0.68), residues: 68 loop : -1.28 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 700 HIS 0.006 0.001 HIS H 432 PHE 0.011 0.001 PHE H 686 TYR 0.020 0.001 TYR H 203 ARG 0.004 0.000 ARG H 591 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9651 (pt) cc_final: 0.9328 (pt) REVERT: H 119 ARG cc_start: 0.8362 (mmt180) cc_final: 0.8028 (mmm-85) REVERT: I 66 THR cc_start: 0.8815 (m) cc_final: 0.8471 (m) REVERT: I 69 LYS cc_start: 0.8861 (ptpp) cc_final: 0.8495 (pttm) outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.2686 time to fit residues: 31.8606 Evaluate side-chains 58 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 HIS H 611 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.004 0.027 8161 Z= 0.223 Angle : 0.554 7.517 11353 Z= 0.300 Chirality : 0.040 0.146 1227 Planarity : 0.004 0.052 1218 Dihedral : 23.669 148.012 1636 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.15 % Allowed : 2.59 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.31), residues: 802 helix: 1.16 (0.27), residues: 392 sheet: -0.70 (0.64), residues: 80 loop : -0.91 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 469 HIS 0.006 0.001 HIS H 432 PHE 0.012 0.001 PHE H 686 TYR 0.014 0.001 TYR H 203 ARG 0.004 0.000 ARG I 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 119 ARG cc_start: 0.8428 (mmt180) cc_final: 0.8071 (mmm-85) REVERT: H 174 ASP cc_start: 0.8699 (m-30) cc_final: 0.8113 (m-30) REVERT: H 488 MET cc_start: 0.8125 (ptt) cc_final: 0.6864 (ppp) REVERT: H 529 LEU cc_start: 0.9243 (tp) cc_final: 0.9039 (tp) REVERT: H 677 MET cc_start: 0.8953 (tpp) cc_final: 0.8598 (tpt) REVERT: I 18 LYS cc_start: 0.8308 (mmtm) cc_final: 0.8030 (mmmm) REVERT: I 70 TYR cc_start: 0.7644 (m-80) cc_final: 0.6790 (m-80) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.2449 time to fit residues: 22.7731 Evaluate side-chains 53 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 19 HIS ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 520 ASN H 611 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8161 Z= 0.264 Angle : 0.585 7.467 11353 Z= 0.317 Chirality : 0.041 0.135 1227 Planarity : 0.004 0.049 1218 Dihedral : 23.768 147.880 1636 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.31), residues: 802 helix: 1.60 (0.27), residues: 380 sheet: -0.54 (0.62), residues: 79 loop : -0.75 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 469 HIS 0.008 0.002 HIS H 432 PHE 0.011 0.001 PHE H 686 TYR 0.012 0.002 TYR H 203 ARG 0.004 0.001 ARG H 599 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9472 (pt) cc_final: 0.9149 (pt) REVERT: H 119 ARG cc_start: 0.8487 (mmt180) cc_final: 0.8126 (mmm-85) REVERT: H 167 MET cc_start: 0.9314 (ttm) cc_final: 0.8918 (mtm) REVERT: H 170 TYR cc_start: 0.6928 (t80) cc_final: 0.6725 (t80) REVERT: H 174 ASP cc_start: 0.8685 (m-30) cc_final: 0.8072 (m-30) REVERT: H 488 MET cc_start: 0.8160 (ptt) cc_final: 0.7869 (ppp) REVERT: H 677 MET cc_start: 0.8976 (tpp) cc_final: 0.8654 (tpt) REVERT: I 18 LYS cc_start: 0.8409 (mmtm) cc_final: 0.8108 (mmmm) REVERT: I 30 GLU cc_start: 0.7971 (pp20) cc_final: 0.7503 (pp20) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2412 time to fit residues: 21.9032 Evaluate side-chains 54 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 347 GLN H 611 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8161 Z= 0.264 Angle : 0.583 7.261 11353 Z= 0.315 Chirality : 0.040 0.131 1227 Planarity : 0.004 0.058 1218 Dihedral : 23.816 147.299 1636 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.31), residues: 802 helix: 1.61 (0.27), residues: 381 sheet: -0.27 (0.63), residues: 77 loop : -0.71 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 469 HIS 0.007 0.002 HIS H 432 PHE 0.021 0.001 PHE H 686 TYR 0.010 0.001 TYR H 203 ARG 0.003 0.001 ARG H 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9516 (pt) cc_final: 0.9160 (pt) REVERT: H 167 MET cc_start: 0.9419 (ttm) cc_final: 0.8855 (mtm) REVERT: H 174 ASP cc_start: 0.8635 (m-30) cc_final: 0.8037 (m-30) REVERT: H 488 MET cc_start: 0.8171 (ptt) cc_final: 0.7864 (ppp) REVERT: H 677 MET cc_start: 0.8872 (tpp) cc_final: 0.8437 (tpp) REVERT: I 70 TYR cc_start: 0.7154 (m-80) cc_final: 0.6882 (m-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2488 time to fit residues: 21.3966 Evaluate side-chains 49 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 69 optimal weight: 0.0370 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 611 ASN I 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8161 Z= 0.246 Angle : 0.575 7.313 11353 Z= 0.315 Chirality : 0.040 0.136 1227 Planarity : 0.004 0.056 1218 Dihedral : 23.729 146.304 1636 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.31), residues: 802 helix: 1.62 (0.27), residues: 382 sheet: -0.19 (0.64), residues: 77 loop : -0.52 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 651 HIS 0.006 0.001 HIS H 432 PHE 0.017 0.001 PHE H 686 TYR 0.014 0.001 TYR I 70 ARG 0.003 0.001 ARG H 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9513 (pt) cc_final: 0.9164 (pt) REVERT: H 167 MET cc_start: 0.9414 (ttm) cc_final: 0.8808 (mtm) REVERT: H 170 TYR cc_start: 0.6871 (t80) cc_final: 0.6529 (t80) REVERT: H 174 ASP cc_start: 0.8615 (m-30) cc_final: 0.7979 (m-30) REVERT: H 228 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7727 (tm-30) REVERT: H 488 MET cc_start: 0.8405 (ptt) cc_final: 0.8159 (ppp) REVERT: H 567 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7467 (tm-30) REVERT: H 677 MET cc_start: 0.8952 (tpp) cc_final: 0.8631 (tpt) REVERT: H 686 PHE cc_start: 0.7958 (t80) cc_final: 0.7204 (t80) REVERT: I 18 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8510 (mmmt) REVERT: I 30 GLU cc_start: 0.8164 (pp20) cc_final: 0.7849 (pp20) REVERT: I 36 LYS cc_start: 0.9068 (pttt) cc_final: 0.8655 (pptt) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2199 time to fit residues: 19.0166 Evaluate side-chains 53 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 611 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8161 Z= 0.177 Angle : 0.532 7.116 11353 Z= 0.292 Chirality : 0.039 0.136 1227 Planarity : 0.003 0.056 1218 Dihedral : 23.579 144.704 1636 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.32), residues: 802 helix: 1.79 (0.28), residues: 384 sheet: 0.00 (0.65), residues: 77 loop : -0.41 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 651 HIS 0.004 0.001 HIS H 432 PHE 0.014 0.001 PHE H 686 TYR 0.009 0.001 TYR H 203 ARG 0.007 0.000 ARG I 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9469 (pt) cc_final: 0.9259 (pt) REVERT: H 167 MET cc_start: 0.9393 (ttm) cc_final: 0.9053 (ttm) REVERT: H 174 ASP cc_start: 0.8598 (m-30) cc_final: 0.7991 (m-30) REVERT: H 488 MET cc_start: 0.8344 (ptt) cc_final: 0.8118 (ppp) REVERT: H 567 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7383 (tm-30) REVERT: H 677 MET cc_start: 0.8951 (tpp) cc_final: 0.8643 (tpt) REVERT: H 686 PHE cc_start: 0.7878 (t80) cc_final: 0.7038 (t80) REVERT: I 30 GLU cc_start: 0.8138 (pp20) cc_final: 0.7855 (pp20) REVERT: I 36 LYS cc_start: 0.9028 (pttt) cc_final: 0.8626 (pptt) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1936 time to fit residues: 17.5566 Evaluate side-chains 53 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 0.0010 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 611 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8161 Z= 0.200 Angle : 0.541 7.068 11353 Z= 0.296 Chirality : 0.039 0.147 1227 Planarity : 0.004 0.057 1218 Dihedral : 23.516 144.841 1636 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.32), residues: 802 helix: 1.82 (0.28), residues: 382 sheet: 0.02 (0.65), residues: 77 loop : -0.33 (0.37), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 651 HIS 0.005 0.001 HIS H 432 PHE 0.014 0.001 PHE H 555 TYR 0.009 0.001 TYR H 203 ARG 0.002 0.000 ARG H 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9495 (pt) cc_final: 0.9290 (pt) REVERT: H 135 MET cc_start: 0.7463 (mmm) cc_final: 0.7018 (mmm) REVERT: H 167 MET cc_start: 0.9505 (ttm) cc_final: 0.8629 (mtm) REVERT: H 488 MET cc_start: 0.8343 (ptt) cc_final: 0.8107 (ppp) REVERT: H 567 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7418 (tm-30) REVERT: H 677 MET cc_start: 0.8911 (tpp) cc_final: 0.8590 (tpt) REVERT: H 686 PHE cc_start: 0.7404 (t80) cc_final: 0.6555 (t80) REVERT: I 30 GLU cc_start: 0.8118 (pp20) cc_final: 0.7827 (pp20) REVERT: I 36 LYS cc_start: 0.9035 (pttt) cc_final: 0.8642 (pptt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2052 time to fit residues: 17.5767 Evaluate side-chains 51 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 0.0170 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 73 optimal weight: 0.0070 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8161 Z= 0.148 Angle : 0.518 6.857 11353 Z= 0.286 Chirality : 0.039 0.154 1227 Planarity : 0.003 0.057 1218 Dihedral : 23.329 143.255 1636 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.32), residues: 802 helix: 1.90 (0.28), residues: 384 sheet: 0.23 (0.68), residues: 71 loop : -0.24 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 651 HIS 0.003 0.001 HIS H 432 PHE 0.012 0.001 PHE H 686 TYR 0.009 0.001 TYR H 203 ARG 0.008 0.000 ARG I 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 135 MET cc_start: 0.7718 (mmm) cc_final: 0.7261 (mmm) REVERT: H 167 MET cc_start: 0.9469 (ttm) cc_final: 0.9101 (ttm) REVERT: H 174 ASP cc_start: 0.8795 (m-30) cc_final: 0.8577 (m-30) REVERT: H 488 MET cc_start: 0.8308 (ptt) cc_final: 0.8085 (ppp) REVERT: H 567 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7294 (tm-30) REVERT: H 649 MET cc_start: 0.8601 (pmm) cc_final: 0.7797 (pmm) REVERT: H 677 MET cc_start: 0.8932 (tpp) cc_final: 0.8611 (tpt) REVERT: H 686 PHE cc_start: 0.7463 (t80) cc_final: 0.6683 (t80) REVERT: I 30 GLU cc_start: 0.8040 (pp20) cc_final: 0.7751 (pp20) REVERT: I 36 LYS cc_start: 0.8989 (pttt) cc_final: 0.8786 (pptt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1653 time to fit residues: 15.8448 Evaluate side-chains 50 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 520 ASN H 611 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8161 Z= 0.377 Angle : 0.712 8.336 11353 Z= 0.381 Chirality : 0.044 0.167 1227 Planarity : 0.005 0.053 1218 Dihedral : 23.805 145.649 1636 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.31), residues: 802 helix: 1.33 (0.27), residues: 373 sheet: -0.86 (0.58), residues: 90 loop : -0.23 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 128 HIS 0.008 0.002 HIS H 459 PHE 0.021 0.002 PHE H 555 TYR 0.019 0.002 TYR H 24 ARG 0.005 0.001 ARG I 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 135 MET cc_start: 0.7724 (mmm) cc_final: 0.7290 (mmm) REVERT: H 158 MET cc_start: 0.9157 (mmm) cc_final: 0.8555 (mmm) REVERT: H 167 MET cc_start: 0.9528 (ttm) cc_final: 0.8628 (mtm) REVERT: H 488 MET cc_start: 0.8249 (ptt) cc_final: 0.7911 (ppp) REVERT: H 677 MET cc_start: 0.8941 (tpp) cc_final: 0.8620 (tpt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1751 time to fit residues: 14.7367 Evaluate side-chains 45 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 611 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.056837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.042213 restraints weight = 42096.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.043362 restraints weight = 23918.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.044133 restraints weight = 16420.931| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8161 Z= 0.181 Angle : 0.566 7.343 11353 Z= 0.308 Chirality : 0.040 0.148 1227 Planarity : 0.004 0.055 1218 Dihedral : 23.519 142.769 1636 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.32), residues: 802 helix: 1.84 (0.28), residues: 380 sheet: 0.04 (0.66), residues: 71 loop : -0.20 (0.37), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 651 HIS 0.004 0.001 HIS H 432 PHE 0.015 0.001 PHE H 686 TYR 0.016 0.001 TYR H 42 ARG 0.006 0.000 ARG I 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1579.05 seconds wall clock time: 29 minutes 47.03 seconds (1787.03 seconds total)