Starting phenix.real_space_refine on Fri Dec 8 08:30:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/12_2023/6n7w_0365_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/12_2023/6n7w_0365.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/12_2023/6n7w_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_0365/12_2023/6n7w_0365_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/12_2023/6n7w_0365_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/12_2023/6n7w_0365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/12_2023/6n7w_0365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/12_2023/6n7w_0365_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/12_2023/6n7w_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-1.21rc1-5172/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: 5.17, per 1000 atoms: 0.66 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: 3.46 Conformation dependent library (CDL) restraints added in 1.1 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: 3.22 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: 3.06 Time building geometry restraints manager: 3.70 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: 2.480 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: 0.000 Extract box with map and model: 3.890 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 27.280 Find NCS groups from input model: 0.200 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.870 ------------------------------------------------------------------------------- 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 : 0.822 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 outliers start: 3 outliers final: 0 residues processed: 150 average time/residue: 0.3019 time to fit residues: 56.7101 Evaluate side-chains 65 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9714 ------------------------------------------------------------------------------- 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: 0.9980 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 615 GLN H 653 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2460 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= 0.166 Angle : 0.528 7.541 11353 Z= 0.287 Chirality : 0.038 0.138 1227 Planarity : 0.004 0.060 1218 Dihedral : 23.446 147.453 1636 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.15 % Allowed : 1.67 % Favored : 98.17 % 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: -0.49 (0.30), residues: 802 helix: 0.57 (0.26), residues: 392 sheet: -0.40 (0.70), residues: 64 loop : -1.33 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 700 HIS 0.004 0.001 HIS H 432 PHE 0.010 0.001 PHE H 686 TYR 0.020 0.001 TYR H 203 ARG 0.004 0.000 ARG I 73 *********************** 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 99 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.2481 time to fit residues: 32.0563 Evaluate side-chains 53 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1106 time to fit residues: 1.1920 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 520 ASN ** H 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8161 Z= 0.257 Angle : 0.599 7.562 11353 Z= 0.321 Chirality : 0.041 0.129 1227 Planarity : 0.004 0.054 1218 Dihedral : 23.787 148.785 1636 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % 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: 0.14 (0.31), residues: 802 helix: 1.16 (0.27), residues: 387 sheet: -0.97 (0.62), residues: 82 loop : -0.83 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 469 HIS 0.008 0.001 HIS H 432 PHE 0.014 0.002 PHE H 686 TYR 0.014 0.002 TYR H 203 ARG 0.005 0.001 ARG H 591 *********************** 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 75 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2374 time to fit residues: 23.7226 Evaluate side-chains 52 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1225 ------------------------------------------------------------------------------- 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: 0.6980 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 8161 Z= 0.275 Angle : 0.596 7.458 11353 Z= 0.322 Chirality : 0.040 0.127 1227 Planarity : 0.004 0.051 1218 Dihedral : 23.805 147.860 1636 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.15 % Allowed : 1.98 % Favored : 97.87 % 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: 0.44 (0.31), residues: 802 helix: 1.36 (0.27), residues: 388 sheet: -0.49 (0.63), residues: 76 loop : -0.74 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 469 HIS 0.007 0.002 HIS H 432 PHE 0.015 0.002 PHE H 686 TYR 0.011 0.001 TYR H 203 ARG 0.006 0.001 ARG I 73 *********************** 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: 1 poor density : 67 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.2850 time to fit residues: 26.0832 Evaluate side-chains 55 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5017 ------------------------------------------------------------------------------- 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: 3.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.0270 chunk 74 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- 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 266 GLN H 347 GLN ** H 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4613 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= 0.258 Angle : 0.590 7.311 11353 Z= 0.318 Chirality : 0.041 0.148 1227 Planarity : 0.004 0.054 1218 Dihedral : 23.775 146.874 1636 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 0.66 (0.31), residues: 802 helix: 1.57 (0.27), residues: 385 sheet: -0.39 (0.64), residues: 76 loop : -0.64 (0.35), residues: 341 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 0.016 0.001 PHE H 686 TYR 0.010 0.001 TYR H 203 ARG 0.003 0.000 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 65 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2265 time to fit residues: 20.0554 Evaluate side-chains 52 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0442 ------------------------------------------------------------------------------- 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: 0.8980 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4774 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= 0.237 Angle : 0.566 7.386 11353 Z= 0.307 Chirality : 0.040 0.134 1227 Planarity : 0.004 0.057 1218 Dihedral : 23.707 145.727 1636 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: 0.73 (0.31), residues: 802 helix: 1.60 (0.27), residues: 388 sheet: -0.19 (0.65), residues: 76 loop : -0.63 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 651 HIS 0.006 0.001 HIS H 432 PHE 0.012 0.001 PHE H 686 TYR 0.009 0.001 TYR H 203 ARG 0.003 0.000 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 64 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2564 time to fit residues: 21.8391 Evaluate side-chains 51 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1044 ------------------------------------------------------------------------------- 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: 0.5980 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 520 ASN ** H 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8161 Z= 0.302 Angle : 0.633 7.639 11353 Z= 0.340 Chirality : 0.041 0.137 1227 Planarity : 0.004 0.052 1218 Dihedral : 23.820 145.053 1636 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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: 0.72 (0.31), residues: 802 helix: 1.59 (0.27), residues: 375 sheet: -0.33 (0.64), residues: 79 loop : -0.52 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 651 HIS 0.006 0.002 HIS H 432 PHE 0.014 0.002 PHE H 555 TYR 0.012 0.002 TYR H 24 ARG 0.005 0.001 ARG H 339 *********************** 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 61 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2273 time to fit residues: 18.9704 Evaluate side-chains 47 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0371 ------------------------------------------------------------------------------- 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: 0.6980 chunk 16 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5110 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= 0.202 Angle : 0.562 7.380 11353 Z= 0.306 Chirality : 0.040 0.135 1227 Planarity : 0.004 0.056 1218 Dihedral : 23.676 142.765 1636 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % 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: 0.93 (0.32), residues: 802 helix: 1.73 (0.27), residues: 380 sheet: -0.23 (0.65), residues: 77 loop : -0.39 (0.37), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 651 HIS 0.005 0.001 HIS H 432 PHE 0.019 0.001 PHE H 524 TYR 0.014 0.001 TYR I 70 ARG 0.005 0.000 ARG H 339 *********************** 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 63 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2032 time to fit residues: 17.9937 Evaluate side-chains 48 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0098 ------------------------------------------------------------------------------- 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: 0.0670 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 chunk 50 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.5064 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= 0.166 Angle : 0.540 7.069 11353 Z= 0.295 Chirality : 0.039 0.136 1227 Planarity : 0.003 0.054 1218 Dihedral : 23.459 142.043 1636 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 1.03 (0.32), residues: 802 helix: 1.80 (0.28), residues: 383 sheet: -0.10 (0.65), residues: 76 loop : -0.37 (0.37), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 651 HIS 0.004 0.001 HIS H 432 PHE 0.013 0.001 PHE H 686 TYR 0.010 0.001 TYR H 203 ARG 0.005 0.000 ARG H 339 *********************** 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 59 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1969 time to fit residues: 16.5201 Evaluate side-chains 49 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0072 ------------------------------------------------------------------------------- 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: 1.9990 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 520 ASN ** H 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8161 Z= 0.270 Angle : 0.611 8.732 11353 Z= 0.329 Chirality : 0.041 0.161 1227 Planarity : 0.004 0.055 1218 Dihedral : 23.578 142.961 1636 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 0.91 (0.31), residues: 802 helix: 1.70 (0.27), residues: 375 sheet: -0.40 (0.63), residues: 80 loop : -0.30 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 625 HIS 0.005 0.001 HIS H 432 PHE 0.014 0.001 PHE H 524 TYR 0.012 0.001 TYR H 24 ARG 0.003 0.001 ARG H 339 ********************** 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 : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2024 time to fit residues: 16.4802 Evaluate side-chains 47 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0548 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 0.0030 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 8 optimal weight: 0.0040 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.5004 ------------------------------------------------------------------------------- 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.057452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.043060 restraints weight = 41415.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.044253 restraints weight = 23181.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.044964 restraints weight = 15712.516| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8161 Z= 0.162 Angle : 0.543 7.042 11353 Z= 0.296 Chirality : 0.039 0.134 1227 Planarity : 0.003 0.055 1218 Dihedral : 23.406 141.156 1636 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.11 (0.32), residues: 802 helix: 1.81 (0.28), residues: 383 sheet: -0.01 (0.67), residues: 71 loop : -0.26 (0.37), residues: 348 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 0.013 0.001 PHE H 686 TYR 0.021 0.001 TYR I 70 ARG 0.005 0.000 ARG H 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1565.95 seconds wall clock time: 29 minutes 46.35 seconds (1786.35 seconds total)