Starting phenix.real_space_refine (version: dev) on Mon Apr 4 17:04:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/04_2022/6n7w_0365_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/04_2022/6n7w_0365.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/04_2022/6n7w_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_0365/04_2022/6n7w_0365_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/04_2022/6n7w_0365_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/04_2022/6n7w_0365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/04_2022/6n7w_0365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/04_2022/6n7w_0365_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7w_0365/04_2022/6n7w_0365_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Convert atoms to be neutral 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-4553/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, 'PTRANS': 4, 'TRANS': 99, 'PCIS': 1} 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: {'undetermined': 1, 'DNA': 24} Link IDs: {None: 1, 'rna3p': 23} 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: 5.08, per 1000 atoms: 0.65 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: 4.42 Conformation dependent library (CDL) restraints added in 933.9 milliseconds 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: 3.05 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: 3.12 Time building geometry restraints manager: 4.60 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 1.272 1.524 -0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" C4' 2DA P 25 " pdb=" O4' 2DA P 25 " ideal model delta sigma weight residual 1.291 1.445 -0.154 2.00e-02 2.50e+03 5.92e+01 bond pdb=" C1' 2DA P 25 " pdb=" N9 2DA P 25 " ideal model delta sigma weight residual 1.344 1.493 -0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" C6 2DA P 25 " pdb=" N6 2DA P 25 " ideal model delta sigma weight residual 1.455 1.339 0.116 2.00e-02 2.50e+03 3.39e+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 ... (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=" C1' 2DA P 25 " pdb=" N9 2DA P 25 " pdb=" C8 2DA P 25 " ideal model delta sigma weight residual 137.03 115.81 21.22 3.00e+00 1.11e-01 5.00e+01 angle pdb=" C1' 2DA P 25 " pdb=" N9 2DA P 25 " pdb=" C4 2DA P 25 " ideal model delta sigma weight residual 114.81 133.87 -19.06 3.00e+00 1.11e-01 4.04e+01 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=" N6 2DA P 25 " pdb=" C6 2DA P 25 " pdb=" N1 2DA P 25 " ideal model delta sigma weight residual 106.32 119.17 -12.85 3.00e+00 1.11e-01 1.84e+01 angle pdb=" C5 2DA P 25 " pdb=" C6 2DA P 25 " pdb=" N6 2DA P 25 " ideal model delta sigma weight residual 133.69 120.91 12.78 3.00e+00 1.11e-01 1.81e+01 ... (remaining 11348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.21: 4161 30.21 - 60.42: 390 60.42 - 90.63: 14 90.63 - 120.84: 1 120.84 - 151.05: 1 Dihedral angle restraints: 4567 sinusoidal: 2255 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 4564 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 3.410 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.070 Process input model: 28.450 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 0.252 8161 Z= 0.316 Angle : 0.790 21.218 11353 Z= 0.421 Chirality : 0.045 0.249 1227 Planarity : 0.016 0.328 1218 Dihedral : 19.166 151.054 3087 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 % 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 *********************** 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 : 0.853 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: 0.2561 time to fit residues: 48.5941 Evaluate side-chains 65 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0665 ------------------------------------------------------------------------------- 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: 0.3980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 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: 0.8191 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 8161 Z= 0.171 Angle : 0.531 7.507 11353 Z= 0.287 Chirality : 0.038 0.132 1227 Planarity : 0.005 0.061 1218 Dihedral : 23.524 149.212 1567 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.15 % 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: -0.50 (0.30), residues: 802 helix: 0.56 (0.26), residues: 392 sheet: -0.40 (0.70), residues: 64 loop : -1.33 (0.34), residues: 346 *********************** 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 : 0.785 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: 0.2323 time to fit residues: 30.3042 Evaluate side-chains 52 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1008 time to fit residues: 1.2056 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 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 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: 0.8336 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 8161 Z= 0.249 Angle : 0.590 7.514 11353 Z= 0.316 Chirality : 0.040 0.128 1227 Planarity : 0.004 0.054 1218 Dihedral : 23.820 150.352 1567 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.00 % 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: 0.17 (0.31), residues: 802 helix: 1.18 (0.27), residues: 389 sheet: -0.81 (0.63), residues: 80 loop : -0.88 (0.35), residues: 333 *********************** 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 77 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.846 Fit side-chains 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: 77 average time/residue: 0.2362 time to fit residues: 24.3970 Evaluate side-chains 51 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0420 ------------------------------------------------------------------------------- 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: 4.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 19 HIS ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN H 520 ASN ** H 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 8161 Z= 0.291 Angle : 0.615 7.459 11353 Z= 0.331 Chirality : 0.041 0.147 1227 Planarity : 0.004 0.051 1218 Dihedral : 24.017 150.591 1567 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.00 % 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: 0.44 (0.31), residues: 802 helix: 1.39 (0.27), residues: 385 sheet: -0.61 (0.63), residues: 76 loop : -0.73 (0.36), residues: 341 *********************** 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 67 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2253 time to fit residues: 20.4272 Evaluate side-chains 53 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0314 ------------------------------------------------------------------------------- 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: 1.9990 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.0050 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 74 optimal weight: 0.0060 chunk 20 optimal weight: 0.6980 overall best weight: 0.3610 ------------------------------------------------------------------------------- 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 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 8161 Z= 0.143 Angle : 0.513 7.001 11353 Z= 0.278 Chirality : 0.038 0.152 1227 Planarity : 0.003 0.056 1218 Dihedral : 23.751 147.049 1567 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 0.00 % 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: 0.93 (0.32), residues: 802 helix: 1.84 (0.28), residues: 388 sheet: -0.10 (0.65), residues: 76 loop : -0.65 (0.36), residues: 338 *********************** 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 68 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2108 time to fit residues: 19.9226 Evaluate side-chains 52 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0979 ------------------------------------------------------------------------------- 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: 2.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 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: 0.8460 moved from start: 0.5098 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= 0.370 Angle : 0.675 7.520 11353 Z= 0.361 Chirality : 0.043 0.135 1227 Planarity : 0.004 0.053 1218 Dihedral : 24.082 149.838 1567 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 0.00 % 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: 0.60 (0.31), residues: 802 helix: 1.57 (0.27), residues: 374 sheet: -0.22 (0.66), residues: 70 loop : -0.70 (0.34), residues: 358 *********************** 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 53 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2085 time to fit residues: 15.6347 Evaluate side-chains 43 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.681 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8731 ------------------------------------------------------------------------------- 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: 0.9980 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 0.0030 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8161 Z= 0.222 Angle : 0.573 7.417 11353 Z= 0.309 Chirality : 0.040 0.138 1227 Planarity : 0.004 0.055 1218 Dihedral : 23.923 146.488 1567 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.00 % 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: 0.91 (0.32), residues: 802 helix: 1.73 (0.27), residues: 386 sheet: 0.01 (0.68), residues: 70 loop : -0.53 (0.36), residues: 346 *********************** 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 : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2188 time to fit residues: 18.5165 Evaluate side-chains 50 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0843 ------------------------------------------------------------------------------- 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: 0.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.0020 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8161 Z= 0.210 Angle : 0.560 7.181 11353 Z= 0.302 Chirality : 0.040 0.135 1227 Planarity : 0.004 0.055 1218 Dihedral : 23.764 144.669 1567 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 0.00 % 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: 1.05 (0.32), residues: 802 helix: 1.87 (0.27), residues: 386 sheet: -0.04 (0.66), residues: 70 loop : -0.47 (0.37), residues: 346 *********************** 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 : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2090 time to fit residues: 17.7937 Evaluate side-chains 50 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6446 ------------------------------------------------------------------------------- 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: 2.9990 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** H 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8161 Z= 0.203 Angle : 0.554 7.093 11353 Z= 0.300 Chirality : 0.040 0.149 1227 Planarity : 0.004 0.056 1218 Dihedral : 23.707 144.077 1567 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 0.00 % 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: 1.04 (0.32), residues: 802 helix: 1.89 (0.27), residues: 382 sheet: 0.04 (0.67), residues: 70 loop : -0.51 (0.36), residues: 350 *********************** 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 61 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1944 time to fit residues: 16.8654 Evaluate side-chains 48 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0093 ------------------------------------------------------------------------------- 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: 0.7980 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 0.0060 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8384 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8161 Z= 0.180 Angle : 0.549 6.958 11353 Z= 0.297 Chirality : 0.039 0.171 1227 Planarity : 0.003 0.056 1218 Dihedral : 23.582 143.326 1567 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 0.00 % 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: 1.16 (0.32), residues: 802 helix: 1.94 (0.28), residues: 382 sheet: 0.02 (0.67), residues: 71 loop : -0.36 (0.37), residues: 349 ********************** 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 60 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2042 time to fit residues: 17.2528 Evaluate side-chains 51 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0570 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 0.0870 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.057249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.042662 restraints weight = 41605.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.043831 restraints weight = 23412.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.044593 restraints weight = 15988.338| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8161 Z= 0.184 Angle : 0.547 6.879 11353 Z= 0.296 Chirality : 0.039 0.136 1227 Planarity : 0.003 0.055 1218 Dihedral : 23.494 143.257 1567 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.00 % 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: 1.25 (0.32), residues: 802 helix: 1.98 (0.28), residues: 382 sheet: 0.13 (0.67), residues: 71 loop : -0.28 (0.37), residues: 349 =============================================================================== Job complete usr+sys time: 1480.42 seconds wall clock time: 27 minutes 45.63 seconds (1665.63 seconds total)