Starting phenix.real_space_refine on Tue Feb 13 04:20:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh4_14721/02_2024/7zh4_14721_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh4_14721/02_2024/7zh4_14721.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh4_14721/02_2024/7zh4_14721_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh4_14721/02_2024/7zh4_14721_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh4_14721/02_2024/7zh4_14721_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh4_14721/02_2024/7zh4_14721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh4_14721/02_2024/7zh4_14721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh4_14721/02_2024/7zh4_14721_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh4_14721/02_2024/7zh4_14721_updated.pdb" } resolution = 2.49 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= 0.180 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 13 5.16 5 C 1869 2.51 5 N 483 2.21 5 O 591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 2957 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 607 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2311 Unusual residues: {' ZN': 1, 'JDA': 1} Inner-chain residues flagged as termini: ['pdbres="LEU D 785 "'] Classifications: {'peptide': 285, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274, None: 2} Not linked: pdbres="LEU D 785 " pdbres=" ZN D1000 " Not linked: pdbres=" ZN D1000 " pdbres="JDA D1001 " Chain breaks: 6 Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1467 SG CYS D 440 35.067 73.958 21.289 1.00 8.28 S ATOM 1490 SG CYS D 443 36.874 74.553 18.050 1.00 9.34 S ATOM 1865 SG CYS D 506 38.863 73.268 20.965 1.00 7.56 S ATOM 1888 SG CYS D 509 37.602 76.874 20.899 1.00 8.94 S Time building chain proxies: 2.11, per 1000 atoms: 0.71 Number of scatterers: 2957 At special positions: 0 Unit cell: (64.66, 87.98, 58.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 13 16.00 O 591 8.00 N 483 7.00 C 1869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 458.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 443 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 509 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 506 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 440 " Number of angles added : 6 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 686 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 5 sheets defined 33.7% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'C' and resid 23 through 34 Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 56 through 59 No H-bonds generated for 'chain 'C' and resid 56 through 59' Processing helix chain 'D' and resid 86 through 100 removed outlier: 5.711A pdb=" N TYR D 91 " --> pdb=" O ASN D 88 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN D 93 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR D 100 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 119 Processing helix chain 'D' and resid 144 through 165 Processing helix chain 'D' and resid 200 through 219 Processing helix chain 'D' and resid 425 through 430 Processing helix chain 'D' and resid 485 through 493 Processing helix chain 'D' and resid 500 through 502 No H-bonds generated for 'chain 'D' and resid 500 through 502' Processing helix chain 'D' and resid 565 through 567 No H-bonds generated for 'chain 'D' and resid 565 through 567' Processing helix chain 'D' and resid 760 through 766 Processing helix chain 'D' and resid 769 through 771 No H-bonds generated for 'chain 'D' and resid 769 through 771' Processing sheet with id= A, first strand: chain 'C' and resid 12 through 17 Processing sheet with id= B, first strand: chain 'D' and resid 446 through 453 Processing sheet with id= C, first strand: chain 'D' and resid 456 through 459 removed outlier: 3.586A pdb=" N ALA D 580 " --> pdb=" O PHE D 781 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS D 783 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU D 578 " --> pdb=" O LYS D 783 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE D 579 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 596 " --> pdb=" O PHE D 750 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 504 through 506 Processing sheet with id= E, first strand: chain 'D' and resid 583 through 585 136 hydrogen bonds defined for protein. 345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 924 1.34 - 1.46: 574 1.46 - 1.58: 1452 1.58 - 1.69: 0 1.69 - 1.81: 17 Bond restraints: 2967 Sorted by residual: bond pdb=" C4 JDA D1001 " pdb=" N2 JDA D1001 " ideal model delta sigma weight residual 1.455 1.341 0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C1 JDA D1001 " pdb=" C4 JDA D1001 " ideal model delta sigma weight residual 1.355 1.410 -0.055 2.00e-02 2.50e+03 7.44e+00 bond pdb=" N4 JDA D1001 " pdb=" N5 JDA D1001 " ideal model delta sigma weight residual 1.362 1.315 0.047 2.00e-02 2.50e+03 5.56e+00 bond pdb=" C14 JDA D1001 " pdb=" C3 JDA D1001 " ideal model delta sigma weight residual 1.528 1.485 0.043 2.00e-02 2.50e+03 4.68e+00 bond pdb=" C13 JDA D1001 " pdb=" N4 JDA D1001 " ideal model delta sigma weight residual 1.322 1.358 -0.036 2.00e-02 2.50e+03 3.29e+00 ... (remaining 2962 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.48: 63 106.48 - 113.37: 1684 113.37 - 120.26: 1003 120.26 - 127.15: 1225 127.15 - 134.03: 26 Bond angle restraints: 4001 Sorted by residual: angle pdb=" C JDA D1001 " pdb=" C1 JDA D1001 " pdb=" C2 JDA D1001 " ideal model delta sigma weight residual 98.42 121.99 -23.57 3.00e+00 1.11e-01 6.17e+01 angle pdb=" C JDA D1001 " pdb=" C1 JDA D1001 " pdb=" C4 JDA D1001 " ideal model delta sigma weight residual 141.51 123.06 18.45 3.00e+00 1.11e-01 3.78e+01 angle pdb=" N1 JDA D1001 " pdb=" C4 JDA D1001 " pdb=" N2 JDA D1001 " ideal model delta sigma weight residual 129.48 117.79 11.69 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C SER D 117 " pdb=" N ARG D 118 " pdb=" CA ARG D 118 " ideal model delta sigma weight residual 121.94 115.09 6.85 2.00e+00 2.50e-01 1.17e+01 angle pdb=" C1 JDA D1001 " pdb=" C4 JDA D1001 " pdb=" N2 JDA D1001 " ideal model delta sigma weight residual 110.56 120.04 -9.48 3.00e+00 1.11e-01 9.99e+00 ... (remaining 3996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 1622 16.94 - 33.88: 126 33.88 - 50.82: 27 50.82 - 67.76: 10 67.76 - 84.71: 3 Dihedral angle restraints: 1788 sinusoidal: 737 harmonic: 1051 Sorted by residual: dihedral pdb=" CA PHE D 492 " pdb=" C PHE D 492 " pdb=" N ALA D 493 " pdb=" CA ALA D 493 " ideal model delta harmonic sigma weight residual -180.00 -163.13 -16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP D 463 " pdb=" CB ASP D 463 " pdb=" CG ASP D 463 " pdb=" OD1 ASP D 463 " ideal model delta sinusoidal sigma weight residual -30.00 -87.42 57.42 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" C4 JDA D1001 " pdb=" C5 JDA D1001 " pdb=" N2 JDA D1001 " pdb=" C6 JDA D1001 " ideal model delta sinusoidal sigma weight residual 180.13 95.42 84.71 1 3.00e+01 1.11e-03 9.68e+00 ... (remaining 1785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 264 0.026 - 0.052: 122 0.052 - 0.078: 45 0.078 - 0.104: 18 0.104 - 0.130: 13 Chirality restraints: 462 Sorted by residual: chirality pdb=" CA VAL D 755 " pdb=" N VAL D 755 " pdb=" C VAL D 755 " pdb=" CB VAL D 755 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE C 36 " pdb=" N ILE C 36 " pdb=" C ILE C 36 " pdb=" CB ILE C 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE D 456 " pdb=" N ILE D 456 " pdb=" C ILE D 456 " pdb=" CB ILE D 456 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 459 not shown) Planarity restraints: 500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 JDA D1001 " 0.016 2.00e-02 2.50e+03 1.82e-02 6.63e+00 pdb=" C11 JDA D1001 " 0.007 2.00e-02 2.50e+03 pdb=" C5 JDA D1001 " -0.022 2.00e-02 2.50e+03 pdb=" C6 JDA D1001 " -0.003 2.00e-02 2.50e+03 pdb=" C7 JDA D1001 " 0.007 2.00e-02 2.50e+03 pdb=" C8 JDA D1001 " 0.016 2.00e-02 2.50e+03 pdb=" C9 JDA D1001 " 0.015 2.00e-02 2.50e+03 pdb=" N3 JDA D1001 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 JDA D1001 " 0.011 2.00e-02 2.50e+03 1.53e-02 3.53e+00 pdb=" C13 JDA D1001 " -0.013 2.00e-02 2.50e+03 pdb=" C9 JDA D1001 " -0.021 2.00e-02 2.50e+03 pdb=" N3 JDA D1001 " 0.020 2.00e-02 2.50e+03 pdb=" N4 JDA D1001 " -0.011 2.00e-02 2.50e+03 pdb=" N5 JDA D1001 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N JDA D1001 " -0.006 2.00e-02 2.50e+03 9.88e-03 2.20e+00 pdb=" C JDA D1001 " 0.017 2.00e-02 2.50e+03 pdb=" C1 JDA D1001 " -0.005 2.00e-02 2.50e+03 pdb=" C14 JDA D1001 " 0.000 2.00e-02 2.50e+03 pdb=" C2 JDA D1001 " -0.012 2.00e-02 2.50e+03 pdb=" C3 JDA D1001 " 0.010 2.00e-02 2.50e+03 pdb=" C4 JDA D1001 " -0.002 2.00e-02 2.50e+03 pdb=" N1 JDA D1001 " 0.010 2.00e-02 2.50e+03 pdb=" N2 JDA D1001 " -0.013 2.00e-02 2.50e+03 ... (remaining 497 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 505 2.76 - 3.30: 2593 3.30 - 3.83: 5143 3.83 - 4.37: 6428 4.37 - 4.90: 10498 Nonbonded interactions: 25167 Sorted by model distance: nonbonded pdb=" OE1 GLU D 202 " pdb=" O HOH D1101 " model vdw 2.231 2.440 nonbonded pdb=" O GLN D 431 " pdb=" NZ LYS D 523 " model vdw 2.234 2.520 nonbonded pdb=" O LEU C 73 " pdb=" OH TYR D 594 " model vdw 2.252 2.440 nonbonded pdb=" NH2 ARG D 450 " pdb=" OD2 ASP D 522 " model vdw 2.258 2.520 nonbonded pdb=" O GLU C 64 " pdb=" O HOH C 101 " model vdw 2.297 2.440 ... (remaining 25162 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 7.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.670 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 : 0.005 0.114 2967 Z= 0.329 Angle : 0.880 23.572 4001 Z= 0.395 Chirality : 0.040 0.130 462 Planarity : 0.004 0.035 500 Dihedral : 14.071 84.706 1102 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.97 (0.40), residues: 346 helix: -0.26 (0.43), residues: 119 sheet: -0.85 (0.41), residues: 103 loop : -0.54 (0.52), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 747 HIS 0.003 0.001 HIS C 68 PHE 0.020 0.003 PHE D 505 TYR 0.011 0.002 TYR D 576 ARG 0.004 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.330 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 1.6003 time to fit residues: 78.5471 Evaluate side-chains 45 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 0.0030 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2967 Z= 0.193 Angle : 0.535 6.319 4001 Z= 0.277 Chirality : 0.039 0.139 462 Planarity : 0.004 0.028 500 Dihedral : 6.850 85.488 381 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.51 % Allowed : 7.23 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.08 (0.42), residues: 346 helix: 0.97 (0.48), residues: 118 sheet: -0.57 (0.41), residues: 103 loop : -0.05 (0.53), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 747 HIS 0.002 0.001 HIS C 68 PHE 0.013 0.002 PHE D 505 TYR 0.009 0.002 TYR D 576 ARG 0.002 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.377 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 1.6831 time to fit residues: 87.7599 Evaluate side-chains 49 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 486 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 0.0170 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN D 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2967 Z= 0.206 Angle : 0.516 5.476 4001 Z= 0.267 Chirality : 0.038 0.137 462 Planarity : 0.003 0.027 500 Dihedral : 6.702 85.148 381 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.11 % Allowed : 8.43 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.43), residues: 346 helix: 1.55 (0.50), residues: 112 sheet: -0.34 (0.42), residues: 103 loop : 0.01 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 747 HIS 0.002 0.001 HIS C 68 PHE 0.014 0.002 PHE D 505 TYR 0.008 0.001 TYR D 576 ARG 0.002 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.388 Fit side-chains REVERT: D 754 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7574 (pt0) outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 1.7109 time to fit residues: 90.9220 Evaluate side-chains 48 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 754 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN D 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2967 Z= 0.230 Angle : 0.524 4.967 4001 Z= 0.271 Chirality : 0.038 0.133 462 Planarity : 0.003 0.027 500 Dihedral : 6.720 85.275 381 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.41 % Allowed : 9.04 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.68 (0.43), residues: 346 helix: 1.67 (0.50), residues: 112 sheet: -0.16 (0.43), residues: 103 loop : 0.06 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 747 HIS 0.002 0.001 HIS C 68 PHE 0.015 0.002 PHE D 505 TYR 0.009 0.002 TYR D 576 ARG 0.002 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.358 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 50 average time/residue: 1.5779 time to fit residues: 80.7146 Evaluate side-chains 49 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 486 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN D 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2967 Z= 0.344 Angle : 0.593 5.789 4001 Z= 0.305 Chirality : 0.041 0.146 462 Planarity : 0.004 0.029 500 Dihedral : 6.932 84.677 381 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.41 % Allowed : 9.64 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.68 (0.44), residues: 346 helix: 1.58 (0.50), residues: 112 sheet: -0.13 (0.43), residues: 103 loop : 0.11 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP D 747 HIS 0.002 0.001 HIS C 68 PHE 0.019 0.003 PHE D 505 TYR 0.012 0.002 TYR D 512 ARG 0.004 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.349 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 1.6122 time to fit residues: 82.3861 Evaluate side-chains 51 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 764 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2967 Z= 0.184 Angle : 0.486 4.548 4001 Z= 0.252 Chirality : 0.037 0.128 462 Planarity : 0.003 0.028 500 Dihedral : 6.619 85.402 381 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.11 % Allowed : 10.24 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.84 (0.44), residues: 346 helix: 1.81 (0.50), residues: 112 sheet: -0.12 (0.44), residues: 103 loop : 0.19 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 567 HIS 0.002 0.001 HIS C 68 PHE 0.011 0.002 PHE D 505 TYR 0.009 0.001 TYR D 504 ARG 0.002 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.354 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 1.5203 time to fit residues: 76.1980 Evaluate side-chains 48 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 764 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2967 Z= 0.142 Angle : 0.449 4.020 4001 Z= 0.235 Chirality : 0.036 0.125 462 Planarity : 0.003 0.025 500 Dihedral : 6.361 85.357 381 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.41 % Allowed : 10.54 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.96 (0.44), residues: 346 helix: 1.94 (0.50), residues: 112 sheet: -0.03 (0.45), residues: 103 loop : 0.20 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 747 HIS 0.002 0.001 HIS D 111 PHE 0.008 0.001 PHE D 505 TYR 0.008 0.001 TYR D 504 ARG 0.001 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.302 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 1.5915 time to fit residues: 81.3270 Evaluate side-chains 52 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 535 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2967 Z= 0.154 Angle : 0.455 4.128 4001 Z= 0.236 Chirality : 0.037 0.126 462 Planarity : 0.003 0.025 500 Dihedral : 6.308 85.099 381 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.11 % Allowed : 10.84 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.07 (0.45), residues: 346 helix: 2.01 (0.50), residues: 112 sheet: 0.02 (0.45), residues: 103 loop : 0.31 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 747 HIS 0.002 0.001 HIS C 68 PHE 0.010 0.001 PHE D 505 TYR 0.008 0.001 TYR D 504 ARG 0.001 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.356 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 1.6320 time to fit residues: 80.0238 Evaluate side-chains 51 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 524 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN D 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2967 Z= 0.223 Angle : 0.503 4.620 4001 Z= 0.260 Chirality : 0.038 0.133 462 Planarity : 0.003 0.026 500 Dihedral : 6.478 85.055 381 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.41 % Allowed : 10.54 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.06 (0.44), residues: 346 helix: 1.94 (0.50), residues: 112 sheet: 0.05 (0.45), residues: 103 loop : 0.33 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 487 HIS 0.002 0.001 HIS C 68 PHE 0.014 0.002 PHE D 505 TYR 0.009 0.002 TYR D 504 ARG 0.002 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: D 754 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7651 (pt0) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 1.5945 time to fit residues: 79.8591 Evaluate side-chains 52 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 754 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2967 Z= 0.201 Angle : 0.489 4.320 4001 Z= 0.253 Chirality : 0.038 0.130 462 Planarity : 0.003 0.026 500 Dihedral : 6.451 85.142 381 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.41 % Allowed : 10.54 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.06 (0.45), residues: 346 helix: 1.93 (0.50), residues: 112 sheet: 0.03 (0.45), residues: 103 loop : 0.36 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 567 HIS 0.002 0.001 HIS C 68 PHE 0.013 0.002 PHE D 505 TYR 0.009 0.001 TYR D 504 ARG 0.002 0.000 ARG C 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 692 Ramachandran restraints generated. 346 Oldfield, 0 Emsley, 346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.356 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 1.5975 time to fit residues: 78.4126 Evaluate side-chains 50 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 524 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.106942 restraints weight = 2778.289| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.49 r_work: 0.3019 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2967 Z= 0.176 Angle : 0.477 4.222 4001 Z= 0.246 Chirality : 0.037 0.125 462 Planarity : 0.003 0.026 500 Dihedral : 6.389 85.225 381 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.81 % Allowed : 11.14 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.09 (0.45), residues: 346 helix: 1.91 (0.50), residues: 112 sheet: 0.04 (0.45), residues: 102 loop : 0.42 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 567 HIS 0.002 0.001 HIS C 68 PHE 0.011 0.002 PHE D 505 TYR 0.008 0.001 TYR D 504 ARG 0.002 0.000 ARG C 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1838.92 seconds wall clock time: 33 minutes 18.69 seconds (1998.69 seconds total)