Starting phenix.real_space_refine (version: dev) on Fri Feb 17 21:22:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/02_2023/7wrq_32735_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/02_2023/7wrq_32735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/02_2023/7wrq_32735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/02_2023/7wrq_32735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/02_2023/7wrq_32735_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/02_2023/7wrq_32735_neut.pdb" } resolution = 3.6 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= -0.001 sd= 0.032 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 Process input model Symmetric amino acids flipped Residue "A GLU 114": "OE1" <-> "OE2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "B ARG 36": not complete - not flipped Residue "B GLU 73": "OE1" <-> "OE2" Residue "B ARG 230": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6247 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4384 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 32, 'TRANS': 533} Chain: "B" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1269 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 16, 'TRANS': 150} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 499 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.28, per 1000 atoms: 0.69 Number of scatterers: 6247 At special positions: 0 Unit cell: (63.576, 98.896, 123.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1151 8.00 N 1125 7.00 C 3930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 45 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A 373 " - pdb=" SG CYS A 397 " distance=1.73 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 566 " - pdb=" SG CYS A 571 " distance=2.09 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 42 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 43 " distance=2.01 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 46 " distance=2.10 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 67 " distance=2.19 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 213 " distance=2.02 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.04 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 258 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 52 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A 701 " - " ASN A 64 " " NAG A 702 " - " ASN A 96 " " NAG A 703 " - " ASN A 515 " " NAG A 704 " - " ASN A 580 " " NAG D 1 " - " ASN A 368 " Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 8.6% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.754A pdb=" N LEU A 502 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 Processing helix chain 'B' and resid 17 through 24 Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 186 through 195 removed outlier: 3.883A pdb=" N ASP B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 19 Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 53 through 59 removed outlier: 3.567A pdb=" N LEU C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.722A pdb=" N VAL A 58 " --> pdb=" O TRP A 80 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 79 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 200 removed outlier: 3.523A pdb=" N LEU A 199 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 224 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 223 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 248 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 367 removed outlier: 3.666A pdb=" N MET A 367 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 464 removed outlier: 7.082A pdb=" N LEU A 463 " --> pdb=" O ASP A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.300A pdb=" N VAL B 10 " --> pdb=" O LEU B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 222 through 223 50 hydrogen bonds defined for protein. 132 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: 1.39 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1181 1.32 - 1.45: 1573 1.45 - 1.58: 3579 1.58 - 1.70: 0 1.70 - 1.83: 44 Bond restraints: 6377 Sorted by residual: bond pdb=" C GLU A 567 " pdb=" N GLY A 568 " ideal model delta sigma weight residual 1.331 1.574 -0.244 1.46e-02 4.69e+03 2.79e+02 bond pdb=" C VAL B 30 " pdb=" N CYS B 31 " ideal model delta sigma weight residual 1.332 1.525 -0.192 1.40e-02 5.10e+03 1.89e+02 bond pdb=" C ILE A 565 " pdb=" N CYS A 566 " ideal model delta sigma weight residual 1.331 1.206 0.125 1.24e-02 6.50e+03 1.01e+02 bond pdb=" C LEU C 64 " pdb=" N LYS C 65 " ideal model delta sigma weight residual 1.329 1.463 -0.134 1.40e-02 5.10e+03 9.10e+01 bond pdb=" C GLU A 394 " pdb=" N GLY A 395 " ideal model delta sigma weight residual 1.333 1.460 -0.127 1.41e-02 5.03e+03 8.09e+01 ... (remaining 6372 not shown) Histogram of bond angle deviations from ideal: 98.94 - 107.17: 283 107.17 - 115.39: 3762 115.39 - 123.62: 4268 123.62 - 131.84: 318 131.84 - 140.07: 14 Bond angle restraints: 8645 Sorted by residual: angle pdb=" O ILE A 565 " pdb=" C ILE A 565 " pdb=" N CYS A 566 " ideal model delta sigma weight residual 122.57 106.94 15.63 1.25e+00 6.40e-01 1.56e+02 angle pdb=" O GLU A 394 " pdb=" C GLU A 394 " pdb=" N GLY A 395 " ideal model delta sigma weight residual 122.85 135.51 -12.66 1.14e+00 7.69e-01 1.23e+02 angle pdb=" C ALA B 32 " pdb=" N GLU B 33 " pdb=" CA GLU B 33 " ideal model delta sigma weight residual 122.68 138.10 -15.42 1.47e+00 4.63e-01 1.10e+02 angle pdb=" C SER A 62 " pdb=" N ARG A 63 " pdb=" CA ARG A 63 " ideal model delta sigma weight residual 121.69 140.07 -18.38 1.85e+00 2.92e-01 9.87e+01 angle pdb=" O ALA A 603 " pdb=" C ALA A 603 " pdb=" N PRO A 604 " ideal model delta sigma weight residual 121.32 109.96 11.36 1.15e+00 7.56e-01 9.75e+01 ... (remaining 8640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 3817 35.98 - 71.97: 81 71.97 - 107.95: 5 107.95 - 143.93: 0 143.93 - 179.91: 1 Dihedral angle restraints: 3904 sinusoidal: 1644 harmonic: 2260 Sorted by residual: dihedral pdb=" CD ARG B 36 " pdb=" NE ARG B 36 " pdb=" CZ ARG B 36 " pdb=" NH1 ARG B 36 " ideal model delta sinusoidal sigma weight residual 0.00 -179.91 179.91 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG A 160 " pdb=" NE ARG A 160 " pdb=" CZ ARG A 160 " pdb=" NH1 ARG A 160 " ideal model delta sinusoidal sigma weight residual 0.00 -79.75 79.75 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB CYS B 24 " pdb=" SG CYS B 24 " pdb=" SG CYS B 43 " pdb=" CB CYS B 43 " ideal model delta sinusoidal sigma weight residual 93.00 167.98 -74.98 1 1.00e+01 1.00e-02 7.11e+01 ... (remaining 3901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 834 0.096 - 0.193: 114 0.193 - 0.289: 20 0.289 - 0.386: 4 0.386 - 0.482: 3 Chirality restraints: 975 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.30e+02 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 368 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CA LEU A 398 " pdb=" N LEU A 398 " pdb=" C LEU A 398 " pdb=" CB LEU A 398 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.60e+00 ... (remaining 972 not shown) Planarity restraints: 1142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.345 2.00e-02 2.50e+03 2.93e-01 1.07e+03 pdb=" C7 NAG D 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.514 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 702 " -0.286 2.00e-02 2.50e+03 2.45e-01 7.53e+02 pdb=" C7 NAG A 702 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A 702 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A 702 " 0.429 2.00e-02 2.50e+03 pdb=" O7 NAG A 702 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " 0.212 2.00e-02 2.50e+03 1.76e-01 3.89e+02 pdb=" C7 NAG A 704 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " -0.290 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " -0.015 2.00e-02 2.50e+03 ... (remaining 1139 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2230 2.87 - 3.37: 4769 3.37 - 3.88: 8412 3.88 - 4.39: 9122 4.39 - 4.90: 16849 Nonbonded interactions: 41382 Sorted by model distance: nonbonded pdb=" O SER A 195 " pdb=" OG SER A 195 " model vdw 2.357 2.440 nonbonded pdb=" O GLU B 189 " pdb=" OG1 THR B 193 " model vdw 2.361 2.440 nonbonded pdb=" O SER C 34 " pdb=" OG SER C 34 " model vdw 2.386 2.440 nonbonded pdb=" N GLN A 95 " pdb=" O GLN A 95 " model vdw 2.398 2.496 nonbonded pdb=" NH1 ARG A 269 " pdb=" OH TYR B 183 " model vdw 2.417 2.520 ... (remaining 41377 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 3930 2.51 5 N 1125 2.21 5 O 1151 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: 1.890 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: 5.550 Check model and map are aligned: 0.090 Process input model: 19.420 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.011 0.244 6377 Z= 0.730 Angle : 1.283 18.381 8645 Z= 0.828 Chirality : 0.075 0.482 975 Planarity : 0.024 0.484 1137 Dihedral : 14.492 179.913 2400 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.51 % Allowed : 19.87 % Favored : 79.62 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.14 % 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: -5.87 (0.21), residues: 790 helix: -2.24 (0.61), residues: 60 sheet: -4.22 (0.40), residues: 100 loop : -4.45 (0.17), residues: 630 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.2395 time to fit residues: 27.0393 Evaluate side-chains 46 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.705 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0551 time to fit residues: 1.2467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS B 196 HIS B 209 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 6377 Z= 0.229 Angle : 0.670 6.480 8645 Z= 0.344 Chirality : 0.043 0.217 975 Planarity : 0.005 0.052 1137 Dihedral : 8.011 179.976 917 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.53 % Favored : 87.22 % Rotamer Outliers : 1.66 % 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: -5.21 (0.23), residues: 790 helix: -1.70 (0.57), residues: 74 sheet: -3.96 (0.37), residues: 112 loop : -3.95 (0.19), residues: 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 55 average time/residue: 0.2407 time to fit residues: 17.3316 Evaluate side-chains 46 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0581 time to fit residues: 1.4528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.059 6377 Z= 0.512 Angle : 0.826 9.128 8645 Z= 0.417 Chirality : 0.049 0.202 975 Planarity : 0.005 0.054 1137 Dihedral : 8.269 179.181 917 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.85 % Favored : 82.03 % Rotamer Outliers : 1.66 % 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: -4.97 (0.23), residues: 790 helix: -1.40 (0.58), residues: 74 sheet: -3.40 (0.62), residues: 51 loop : -3.94 (0.19), residues: 665 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.706 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 53 average time/residue: 0.2434 time to fit residues: 16.7076 Evaluate side-chains 47 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0578 time to fit residues: 1.7207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 6377 Z= 0.205 Angle : 0.631 9.438 8645 Z= 0.321 Chirality : 0.042 0.212 975 Planarity : 0.005 0.048 1137 Dihedral : 7.890 179.790 917 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.14 % Favored : 88.73 % Rotamer Outliers : 1.06 % 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: -4.57 (0.25), residues: 790 helix: -1.26 (0.57), residues: 75 sheet: -3.43 (0.54), residues: 65 loop : -3.58 (0.20), residues: 650 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.751 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 0.2292 time to fit residues: 15.4430 Evaluate side-chains 46 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0562 time to fit residues: 1.3013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 67 optimal weight: 0.3980 chunk 19 optimal weight: 0.0040 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 6377 Z= 0.308 Angle : 0.663 9.323 8645 Z= 0.338 Chirality : 0.044 0.201 975 Planarity : 0.005 0.048 1137 Dihedral : 7.881 179.419 917 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.08 % Favored : 83.80 % Rotamer Outliers : 1.66 % 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: -4.49 (0.25), residues: 790 helix: -1.04 (0.59), residues: 75 sheet: -3.03 (0.63), residues: 51 loop : -3.60 (0.20), residues: 664 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.802 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 0.2561 time to fit residues: 17.1598 Evaluate side-chains 46 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0601 time to fit residues: 1.5571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 0.0770 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 6377 Z= 0.235 Angle : 0.629 9.490 8645 Z= 0.320 Chirality : 0.042 0.204 975 Planarity : 0.004 0.046 1137 Dihedral : 7.789 179.514 917 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.77 % Favored : 88.10 % Rotamer Outliers : 1.06 % 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: -4.30 (0.25), residues: 790 helix: -0.34 (0.63), residues: 62 sheet: -2.78 (0.69), residues: 46 loop : -3.49 (0.20), residues: 682 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.644 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 50 average time/residue: 0.2301 time to fit residues: 15.1401 Evaluate side-chains 44 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0627 time to fit residues: 1.2791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.0050 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 6377 Z= 0.199 Angle : 0.611 9.355 8645 Z= 0.308 Chirality : 0.041 0.200 975 Planarity : 0.004 0.046 1137 Dihedral : 7.665 179.658 917 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.41 % Favored : 87.47 % Rotamer Outliers : 1.21 % 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: -4.15 (0.26), residues: 790 helix: -0.02 (0.65), residues: 62 sheet: -2.94 (0.75), residues: 41 loop : -3.37 (0.20), residues: 687 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.935 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 47 average time/residue: 0.2321 time to fit residues: 15.0594 Evaluate side-chains 45 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0708 time to fit residues: 1.5335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.0870 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 6377 Z= 0.239 Angle : 0.629 9.462 8645 Z= 0.315 Chirality : 0.042 0.194 975 Planarity : 0.004 0.047 1137 Dihedral : 7.675 179.617 917 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.91 % Favored : 86.96 % Rotamer Outliers : 0.60 % 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: -4.06 (0.26), residues: 790 helix: 0.14 (0.67), residues: 62 sheet: -3.40 (0.59), residues: 59 loop : -3.25 (0.21), residues: 669 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 46 average time/residue: 0.2132 time to fit residues: 13.4627 Evaluate side-chains 41 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.700 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0557 time to fit residues: 1.0315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 46 optimal weight: 0.0980 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 6377 Z= 0.176 Angle : 0.596 9.341 8645 Z= 0.299 Chirality : 0.040 0.197 975 Planarity : 0.004 0.047 1137 Dihedral : 7.575 179.989 917 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.63 % Favored : 89.24 % Rotamer Outliers : 0.76 % 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: -3.81 (0.26), residues: 790 helix: 0.30 (0.68), residues: 62 sheet: -2.68 (0.97), residues: 26 loop : -3.15 (0.21), residues: 702 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.814 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 43 average time/residue: 0.2244 time to fit residues: 13.0879 Evaluate side-chains 46 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0593 time to fit residues: 1.4025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 6377 Z= 0.286 Angle : 0.657 9.430 8645 Z= 0.330 Chirality : 0.043 0.194 975 Planarity : 0.004 0.048 1137 Dihedral : 7.699 179.584 917 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.18 % Favored : 85.70 % Rotamer Outliers : 0.15 % 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: -3.86 (0.27), residues: 790 helix: 0.36 (0.68), residues: 62 sheet: -3.16 (0.57), residues: 65 loop : -3.12 (0.21), residues: 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.727 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.2179 time to fit residues: 12.8241 Evaluate side-chains 41 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.4980 chunk 61 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.086021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.059634 restraints weight = 15410.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.062002 restraints weight = 8713.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.063595 restraints weight = 6130.398| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 6377 Z= 0.194 Angle : 0.612 9.307 8645 Z= 0.307 Chirality : 0.041 0.200 975 Planarity : 0.004 0.048 1137 Dihedral : 7.590 179.934 917 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.27 % Favored : 88.61 % Rotamer Outliers : 0.76 % 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: -3.69 (0.27), residues: 790 helix: 0.38 (0.67), residues: 62 sheet: -2.60 (0.99), residues: 26 loop : -3.05 (0.21), residues: 702 =============================================================================== Job complete usr+sys time: 1390.53 seconds wall clock time: 26 minutes 8.94 seconds (1568.94 seconds total)