Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 07:33:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/04_2023/7wrq_32735_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/04_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_32735/04_2023/7wrq_32735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/04_2023/7wrq_32735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/04_2023/7wrq_32735_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/04_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 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. 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-1.21rc1-4938/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 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: 3.68, per 1000 atoms: 0.59 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: 2.09 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: 1.43 Time building geometry restraints manager: 2.33 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: 3771 35.98 - 71.97: 81 71.97 - 107.95: 5 107.95 - 143.93: 0 143.93 - 179.91: 1 Dihedral angle restraints: 3858 sinusoidal: 1598 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 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 831 0.096 - 0.193: 116 0.193 - 0.289: 21 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 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: 1.550 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: 5.680 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 18.470 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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= 0.735 Angle : 1.291 18.381 8645 Z= 0.818 Chirality : 0.076 0.482 975 Planarity : 0.024 0.484 1137 Dihedral : 14.576 179.913 2354 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 : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.2337 time to fit residues: 26.3865 Evaluate side-chains 46 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0542 time to fit residues: 1.3400 ------------------------------------------------------------------------------- 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: 0.8262 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 6377 Z= 0.231 Angle : 0.685 6.501 8645 Z= 0.346 Chirality : 0.043 0.153 975 Planarity : 0.005 0.057 1137 Dihedral : 8.063 179.845 871 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.28 % Favored : 87.47 % 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: -3.95 (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 60 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 56 average time/residue: 0.2348 time to fit residues: 17.2241 Evaluate side-chains 44 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0604 time to fit residues: 1.5027 ------------------------------------------------------------------------------- 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: 4.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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: 0.8388 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 6377 Z= 0.380 Angle : 0.747 9.311 8645 Z= 0.375 Chirality : 0.047 0.186 975 Planarity : 0.005 0.052 1137 Dihedral : 8.205 179.578 871 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.58 % Favored : 83.29 % Rotamer Outliers : 1.36 % 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: -4.88 (0.24), residues: 790 helix: -1.31 (0.60), residues: 69 sheet: -3.39 (0.61), residues: 52 loop : -3.85 (0.19), residues: 669 *********************** 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 54 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.756 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.2239 time to fit residues: 15.3887 Evaluate side-chains 47 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0618 time to fit residues: 1.7458 ------------------------------------------------------------------------------- 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: 0.9980 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.8376 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 6377 Z= 0.316 Angle : 0.680 9.236 8645 Z= 0.345 Chirality : 0.044 0.152 975 Planarity : 0.005 0.050 1137 Dihedral : 8.036 179.447 871 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.91 % Favored : 86.96 % 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: -4.63 (0.24), residues: 790 helix: -1.17 (0.58), residues: 74 sheet: -3.42 (0.60), residues: 51 loop : -3.66 (0.19), residues: 665 *********************** 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 56 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 0.2400 time to fit residues: 16.8442 Evaluate side-chains 48 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.754 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.0604 time to fit residues: 1.6715 ------------------------------------------------------------------------------- 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: 6.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 52 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.9602 ------------------------------------------------------------------------------- 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: 0.8350 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 6377 Z= 0.214 Angle : 0.621 9.478 8645 Z= 0.314 Chirality : 0.042 0.158 975 Planarity : 0.004 0.047 1137 Dihedral : 7.820 179.693 871 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.41 % Favored : 87.47 % Rotamer Outliers : 1.36 % 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: -4.40 (0.25), residues: 790 helix: -1.02 (0.59), residues: 75 sheet: -3.03 (0.63), residues: 51 loop : -3.51 (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: 9 poor density : 45 time to evaluate : 0.813 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 52 average time/residue: 0.2332 time to fit residues: 16.0404 Evaluate side-chains 46 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0615 time to fit residues: 1.4891 ------------------------------------------------------------------------------- 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: 3.9990 chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 0.0050 chunk 39 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 overall best weight: 1.1596 ------------------------------------------------------------------------------- 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 B 196 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3097 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= 0.236 Angle : 0.633 9.352 8645 Z= 0.320 Chirality : 0.042 0.149 975 Planarity : 0.004 0.048 1137 Dihedral : 7.799 179.561 871 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.41 % Favored : 87.47 % Rotamer Outliers : 1.51 % 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: -4.23 (0.25), residues: 790 helix: -0.41 (0.62), residues: 69 sheet: -3.41 (0.55), residues: 65 loop : -3.36 (0.21), residues: 656 *********************** 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 53 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 0.2463 time to fit residues: 16.1680 Evaluate side-chains 46 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.825 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.0677 time to fit residues: 1.8389 ------------------------------------------------------------------------------- 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: 0.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.9502 ------------------------------------------------------------------------------- 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: 0.8338 moved from start: 0.3206 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= 0.208 Angle : 0.611 9.419 8645 Z= 0.306 Chirality : 0.041 0.151 975 Planarity : 0.004 0.047 1137 Dihedral : 7.701 179.707 871 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.65 % Favored : 88.23 % 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: -4.08 (0.26), residues: 790 helix: 0.12 (0.65), residues: 62 sheet: -3.38 (0.61), residues: 54 loop : -3.28 (0.21), residues: 674 *********************** 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 48 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 46 average time/residue: 0.2293 time to fit residues: 14.0390 Evaluate side-chains 41 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.729 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0598 time to fit residues: 1.2431 ------------------------------------------------------------------------------- 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: 0.4980 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8328 moved from start: 0.3347 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= 0.195 Angle : 0.601 9.317 8645 Z= 0.300 Chirality : 0.041 0.151 975 Planarity : 0.004 0.047 1137 Dihedral : 7.635 179.809 871 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.14 % Favored : 88.73 % 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: -3.96 (0.26), residues: 790 helix: 0.31 (0.66), residues: 62 sheet: -3.63 (0.64), residues: 49 loop : -3.18 (0.21), residues: 679 *********************** 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 49 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 47 average time/residue: 0.2000 time to fit residues: 13.0743 Evaluate side-chains 43 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.931 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.0651 time to fit residues: 1.4936 ------------------------------------------------------------------------------- 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: 2.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8329 moved from start: 0.3406 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= 0.209 Angle : 0.614 9.445 8645 Z= 0.305 Chirality : 0.041 0.151 975 Planarity : 0.005 0.069 1137 Dihedral : 7.634 179.772 871 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.65 % Favored : 88.23 % 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: -3.83 (0.26), residues: 790 helix: 0.49 (0.67), residues: 62 sheet: -3.43 (0.69), residues: 44 loop : -3.12 (0.21), residues: 684 *********************** 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 50 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 0.2384 time to fit residues: 14.9183 Evaluate side-chains 44 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.756 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0605 time to fit residues: 1.3594 ------------------------------------------------------------------------------- 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: 2.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.0870 chunk 9 optimal weight: 0.5980 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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: 0.8296 moved from start: 0.3527 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= 0.169 Angle : 0.596 9.309 8645 Z= 0.296 Chirality : 0.040 0.152 975 Planarity : 0.004 0.046 1137 Dihedral : 7.539 179.990 871 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.87 % Favored : 90.00 % Rotamer Outliers : 0.45 % 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: -3.65 (0.27), residues: 790 helix: 0.69 (0.68), residues: 62 sheet: -2.55 (1.00), residues: 26 loop : -3.06 (0.21), residues: 702 ********************** 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 46 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 44 average time/residue: 0.2489 time to fit residues: 14.4200 Evaluate side-chains 43 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.752 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0689 time to fit residues: 1.2396 ------------------------------------------------------------------------------- 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: 1.9990 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 0.0570 chunk 63 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.086608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.060292 restraints weight = 15346.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.062671 restraints weight = 8701.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.064319 restraints weight = 6128.754| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3563 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= 0.185 Angle : 0.605 9.463 8645 Z= 0.301 Chirality : 0.040 0.149 975 Planarity : 0.004 0.047 1137 Dihedral : 7.513 179.958 871 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.51 % Favored : 89.37 % 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: -3.65 (0.27), residues: 790 helix: 0.78 (0.67), residues: 62 sheet: -3.36 (0.66), residues: 49 loop : -2.98 (0.22), residues: 679 =============================================================================== Job complete usr+sys time: 1394.57 seconds wall clock time: 25 minutes 51.53 seconds (1551.53 seconds total)