Starting phenix.real_space_refine on Tue Feb 13 13:06:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/02_2024/7wrq_32735_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/02_2024/7wrq_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_2024/7wrq_32735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/02_2024/7wrq_32735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/02_2024/7wrq_32735_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrq_32735/02_2024/7wrq_32735_neut.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-dev-5238/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: 9 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.01, per 1000 atoms: 0.64 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: 2.19 Conformation dependent library (CDL) restraints added in 1.3 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: 0.54 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: 1.23 Time building geometry restraints manager: 2.41 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: 3901 35.98 - 71.97: 88 71.97 - 107.95: 13 107.95 - 143.93: 0 143.93 - 179.91: 1 Dihedral angle restraints: 4003 sinusoidal: 1743 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 4000 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: 2.320 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: 5.890 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 19.760 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.220 ------------------------------------------------------------------------------- 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 : 15.483 179.913 2499 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 % Allowed : 6.65 % Favored : 92.30 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 179 HIS 0.014 0.002 HIS A 389 PHE 0.017 0.002 PHE A 262 TYR 0.012 0.002 TYR B 183 ARG 0.007 0.000 ARG C 56 *********************** 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 : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 545 LYS cc_start: 0.9073 (tttp) cc_final: 0.8872 (tptp) REVERT: B 37 GLU cc_start: 0.9295 (pt0) cc_final: 0.8467 (pm20) REVERT: B 49 SER cc_start: 0.9460 (t) cc_final: 0.9195 (p) REVERT: B 68 GLN cc_start: 0.9127 (mt0) cc_final: 0.8816 (mt0) REVERT: B 72 ASP cc_start: 0.8863 (p0) cc_final: 0.8576 (p0) REVERT: B 209 HIS cc_start: 0.8327 (m170) cc_final: 0.8090 (m170) REVERT: B 243 GLN cc_start: 0.8755 (mp10) cc_final: 0.8243 (mp10) REVERT: B 259 TYR cc_start: 0.8094 (m-80) cc_final: 0.7892 (m-10) REVERT: C 5 LEU cc_start: 0.8986 (tp) cc_final: 0.8707 (tt) outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.2240 time to fit residues: 25.3807 Evaluate side-chains 53 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 571 CYS 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: 7.9990 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: 3.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6377 Z= 0.224 Angle : 0.685 6.462 8645 Z= 0.344 Chirality : 0.043 0.149 975 Planarity : 0.005 0.056 1137 Dihedral : 10.496 179.964 1019 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.41 % Favored : 87.34 % Rotamer: Outliers : 1.96 % Allowed : 10.88 % Favored : 87.16 % 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: -5.23 (0.23), residues: 790 helix: -1.64 (0.59), residues: 68 sheet: -3.99 (0.37), residues: 112 loop : -3.95 (0.19), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 173 HIS 0.014 0.001 HIS A 601 PHE 0.012 0.001 PHE A 416 TYR 0.017 0.001 TYR A 208 ARG 0.009 0.000 ARG C 55 *********************** 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 67 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: B 37 GLU cc_start: 0.9237 (pt0) cc_final: 0.8455 (pm20) REVERT: B 49 SER cc_start: 0.9465 (t) cc_final: 0.9209 (p) REVERT: B 73 GLU cc_start: 0.8285 (tp30) cc_final: 0.8074 (tm-30) REVERT: B 209 HIS cc_start: 0.8365 (m170) cc_final: 0.8122 (m170) REVERT: B 259 TYR cc_start: 0.8154 (m-80) cc_final: 0.7936 (m-10) REVERT: C 46 GLU cc_start: 0.8781 (tt0) cc_final: 0.8078 (tt0) outliers start: 13 outliers final: 5 residues processed: 63 average time/residue: 0.2322 time to fit residues: 19.0014 Evaluate side-chains 49 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain B residue 250 THR 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: 2.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6377 Z= 0.266 Angle : 0.666 9.510 8645 Z= 0.332 Chirality : 0.043 0.167 975 Planarity : 0.005 0.050 1137 Dihedral : 8.768 179.768 1018 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.06 % Favored : 84.81 % Rotamer: Outliers : 1.81 % Allowed : 13.14 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.24), residues: 790 helix: -1.28 (0.59), residues: 69 sheet: -3.19 (0.55), residues: 61 loop : -3.82 (0.19), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 173 HIS 0.002 0.001 HIS B 196 PHE 0.009 0.001 PHE A 416 TYR 0.010 0.001 TYR A 49 ARG 0.003 0.000 ARG C 55 *********************** 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 60 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7739 (m-40) REVERT: B 37 GLU cc_start: 0.9157 (pt0) cc_final: 0.8409 (pm20) REVERT: B 49 SER cc_start: 0.9484 (t) cc_final: 0.9218 (p) REVERT: B 209 HIS cc_start: 0.8395 (m170) cc_final: 0.8189 (m170) REVERT: C 56 ARG cc_start: 0.8892 (mtt90) cc_final: 0.8580 (mtp85) outliers start: 12 outliers final: 6 residues processed: 59 average time/residue: 0.2101 time to fit residues: 16.3777 Evaluate side-chains 53 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.0060 chunk 75 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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: 0.8320 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6377 Z= 0.212 Angle : 0.617 9.267 8645 Z= 0.310 Chirality : 0.041 0.161 975 Planarity : 0.005 0.057 1137 Dihedral : 8.300 179.728 1017 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.52 % Favored : 88.35 % Rotamer: Outliers : 1.36 % Allowed : 14.65 % Favored : 83.99 % 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: -4.52 (0.25), residues: 790 helix: -0.87 (0.60), residues: 69 sheet: -3.04 (0.57), residues: 61 loop : -3.61 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 173 HIS 0.007 0.001 HIS A 601 PHE 0.009 0.001 PHE A 416 TYR 0.032 0.002 TYR A 49 ARG 0.012 0.000 ARG C 55 *********************** 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: 9 poor density : 47 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: B 37 GLU cc_start: 0.9131 (pt0) cc_final: 0.8380 (pm20) REVERT: B 49 SER cc_start: 0.9504 (t) cc_final: 0.9224 (p) REVERT: B 189 GLU cc_start: 0.8780 (tp30) cc_final: 0.8396 (tp30) outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 0.2611 time to fit residues: 17.8232 Evaluate side-chains 51 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 601 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 5.9990 chunk 56 optimal weight: 0.0980 chunk 31 optimal weight: 0.0970 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 B 209 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6377 Z= 0.242 Angle : 0.624 8.207 8645 Z= 0.315 Chirality : 0.042 0.151 975 Planarity : 0.004 0.048 1137 Dihedral : 8.123 179.621 1017 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.04 % Favored : 86.84 % Rotamer: Outliers : 2.42 % Allowed : 14.05 % Favored : 83.53 % 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: -4.34 (0.25), residues: 790 helix: -0.58 (0.59), residues: 69 sheet: -2.83 (0.63), residues: 51 loop : -3.51 (0.20), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 236 HIS 0.008 0.001 HIS B 196 PHE 0.010 0.001 PHE A 416 TYR 0.011 0.001 TYR B 259 ARG 0.006 0.000 ARG C 55 *********************** 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 61 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 208 TYR cc_start: 0.8337 (t80) cc_final: 0.8099 (t80) REVERT: A 372 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7747 (m-40) REVERT: B 37 GLU cc_start: 0.9099 (pt0) cc_final: 0.8374 (pm20) REVERT: B 49 SER cc_start: 0.9511 (t) cc_final: 0.9228 (p) REVERT: B 189 GLU cc_start: 0.8870 (tp30) cc_final: 0.8471 (tp30) outliers start: 16 outliers final: 11 residues processed: 58 average time/residue: 0.2045 time to fit residues: 15.9806 Evaluate side-chains 55 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 601 HIS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 SER 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: 0.5980 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 209 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6377 Z= 0.396 Angle : 0.715 9.107 8645 Z= 0.360 Chirality : 0.045 0.149 975 Planarity : 0.005 0.050 1137 Dihedral : 8.313 179.070 1017 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.33 % Favored : 83.54 % Rotamer: Outliers : 2.57 % Allowed : 15.11 % Favored : 82.33 % 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: -4.39 (0.25), residues: 790 helix: -0.35 (0.64), residues: 69 sheet: -3.20 (0.60), residues: 51 loop : -3.55 (0.20), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 173 HIS 0.025 0.002 HIS A 601 PHE 0.012 0.002 PHE A 602 TYR 0.012 0.001 TYR C 24 ARG 0.006 0.000 ARG C 55 *********************** 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 59 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 372 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7813 (m-40) REVERT: B 37 GLU cc_start: 0.9070 (pt0) cc_final: 0.8290 (pm20) REVERT: B 189 GLU cc_start: 0.8948 (tp30) cc_final: 0.8546 (tp30) outliers start: 17 outliers final: 12 residues processed: 56 average time/residue: 0.2129 time to fit residues: 15.8173 Evaluate side-chains 54 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 0.0050 chunk 46 optimal weight: 0.0270 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5052 ------------------------------------------------------------------------------- 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 209 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3091 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= 0.170 Angle : 0.610 9.539 8645 Z= 0.305 Chirality : 0.041 0.154 975 Planarity : 0.004 0.048 1137 Dihedral : 8.022 179.665 1017 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.52 % Favored : 88.35 % Rotamer: Outliers : 2.27 % Allowed : 16.31 % Favored : 81.42 % 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: -4.13 (0.25), residues: 790 helix: 0.01 (0.65), residues: 62 sheet: -2.72 (0.62), residues: 51 loop : -3.38 (0.20), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 236 HIS 0.024 0.002 HIS B 209 PHE 0.008 0.001 PHE A 416 TYR 0.020 0.001 TYR B 259 ARG 0.006 0.000 ARG C 37 *********************** 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 59 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 372 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7688 (m-40) REVERT: B 37 GLU cc_start: 0.9035 (pt0) cc_final: 0.8291 (pm20) REVERT: B 86 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7165 (mt) REVERT: B 189 GLU cc_start: 0.8875 (tp30) cc_final: 0.8474 (tp30) outliers start: 15 outliers final: 11 residues processed: 55 average time/residue: 0.2162 time to fit residues: 15.8581 Evaluate side-chains 56 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 overall best weight: 1.3422 ------------------------------------------------------------------------------- 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 209 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3190 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= 0.259 Angle : 0.635 9.140 8645 Z= 0.319 Chirality : 0.042 0.149 975 Planarity : 0.004 0.049 1137 Dihedral : 8.019 179.538 1017 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.42 % Favored : 86.46 % Rotamer: Outliers : 2.57 % Allowed : 16.31 % Favored : 81.12 % 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: -4.07 (0.26), residues: 790 helix: 0.18 (0.66), residues: 62 sheet: -2.64 (0.63), residues: 51 loop : -3.35 (0.20), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 236 HIS 0.006 0.001 HIS B 209 PHE 0.010 0.001 PHE A 416 TYR 0.020 0.001 TYR A 208 ARG 0.006 0.000 ARG C 37 *********************** 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 59 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7780 (m-40) REVERT: B 37 GLU cc_start: 0.9004 (pt0) cc_final: 0.8266 (pm20) REVERT: B 59 GLU cc_start: 0.8658 (mp0) cc_final: 0.8380 (mp0) REVERT: B 189 GLU cc_start: 0.8927 (tp30) cc_final: 0.8519 (tp30) outliers start: 17 outliers final: 11 residues processed: 56 average time/residue: 0.2363 time to fit residues: 17.5286 Evaluate side-chains 52 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR 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: 1.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 0.0020 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 209 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3282 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= 0.187 Angle : 0.606 9.404 8645 Z= 0.304 Chirality : 0.041 0.152 975 Planarity : 0.004 0.048 1137 Dihedral : 7.915 179.799 1017 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.39 % Favored : 88.48 % Rotamer: Outliers : 2.11 % Allowed : 16.47 % Favored : 81.42 % 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: -3.94 (0.26), residues: 790 helix: 0.25 (0.66), residues: 62 sheet: -2.58 (0.63), residues: 51 loop : -3.25 (0.21), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 236 HIS 0.008 0.001 HIS B 209 PHE 0.008 0.001 PHE A 416 TYR 0.020 0.001 TYR B 259 ARG 0.004 0.000 ARG C 37 *********************** 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 55 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7729 (m-40) REVERT: B 37 GLU cc_start: 0.8980 (pt0) cc_final: 0.8254 (pm20) REVERT: B 59 GLU cc_start: 0.8614 (mp0) cc_final: 0.8346 (mp0) REVERT: B 189 GLU cc_start: 0.8900 (tp30) cc_final: 0.8696 (tp30) outliers start: 14 outliers final: 10 residues processed: 51 average time/residue: 0.1994 time to fit residues: 13.7207 Evaluate side-chains 51 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 209 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6377 Z= 0.257 Angle : 0.638 9.255 8645 Z= 0.320 Chirality : 0.042 0.148 975 Planarity : 0.004 0.049 1137 Dihedral : 7.953 179.468 1017 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.30 % Favored : 85.57 % Rotamer: Outliers : 2.11 % Allowed : 16.47 % Favored : 81.42 % 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: -3.91 (0.26), residues: 790 helix: 0.33 (0.67), residues: 62 sheet: -2.54 (0.64), residues: 51 loop : -3.24 (0.21), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 236 HIS 0.007 0.001 HIS B 209 PHE 0.010 0.001 PHE A 416 TYR 0.016 0.001 TYR B 259 ARG 0.004 0.000 ARG C 37 ********************** 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 58 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7767 (m-40) REVERT: B 37 GLU cc_start: 0.8982 (pt0) cc_final: 0.8253 (pm20) REVERT: B 59 GLU cc_start: 0.8621 (mp0) cc_final: 0.8344 (mp0) REVERT: B 189 GLU cc_start: 0.8941 (tp30) cc_final: 0.8737 (tp30) outliers start: 14 outliers final: 12 residues processed: 54 average time/residue: 0.2005 time to fit residues: 14.6516 Evaluate side-chains 54 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 601 HIS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.0030 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.0770 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9952 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.085486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.059134 restraints weight = 15619.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.061820 restraints weight = 9846.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.063724 restraints weight = 5914.637| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3404 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= 0.213 Angle : 0.619 9.228 8645 Z= 0.310 Chirality : 0.041 0.151 975 Planarity : 0.004 0.047 1137 Dihedral : 7.895 179.689 1017 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.90 % Favored : 87.97 % Rotamer: Outliers : 2.11 % Allowed : 16.31 % Favored : 81.57 % 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: -3.77 (0.27), residues: 790 helix: 0.10 (0.64), residues: 69 sheet: -2.57 (0.71), residues: 41 loop : -3.12 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 236 HIS 0.003 0.000 HIS A 601 PHE 0.009 0.001 PHE A 416 TYR 0.010 0.001 TYR A 208 ARG 0.004 0.000 ARG C 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1458.63 seconds wall clock time: 27 minutes 3.59 seconds (1623.59 seconds total)