Starting phenix.real_space_refine on Sun Dec 29 20:00:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qpa_14116/12_2024/7qpa_14116_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qpa_14116/12_2024/7qpa_14116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qpa_14116/12_2024/7qpa_14116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qpa_14116/12_2024/7qpa_14116.map" model { file = "/net/cci-nas-00/data/ceres_data/7qpa_14116/12_2024/7qpa_14116_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qpa_14116/12_2024/7qpa_14116_trim.cif" } resolution = 3.18 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= 0.047 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 34 5.16 5 C 3508 2.51 5 N 804 2.21 5 O 926 1.98 5 H 5540 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10814 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5244 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "B" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5244 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "A" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'DLP': 2, 'IAC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 87 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 105 Classifications: {'water': 35} Link IDs: {None: 34} Time building chain proxies: 5.77, per 1000 atoms: 0.53 Number of scatterers: 10814 At special positions: 0 Unit cell: (76.346, 100.932, 67.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 2 15.00 O 926 8.00 N 804 7.00 C 3508 6.00 H 5540 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 753.9 milliseconds 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 87.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 3 through 30 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 51 through 61 removed outlier: 3.866A pdb=" N GLN A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 93 removed outlier: 3.534A pdb=" N PHE A 92 " --> pdb=" O MET A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.726A pdb=" N ARG A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.676A pdb=" N ALA A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.938A pdb=" N ALA A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 207 through 220 removed outlier: 3.674A pdb=" N LEU A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.906A pdb=" N TYR A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.915A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 274 Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 311 through 320 removed outlier: 3.777A pdb=" N ILE A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 339 through 351 removed outlier: 4.108A pdb=" N ILE A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 367 removed outlier: 4.043A pdb=" N LEU A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 29 Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 51 through 61 removed outlier: 3.846A pdb=" N GLN B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 removed outlier: 3.781A pdb=" N MET B 67 " --> pdb=" O PRO B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 93 removed outlier: 3.686A pdb=" N PHE B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.536A pdb=" N ALA B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 148 removed outlier: 4.046A pdb=" N SER B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 163 Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.688A pdb=" N LEU B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.660A pdb=" N TYR B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 257 removed outlier: 3.945A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 274 Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 311 through 320 removed outlier: 3.687A pdb=" N ILE B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.798A pdb=" N THR B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 367 removed outlier: 4.070A pdb=" N LEU B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1134 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: 3.91 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5534 1.03 - 1.23: 13 1.23 - 1.42: 2091 1.42 - 1.62: 3172 1.62 - 1.81: 62 Bond restraints: 10872 Sorted by residual: bond pdb=" N IAC A 401 " pdb=" C8 IAC A 401 " ideal model delta sigma weight residual 1.371 1.315 0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" N IAC B 401 " pdb=" C8 IAC B 401 " ideal model delta sigma weight residual 1.371 1.315 0.056 2.00e-02 2.50e+03 7.76e+00 bond pdb=" O4P DLP A 402 " pdb=" P DLP A 402 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" O4P DLP A 403 " pdb=" P DLP A 403 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C4 DLP A 403 " pdb=" O4P DLP A 403 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.11e+00 ... (remaining 10867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 19377 2.09 - 4.18: 183 4.18 - 6.27: 10 6.27 - 8.36: 4 8.36 - 10.45: 2 Bond angle restraints: 19576 Sorted by residual: angle pdb=" O3P DLP A 403 " pdb=" P DLP A 403 " pdb=" O4P DLP A 403 " ideal model delta sigma weight residual 93.58 104.03 -10.45 3.00e+00 1.11e-01 1.21e+01 angle pdb=" O3P DLP A 402 " pdb=" P DLP A 402 " pdb=" O4P DLP A 402 " ideal model delta sigma weight residual 93.58 103.82 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N VAL A 106 " pdb=" CA VAL A 106 " pdb=" C VAL A 106 " ideal model delta sigma weight residual 113.00 109.51 3.49 1.30e+00 5.92e-01 7.20e+00 angle pdb=" N ILE B 318 " pdb=" CA ILE B 318 " pdb=" C ILE B 318 " ideal model delta sigma weight residual 112.96 110.36 2.60 1.00e+00 1.00e+00 6.78e+00 angle pdb=" C18 IAC A 401 " pdb=" C17 IAC A 401 " pdb=" C7 IAC A 401 " ideal model delta sigma weight residual 115.88 109.02 6.86 3.00e+00 1.11e-01 5.23e+00 ... (remaining 19571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.15: 4688 23.15 - 46.30: 260 46.30 - 69.45: 70 69.45 - 92.60: 8 92.60 - 115.75: 2 Dihedral angle restraints: 5028 sinusoidal: 2762 harmonic: 2266 Sorted by residual: dihedral pdb=" N DLP A 403 " pdb=" C4 DLP A 403 " pdb=" C5 DLP A 403 " pdb=" O4P DLP A 403 " ideal model delta sinusoidal sigma weight residual 288.95 173.20 115.75 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" N DLP A 402 " pdb=" C4 DLP A 402 " pdb=" C5 DLP A 402 " pdb=" O4P DLP A 402 " ideal model delta sinusoidal sigma weight residual 288.95 174.87 114.08 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" CA SER B 113 " pdb=" C SER B 113 " pdb=" N VAL B 114 " pdb=" CA VAL B 114 " ideal model delta harmonic sigma weight residual 180.00 -162.86 -17.14 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 637 0.040 - 0.079: 189 0.079 - 0.119: 30 0.119 - 0.159: 3 0.159 - 0.199: 3 Chirality restraints: 862 Sorted by residual: chirality pdb=" C2 DLP A 403 " pdb=" C1 DLP A 403 " pdb=" C3 DLP A 403 " pdb=" O2 DLP A 403 " both_signs ideal model delta sigma weight residual False -2.35 -2.55 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" C2 DLP A 402 " pdb=" C1 DLP A 402 " pdb=" C3 DLP A 402 " pdb=" O2 DLP A 402 " both_signs ideal model delta sigma weight residual False -2.35 -2.55 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CG LEU B 5 " pdb=" CB LEU B 5 " pdb=" CD1 LEU B 5 " pdb=" CD2 LEU B 5 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 859 not shown) Planarity restraints: 1472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 68 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO B 69 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 69 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 69 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 328 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 329 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 216 " 0.136 9.50e-02 1.11e+02 4.56e-02 2.57e+00 pdb=" NE ARG A 216 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 216 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 216 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 216 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 216 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 216 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 216 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 216 " 0.000 2.00e-02 2.50e+03 ... (remaining 1469 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 62 2.04 - 2.68: 16669 2.68 - 3.32: 33261 3.32 - 3.96: 42515 3.96 - 4.60: 66955 Nonbonded interactions: 159462 Sorted by model distance: nonbonded pdb="HD21 LEU B 5 " pdb=" HE1 HIS B 9 " model vdw 1.404 2.270 nonbonded pdb="HD21 ASN A 117 " pdb=" O HOH A 501 " model vdw 1.644 2.450 nonbonded pdb="HD21 ASN B 117 " pdb=" O HOH B 501 " model vdw 1.647 2.450 nonbonded pdb=" OD1 ASN A 63 " pdb=" H PHE A 65 " model vdw 1.667 2.450 nonbonded pdb=" HZ3 LYS B 334 " pdb=" O HOH B 503 " model vdw 1.707 2.450 ... (remaining 159457 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 0 through 367 or resid 401)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.200 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.010 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 0.004 0.056 5332 Z= 0.286 Angle : 0.638 10.454 7224 Z= 0.310 Chirality : 0.038 0.199 862 Planarity : 0.005 0.060 854 Dihedral : 15.169 115.750 1936 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.33), residues: 646 helix: 1.66 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.71 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 93 HIS 0.010 0.001 HIS A 94 PHE 0.015 0.001 PHE A 330 TYR 0.007 0.001 TYR B 8 ARG 0.010 0.001 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.773 Fit side-chains REVERT: A 67 MET cc_start: 0.8540 (mtm) cc_final: 0.8321 (mtp) REVERT: A 308 ARG cc_start: 0.7457 (mmt-90) cc_final: 0.7256 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.3618 time to fit residues: 44.2659 Evaluate side-chains 83 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5332 Z= 0.227 Angle : 0.561 5.154 7224 Z= 0.290 Chirality : 0.037 0.124 862 Planarity : 0.005 0.047 854 Dihedral : 11.648 104.596 772 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.72 % Allowed : 5.42 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.33), residues: 646 helix: 1.36 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.05 (0.51), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.010 0.001 HIS A 94 PHE 0.016 0.001 PHE A 330 TYR 0.008 0.001 TYR A 362 ARG 0.005 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.763 Fit side-chains REVERT: A 208 MET cc_start: 0.7101 (tpp) cc_final: 0.6769 (tpt) REVERT: B 308 ARG cc_start: 0.7640 (mmt-90) cc_final: 0.7268 (mmt-90) outliers start: 4 outliers final: 4 residues processed: 84 average time/residue: 0.3941 time to fit residues: 43.2117 Evaluate side-chains 80 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 137 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5332 Z= 0.211 Angle : 0.532 5.580 7224 Z= 0.273 Chirality : 0.036 0.125 862 Planarity : 0.005 0.047 854 Dihedral : 11.363 97.515 772 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.72 % Allowed : 6.86 % Favored : 92.42 % 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: 1.04 (0.33), residues: 646 helix: 1.37 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.22 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.004 0.001 HIS A 94 PHE 0.016 0.001 PHE A 330 TYR 0.006 0.001 TYR B 8 ARG 0.005 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.822 Fit side-chains REVERT: A 208 MET cc_start: 0.7077 (tpp) cc_final: 0.6770 (tpt) REVERT: B 308 ARG cc_start: 0.7655 (mmt-90) cc_final: 0.7261 (mmt-90) outliers start: 4 outliers final: 3 residues processed: 81 average time/residue: 0.3816 time to fit residues: 40.6333 Evaluate side-chains 81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 12 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5332 Z= 0.208 Angle : 0.527 5.023 7224 Z= 0.271 Chirality : 0.036 0.131 862 Planarity : 0.005 0.046 854 Dihedral : 11.366 91.721 772 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.72 % Allowed : 8.12 % Favored : 91.16 % 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: 1.06 (0.33), residues: 646 helix: 1.40 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.29 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.010 0.001 HIS A 94 PHE 0.015 0.001 PHE A 330 TYR 0.006 0.001 TYR B 361 ARG 0.005 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.811 Fit side-chains REVERT: A 208 MET cc_start: 0.7065 (tpp) cc_final: 0.6766 (tpt) outliers start: 4 outliers final: 4 residues processed: 83 average time/residue: 0.3750 time to fit residues: 41.0765 Evaluate side-chains 82 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5332 Z= 0.185 Angle : 0.509 5.024 7224 Z= 0.262 Chirality : 0.036 0.157 862 Planarity : 0.005 0.044 854 Dihedral : 11.312 89.667 772 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.08 % Allowed : 8.48 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.34), residues: 646 helix: 1.48 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -2.22 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.007 0.001 HIS A 94 PHE 0.014 0.001 PHE A 330 TYR 0.005 0.001 TYR B 130 ARG 0.003 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.950 Fit side-chains REVERT: A 208 MET cc_start: 0.7056 (tpp) cc_final: 0.6774 (tpt) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.3808 time to fit residues: 40.3496 Evaluate side-chains 76 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain B residue 12 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5332 Z= 0.215 Angle : 0.523 4.865 7224 Z= 0.270 Chirality : 0.037 0.157 862 Planarity : 0.005 0.045 854 Dihedral : 11.348 86.767 772 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.08 % Allowed : 9.03 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.33), residues: 646 helix: 1.38 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -2.14 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.010 0.001 HIS A 94 PHE 0.015 0.001 PHE A 330 TYR 0.006 0.001 TYR A 361 ARG 0.003 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.795 Fit side-chains REVERT: A 208 MET cc_start: 0.7051 (tpp) cc_final: 0.6778 (tpt) outliers start: 6 outliers final: 6 residues processed: 77 average time/residue: 0.3880 time to fit residues: 39.2009 Evaluate side-chains 79 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 54 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.0670 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5332 Z= 0.154 Angle : 0.490 4.697 7224 Z= 0.252 Chirality : 0.036 0.125 862 Planarity : 0.005 0.043 854 Dihedral : 11.054 88.278 772 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.90 % Allowed : 9.21 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.34), residues: 646 helix: 1.55 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -2.06 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.009 0.001 HIS A 94 PHE 0.013 0.001 PHE A 330 TYR 0.005 0.001 TYR B 130 ARG 0.004 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.809 Fit side-chains REVERT: A 208 MET cc_start: 0.7045 (tpp) cc_final: 0.6772 (tpt) REVERT: A 308 ARG cc_start: 0.7397 (mmt-90) cc_final: 0.6651 (mtm180) outliers start: 5 outliers final: 4 residues processed: 82 average time/residue: 0.3689 time to fit residues: 39.7018 Evaluate side-chains 78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain B residue 12 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5332 Z= 0.198 Angle : 0.513 4.697 7224 Z= 0.264 Chirality : 0.037 0.168 862 Planarity : 0.005 0.043 854 Dihedral : 11.067 86.243 772 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.90 % Allowed : 9.75 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.34), residues: 646 helix: 1.49 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -2.13 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 233 HIS 0.009 0.001 HIS A 94 PHE 0.014 0.001 PHE A 330 TYR 0.006 0.001 TYR B 130 ARG 0.002 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.877 Fit side-chains REVERT: A 208 MET cc_start: 0.7071 (tpp) cc_final: 0.6813 (tpt) REVERT: A 308 ARG cc_start: 0.7434 (mmt-90) cc_final: 0.6684 (mtm180) REVERT: B 9 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.6737 (t-90) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.4040 time to fit residues: 41.1937 Evaluate side-chains 75 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5332 Z= 0.222 Angle : 0.524 4.780 7224 Z= 0.271 Chirality : 0.037 0.125 862 Planarity : 0.005 0.043 854 Dihedral : 11.118 82.116 772 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.08 % Allowed : 9.39 % Favored : 89.53 % 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: 1.05 (0.33), residues: 646 helix: 1.39 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.46 (0.47), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.009 0.001 HIS A 94 PHE 0.016 0.001 PHE A 155 TYR 0.007 0.001 TYR B 130 ARG 0.003 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.866 Fit side-chains REVERT: A 9 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.6729 (t-90) REVERT: A 208 MET cc_start: 0.7050 (tpp) cc_final: 0.6785 (tpt) REVERT: A 308 ARG cc_start: 0.7448 (mmt-90) cc_final: 0.6692 (mtm180) REVERT: B 9 HIS cc_start: 0.7350 (OUTLIER) cc_final: 0.6737 (t-90) outliers start: 6 outliers final: 3 residues processed: 77 average time/residue: 0.4040 time to fit residues: 40.9144 Evaluate side-chains 76 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5332 Z= 0.187 Angle : 0.509 4.600 7224 Z= 0.262 Chirality : 0.036 0.126 862 Planarity : 0.006 0.078 854 Dihedral : 10.941 80.499 772 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.08 % Allowed : 9.21 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.33), residues: 646 helix: 1.46 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.45 (0.47), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 233 HIS 0.013 0.001 HIS A 94 PHE 0.013 0.001 PHE A 330 TYR 0.006 0.001 TYR A 361 ARG 0.013 0.001 ARG B 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.891 Fit side-chains REVERT: A 9 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.6685 (t-90) REVERT: A 208 MET cc_start: 0.7042 (tpp) cc_final: 0.6777 (tpt) REVERT: A 308 ARG cc_start: 0.7444 (mmt-90) cc_final: 0.6687 (mtm180) REVERT: B 9 HIS cc_start: 0.7333 (OUTLIER) cc_final: 0.6728 (t-90) REVERT: B 18 TYR cc_start: 0.8694 (m-80) cc_final: 0.8440 (m-80) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 0.3902 time to fit residues: 39.6494 Evaluate side-chains 78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 54 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.167043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137493 restraints weight = 16572.679| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.78 r_work: 0.3347 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5332 Z= 0.212 Angle : 0.520 4.660 7224 Z= 0.268 Chirality : 0.037 0.127 862 Planarity : 0.005 0.057 854 Dihedral : 11.008 76.659 772 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.08 % Allowed : 9.57 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.33), residues: 646 helix: 1.41 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.51 (0.46), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.012 0.001 HIS A 94 PHE 0.014 0.001 PHE A 330 TYR 0.007 0.001 TYR A 361 ARG 0.008 0.001 ARG B 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3152.94 seconds wall clock time: 57 minutes 16.75 seconds (3436.75 seconds total)