Starting phenix.real_space_refine on Fri Mar 15 07:04:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpa_14116/03_2024/7qpa_14116_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpa_14116/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpa_14116/03_2024/7qpa_14116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpa_14116/03_2024/7qpa_14116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpa_14116/03_2024/7qpa_14116_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpa_14116/03_2024/7qpa_14116_trim_updated.pdb" } 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 Residue "A TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.54, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.57 Conformation dependent library (CDL) restraints added in 1.3 seconds 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... running ksdssp... Secondary structure from input PDB file: 37 helices and 0 sheets defined 76.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 36 through 49 Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.866A pdb=" N GLN A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.534A pdb=" N PHE A 92 " --> pdb=" O MET A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 98 No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 105 through 108 No H-bonds generated for 'chain 'A' and resid 105 through 108' Processing helix chain 'A' and resid 110 through 113 No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 121 through 130 removed outlier: 3.676A pdb=" N ALA A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 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 149 through 163 Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 222 through 240 Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.915A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 295 through 307 Processing helix chain 'A' and resid 311 through 319 removed outlier: 3.675A pdb=" N VAL A 316 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 317 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 319 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 340 through 350 removed outlier: 3.656A pdb=" N THR A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 366 Processing helix chain 'B' and resid 4 through 29 Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.846A pdb=" N GLN B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.686A pdb=" N PHE B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 121 through 147 removed outlier: 3.536A pdb=" N ALA B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLU B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) 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 149 through 163 Processing helix chain 'B' and resid 208 through 219 Processing helix chain 'B' and resid 222 through 240 Processing helix chain 'B' and resid 246 through 256 removed outlier: 3.945A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 295 through 307 Processing helix chain 'B' and resid 311 through 319 removed outlier: 3.721A pdb=" N VAL B 316 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 317 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 319 " --> pdb=" O VAL B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 340 through 350 removed outlier: 3.860A pdb=" N SER B 344 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B 345 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE B 348 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE B 349 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY B 350 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 366 323 hydrogen bonds defined for protein. 942 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: 3.48 Time building geometry restraints manager: 9.63 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: 100.24 - 107.08: 317 107.08 - 113.92: 13269 113.92 - 120.77: 3794 120.77 - 127.61: 2123 127.61 - 134.46: 73 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: 73 2.04 - 2.68: 16721 2.68 - 3.32: 33310 3.32 - 3.96: 42607 3.96 - 4.60: 67031 Nonbonded interactions: 159742 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 1.850 nonbonded pdb="HD21 ASN B 117 " pdb=" O HOH B 501 " model vdw 1.647 1.850 nonbonded pdb=" OD1 ASN A 63 " pdb=" H PHE A 65 " model vdw 1.667 1.850 nonbonded pdb=" HZ3 LYS B 334 " pdb=" O HOH B 503 " model vdw 1.707 1.850 ... (remaining 159737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.370 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: 0.170 Extract box with map and model: 2.490 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 39.250 Find NCS groups from input model: 0.350 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.920 ------------------------------------------------------------------------------- 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= 0.274 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 fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.637 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: 0.3515 time to fit residues: 42.6323 Evaluate side-chains 83 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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: 0.8980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7254 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5332 Z= 0.237 Angle : 0.546 4.916 7224 Z= 0.278 Chirality : 0.037 0.139 862 Planarity : 0.005 0.042 854 Dihedral : 11.541 104.564 772 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.72 % Allowed : 5.60 % Favored : 93.68 % 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: 1.33 (0.34), residues: 646 helix: 1.51 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.70 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 233 HIS 0.011 0.001 HIS A 94 PHE 0.015 0.001 PHE A 330 TYR 0.007 0.001 TYR A 362 ARG 0.004 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 fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.840 Fit side-chains REVERT: A 67 MET cc_start: 0.8519 (mtm) cc_final: 0.8260 (mtp) REVERT: A 208 MET cc_start: 0.7092 (tpp) cc_final: 0.6764 (tpt) REVERT: A 308 ARG cc_start: 0.7451 (mmt-90) cc_final: 0.7194 (mmt-90) outliers start: 4 outliers final: 4 residues processed: 84 average time/residue: 0.3507 time to fit residues: 38.7865 Evaluate side-chains 82 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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: 0.5980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7248 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5332 Z= 0.194 Angle : 0.506 4.870 7224 Z= 0.257 Chirality : 0.036 0.130 862 Planarity : 0.005 0.040 854 Dihedral : 11.259 98.416 772 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.90 % Allowed : 6.50 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.34), residues: 646 helix: 1.62 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.67 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.006 0.001 HIS A 94 PHE 0.015 0.001 PHE A 330 TYR 0.007 0.001 TYR B 8 ARG 0.002 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 85 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.797 Fit side-chains REVERT: A 67 MET cc_start: 0.8537 (mtm) cc_final: 0.8272 (mtp) REVERT: A 208 MET cc_start: 0.7079 (tpp) cc_final: 0.6774 (tpt) REVERT: A 308 ARG cc_start: 0.7389 (mmt-90) cc_final: 0.6595 (mtm180) outliers start: 5 outliers final: 5 residues processed: 83 average time/residue: 0.3514 time to fit residues: 38.7106 Evaluate side-chains 85 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 289 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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: 0.7260 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5332 Z= 0.213 Angle : 0.510 4.850 7224 Z= 0.259 Chirality : 0.036 0.131 862 Planarity : 0.005 0.040 854 Dihedral : 11.244 91.836 772 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.08 % Allowed : 7.40 % Favored : 91.52 % 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: 1.44 (0.34), residues: 646 helix: 1.59 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.65 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 233 HIS 0.008 0.001 HIS A 94 PHE 0.014 0.001 PHE A 330 TYR 0.007 0.001 TYR B 130 ARG 0.002 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 83 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.838 Fit side-chains REVERT: A 67 MET cc_start: 0.8558 (mtm) cc_final: 0.8292 (mtp) REVERT: A 208 MET cc_start: 0.7065 (tpp) cc_final: 0.6778 (tpt) REVERT: A 308 ARG cc_start: 0.7428 (mmt-90) cc_final: 0.6644 (mtm180) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.3362 time to fit residues: 35.6392 Evaluate side-chains 81 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 289 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7275 moved from start: 0.1195 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= 0.234 Angle : 0.516 4.883 7224 Z= 0.264 Chirality : 0.037 0.145 862 Planarity : 0.005 0.041 854 Dihedral : 11.432 85.191 772 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.08 % Allowed : 8.12 % Favored : 90.79 % 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: 1.45 (0.34), residues: 646 helix: 1.62 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.58 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 233 HIS 0.008 0.001 HIS A 94 PHE 0.014 0.001 PHE A 330 TYR 0.007 0.001 TYR B 130 ARG 0.002 0.000 ARG A 216 *********************** 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 83 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.827 Fit side-chains REVERT: A 67 MET cc_start: 0.8577 (mtm) cc_final: 0.8191 (mtp) REVERT: A 208 MET cc_start: 0.7059 (tpp) cc_final: 0.6783 (tpt) REVERT: A 308 ARG cc_start: 0.7386 (mmt-90) cc_final: 0.6643 (mtm180) outliers start: 6 outliers final: 6 residues processed: 80 average time/residue: 0.3842 time to fit residues: 40.8461 Evaluate side-chains 83 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 54 LEU Chi-restraints excluded: chain B residue 289 MET 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: 0.8980 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7277 moved from start: 0.1287 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= 0.220 Angle : 0.507 4.800 7224 Z= 0.259 Chirality : 0.036 0.131 862 Planarity : 0.005 0.042 854 Dihedral : 11.362 86.236 772 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.44 % Allowed : 8.12 % 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: 1.45 (0.34), residues: 646 helix: 1.62 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.58 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 233 HIS 0.008 0.001 HIS A 94 PHE 0.014 0.001 PHE A 330 TYR 0.007 0.001 TYR B 361 ARG 0.002 0.000 ARG A 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 81 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.888 Fit side-chains REVERT: A 67 MET cc_start: 0.8585 (mtm) cc_final: 0.8219 (mtp) REVERT: A 208 MET cc_start: 0.7046 (tpp) cc_final: 0.6777 (tpt) REVERT: A 286 ILE cc_start: 0.8419 (tp) cc_final: 0.7697 (pt) REVERT: A 308 ARG cc_start: 0.7351 (mmt-90) cc_final: 0.6639 (mtm180) outliers start: 8 outliers final: 8 residues processed: 76 average time/residue: 0.3762 time to fit residues: 37.6003 Evaluate side-chains 80 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 289 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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: 0.7283 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5332 Z= 0.228 Angle : 0.511 4.782 7224 Z= 0.261 Chirality : 0.036 0.131 862 Planarity : 0.005 0.042 854 Dihedral : 11.277 87.866 772 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.26 % Allowed : 8.66 % Favored : 90.07 % 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 (0.34), residues: 646 helix: 1.61 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.60 (0.49), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 233 HIS 0.008 0.001 HIS A 94 PHE 0.014 0.001 PHE A 330 TYR 0.007 0.001 TYR B 361 ARG 0.001 0.000 ARG A 216 *********************** 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 79 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.834 Fit side-chains REVERT: A 67 MET cc_start: 0.8593 (mtm) cc_final: 0.8242 (mtp) REVERT: A 208 MET cc_start: 0.7052 (tpp) cc_final: 0.6767 (tpt) REVERT: A 286 ILE cc_start: 0.8385 (tp) cc_final: 0.7796 (pt) REVERT: A 308 ARG cc_start: 0.7387 (mmt-90) cc_final: 0.6703 (mtm180) REVERT: B 18 TYR cc_start: 0.8691 (m-80) cc_final: 0.8405 (m-80) outliers start: 7 outliers final: 7 residues processed: 75 average time/residue: 0.3735 time to fit residues: 36.8556 Evaluate side-chains 79 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 A residue 54 LEU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 289 MET 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: 1.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1410 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= 0.217 Angle : 0.504 4.707 7224 Z= 0.258 Chirality : 0.036 0.129 862 Planarity : 0.005 0.043 854 Dihedral : 11.219 88.100 772 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.81 % Allowed : 8.12 % Favored : 90.07 % 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: 1.44 (0.34), residues: 646 helix: 1.61 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.58 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 233 HIS 0.009 0.001 HIS A 94 PHE 0.014 0.001 PHE A 330 TYR 0.007 0.001 TYR B 361 ARG 0.004 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 83 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.815 Fit side-chains REVERT: A 67 MET cc_start: 0.8530 (mtm) cc_final: 0.8234 (mtp) REVERT: A 208 MET cc_start: 0.7047 (tpp) cc_final: 0.6767 (tpt) REVERT: A 286 ILE cc_start: 0.8357 (tp) cc_final: 0.7802 (pt) REVERT: A 308 ARG cc_start: 0.7383 (mmt-90) cc_final: 0.6702 (mtm180) REVERT: A 355 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7975 (tp) REVERT: B 18 TYR cc_start: 0.8689 (m-80) cc_final: 0.8399 (m-80) outliers start: 10 outliers final: 9 residues processed: 77 average time/residue: 0.3701 time to fit residues: 37.5589 Evaluate side-chains 82 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 A residue 54 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 289 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 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: 0.7281 moved from start: 0.1476 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= 0.212 Angle : 0.502 4.696 7224 Z= 0.256 Chirality : 0.036 0.128 862 Planarity : 0.005 0.041 854 Dihedral : 10.888 87.294 772 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.81 % Allowed : 8.30 % 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: 1.47 (0.34), residues: 646 helix: 1.61 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -1.49 (0.50), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 233 HIS 0.009 0.001 HIS A 94 PHE 0.013 0.001 PHE A 330 TYR 0.006 0.001 TYR B 361 ARG 0.004 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 82 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.815 Fit side-chains REVERT: A 67 MET cc_start: 0.8532 (mtm) cc_final: 0.8253 (mtp) REVERT: A 208 MET cc_start: 0.7040 (tpp) cc_final: 0.6765 (tpt) REVERT: A 286 ILE cc_start: 0.8294 (tp) cc_final: 0.7784 (pt) REVERT: A 308 ARG cc_start: 0.7262 (mmt-90) cc_final: 0.6582 (mtm180) REVERT: A 355 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7960 (tp) REVERT: B 18 TYR cc_start: 0.8689 (m-80) cc_final: 0.8390 (m-80) outliers start: 10 outliers final: 8 residues processed: 76 average time/residue: 0.3667 time to fit residues: 36.7126 Evaluate side-chains 80 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 A residue 355 LEU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 289 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7275 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5332 Z= 0.199 Angle : 0.502 4.654 7224 Z= 0.256 Chirality : 0.036 0.127 862 Planarity : 0.006 0.077 854 Dihedral : 10.631 85.809 772 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.81 % Allowed : 8.66 % 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: 1.46 (0.34), residues: 646 helix: 1.57 (0.24), residues: 512 sheet: None (None), residues: 0 loop : -1.34 (0.50), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 233 HIS 0.009 0.001 HIS A 94 PHE 0.013 0.001 PHE A 330 TYR 0.006 0.001 TYR B 361 ARG 0.012 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 83 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.807 Fit side-chains REVERT: A 67 MET cc_start: 0.8532 (mtm) cc_final: 0.8253 (mtp) REVERT: A 208 MET cc_start: 0.7015 (tpp) cc_final: 0.6794 (tpt) REVERT: A 286 ILE cc_start: 0.8296 (tp) cc_final: 0.7784 (pt) REVERT: A 308 ARG cc_start: 0.7253 (mmt-90) cc_final: 0.6573 (mtm180) REVERT: A 355 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7949 (tp) REVERT: B 18 TYR cc_start: 0.8682 (m-80) cc_final: 0.8384 (m-80) outliers start: 10 outliers final: 9 residues processed: 77 average time/residue: 0.3869 time to fit residues: 39.1067 Evaluate side-chains 83 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 A residue 54 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 289 MET 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: 1.9990 chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 9 optimal weight: 0.0470 chunk 44 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.164733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134655 restraints weight = 16398.220| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.83 r_work: 0.3327 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1527 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= 0.174 Angle : 0.489 4.596 7224 Z= 0.248 Chirality : 0.035 0.127 862 Planarity : 0.005 0.057 854 Dihedral : 10.293 82.263 772 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.62 % Allowed : 8.84 % 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: 1.47 (0.34), residues: 646 helix: 1.63 (0.24), residues: 516 sheet: None (None), residues: 0 loop : -1.70 (0.48), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 233 HIS 0.011 0.001 HIS A 94 PHE 0.016 0.001 PHE A 155 TYR 0.010 0.001 TYR A 18 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: 3061.15 seconds wall clock time: 54 minutes 18.48 seconds (3258.48 seconds total)