Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 15:15:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpa_14116/10_2023/7qpa_14116_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpa_14116/10_2023/7qpa_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_14116/10_2023/7qpa_14116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpa_14116/10_2023/7qpa_14116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpa_14116/10_2023/7qpa_14116_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpa_14116/10_2023/7qpa_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 5.03, per 1000 atoms: 0.47 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: 9.86 Conformation dependent library (CDL) restraints added in 1.0 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: 1.22 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: 4.09 Time building geometry restraints manager: 9.96 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: 4042 23.15 - 46.30: 194 46.30 - 69.45: 21 69.45 - 92.60: 7 92.60 - 115.75: 2 Dihedral angle restraints: 4266 sinusoidal: 2000 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 4263 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: 0.470 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: 0.150 Extract box with map and model: 2.520 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 39.320 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.180 ------------------------------------------------------------------------------- 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 : 14.819 115.750 1916 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 *********************** 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 : 0.877 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.3555 time to fit residues: 43.2197 Evaluate side-chains 83 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0739 ------------------------------------------------------------------------------- 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: 0.3980 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5332 Z= 0.228 Angle : 0.546 4.970 7224 Z= 0.276 Chirality : 0.037 0.139 862 Planarity : 0.005 0.044 854 Dihedral : 9.999 102.495 752 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.72 % Allowed : 5.78 % Favored : 93.50 % 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: 1.36 (0.34), residues: 646 helix: 1.54 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.72 (0.50), residues: 128 *********************** 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 84 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.745 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 83 average time/residue: 0.3744 time to fit residues: 40.7846 Evaluate side-chains 81 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1323 time to fit residues: 1.9897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.0040 chunk 58 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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: 0.7239 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5332 Z= 0.181 Angle : 0.502 4.871 7224 Z= 0.254 Chirality : 0.036 0.130 862 Planarity : 0.005 0.047 854 Dihedral : 9.526 92.853 752 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % 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: 1.51 (0.34), residues: 646 helix: 1.65 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.70 (0.51), residues: 128 *********************** 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 78 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.880 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3755 time to fit residues: 38.7887 Evaluate side-chains 78 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.872 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 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: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.7272 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5332 Z= 0.251 Angle : 0.538 4.994 7224 Z= 0.272 Chirality : 0.037 0.135 862 Planarity : 0.005 0.042 854 Dihedral : 9.462 84.893 752 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 8.84 % 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: 1.33 (0.34), residues: 646 helix: 1.51 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.69 (0.51), residues: 128 *********************** 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 77 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.728 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.3697 time to fit residues: 37.7488 Evaluate side-chains 77 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.854 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.0370 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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: 0.7256 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5332 Z= 0.191 Angle : 0.505 4.860 7224 Z= 0.255 Chirality : 0.036 0.128 862 Planarity : 0.004 0.042 854 Dihedral : 9.314 79.656 752 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.18 % Allowed : 8.48 % Favored : 91.34 % 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: 1.41 (0.34), residues: 646 helix: 1.57 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.68 (0.51), residues: 128 *********************** 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 79 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.793 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 78 average time/residue: 0.3792 time to fit residues: 38.9469 Evaluate side-chains 78 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1901 time to fit residues: 1.3177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.9980 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: 0.9990 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 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: 0.7280 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5332 Z= 0.237 Angle : 0.523 4.938 7224 Z= 0.266 Chirality : 0.036 0.132 862 Planarity : 0.005 0.043 854 Dihedral : 9.344 81.066 752 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.54 % Allowed : 8.84 % Favored : 90.61 % 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: 1.41 (0.34), residues: 646 helix: 1.60 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.62 (0.49), residues: 136 *********************** 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 77 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.901 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 74 average time/residue: 0.3857 time to fit residues: 37.4992 Evaluate side-chains 75 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1361 time to fit residues: 1.7629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 18 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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: 0.7253 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5332 Z= 0.167 Angle : 0.489 4.783 7224 Z= 0.247 Chirality : 0.035 0.126 862 Planarity : 0.004 0.042 854 Dihedral : 9.102 77.834 752 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.18 % Allowed : 9.39 % 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: 1.59 (0.34), residues: 646 helix: 1.74 (0.24), residues: 510 sheet: None (None), residues: 0 loop : -1.59 (0.50), residues: 136 *********************** 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 76 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.772 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.3943 time to fit residues: 39.5271 Evaluate side-chains 74 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7276 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 : 0.004 0.028 5332 Z= 0.244 Angle : 0.529 4.944 7224 Z= 0.268 Chirality : 0.037 0.162 862 Planarity : 0.004 0.042 854 Dihedral : 9.160 79.838 752 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.36 % Allowed : 9.39 % Favored : 90.25 % 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 : -1.58 (0.50), residues: 136 *********************** 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 fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.757 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 75 average time/residue: 0.3990 time to fit residues: 38.9467 Evaluate side-chains 75 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1367 time to fit residues: 1.3641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.0370 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 60 optimal weight: 0.0980 chunk 28 optimal weight: 0.5980 overall best weight: 0.3458 ------------------------------------------------------------------------------- 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: 0.7240 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5332 Z= 0.147 Angle : 0.484 5.412 7224 Z= 0.243 Chirality : 0.036 0.145 862 Planarity : 0.004 0.043 854 Dihedral : 8.707 75.562 752 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.18 % Allowed : 9.75 % 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: 1.62 (0.34), residues: 646 helix: 1.74 (0.24), residues: 514 sheet: None (None), residues: 0 loop : -1.63 (0.50), residues: 132 *********************** 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 fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.825 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.4136 time to fit residues: 41.6021 Evaluate side-chains 78 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1388 time to fit residues: 1.3668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 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: 0.7273 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5332 Z= 0.229 Angle : 0.517 4.932 7224 Z= 0.261 Chirality : 0.037 0.148 862 Planarity : 0.004 0.042 854 Dihedral : 8.896 78.861 752 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % 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: 514 sheet: None (None), residues: 0 loop : -1.66 (0.50), residues: 132 ********************** 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 73 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.766 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3919 time to fit residues: 37.4362 Evaluate side-chains 72 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.163588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133612 restraints weight = 16405.133| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.82 r_work: 0.3317 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5332 Z= 0.204 Angle : 0.507 4.856 7224 Z= 0.256 Chirality : 0.036 0.127 862 Planarity : 0.005 0.076 854 Dihedral : 8.923 78.482 752 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 10.11 % 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: 1.45 (0.34), residues: 646 helix: 1.62 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.68 (0.50), residues: 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3050.94 seconds wall clock time: 54 minutes 21.29 seconds (3261.29 seconds total)