Starting phenix.real_space_refine on Sun Apr 7 19:32:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp9_14115/04_2024/7qp9_14115_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp9_14115/04_2024/7qp9_14115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp9_14115/04_2024/7qp9_14115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp9_14115/04_2024/7qp9_14115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp9_14115/04_2024/7qp9_14115_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qp9_14115/04_2024/7qp9_14115_trim_updated.pdb" } resolution = 2.89 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= 0.000 sd= 0.022 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 4 5.49 5 S 34 5.16 5 C 3576 2.51 5 N 804 2.21 5 O 1001 1.98 5 H 5668 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11087 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5245 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "B" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5245 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'DLP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'DLP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 198 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 183 Classifications: {'water': 61} Link IDs: {None: 60} Time building chain proxies: 5.52, per 1000 atoms: 0.50 Number of scatterers: 11087 At special positions: 0 Unit cell: (89.933, 88.639, 64.053, 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 4 15.00 O 1001 8.00 N 804 7.00 C 3576 6.00 H 5668 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: 9.50 Conformation dependent library (CDL) restraints added in 1.1 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: 34 helices and 0 sheets defined 76.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 6 through 29 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 69 through 91 Processing helix chain 'A' and resid 102 through 113 Processing helix chain 'A' and resid 123 through 129 removed outlier: 3.709A pdb=" N ALA A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 163 removed outlier: 4.868A pdb=" N TYR A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 218 Processing helix chain 'A' and resid 222 through 240 Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.675A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 removed outlier: 3.761A pdb=" N SER A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) 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 320 Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'B' and resid 6 through 29 Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 69 through 91 Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 123 through 129 removed outlier: 3.684A pdb=" N ALA B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 163 removed outlier: 4.897A pdb=" N TYR B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N THR B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 218 Processing helix chain 'B' and resid 222 through 240 Processing helix chain 'B' and resid 246 through 256 removed outlier: 3.672A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 273 removed outlier: 3.756A pdb=" N SER B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) 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 322 removed outlier: 3.849A pdb=" N ALA B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 340 through 366 removed outlier: 4.283A pdb=" N LEU B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 353 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix 342 hydrogen bonds defined for protein. 1026 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: 3.89 Time building geometry restraints manager: 9.88 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: 5662 1.03 - 1.23: 15 1.23 - 1.42: 2081 1.42 - 1.61: 3258 1.61 - 1.81: 62 Bond restraints: 11078 Sorted by residual: bond pdb=" O4P DLP B 501 " pdb=" P DLP B 501 " ideal model delta sigma weight residual 1.649 1.595 0.054 2.00e-02 2.50e+03 7.39e+00 bond pdb=" O4P DLP A 502 " pdb=" P DLP A 502 " ideal model delta sigma weight residual 1.649 1.595 0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" O4P DLP A 501 " pdb=" P DLP A 501 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" O4P DLP B 502 " pdb=" P DLP B 502 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" C4 DLP A 502 " pdb=" O4P DLP A 502 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 4.08e+00 ... (remaining 11073 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.92: 340 106.92 - 113.70: 13264 113.70 - 120.48: 3452 120.48 - 127.26: 2595 127.26 - 134.04: 76 Bond angle restraints: 19727 Sorted by residual: angle pdb=" O3P DLP B 502 " pdb=" P DLP B 502 " pdb=" O4P DLP B 502 " ideal model delta sigma weight residual 93.58 105.18 -11.60 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O3P DLP A 502 " pdb=" P DLP A 502 " pdb=" O4P DLP A 502 " ideal model delta sigma weight residual 93.58 105.17 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O3P DLP B 501 " pdb=" P DLP B 501 " pdb=" O4P DLP B 501 " ideal model delta sigma weight residual 93.58 103.98 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" O3P DLP A 501 " pdb=" P DLP A 501 " pdb=" O4P DLP A 501 " ideal model delta sigma weight residual 93.58 103.90 -10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C1 DLP B 501 " pdb=" C2 DLP B 501 " pdb=" O2 DLP B 501 " ideal model delta sigma weight residual 111.29 105.02 6.27 3.00e+00 1.11e-01 4.37e+00 ... (remaining 19722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 4754 23.43 - 46.85: 268 46.85 - 70.28: 72 70.28 - 93.70: 16 93.70 - 117.13: 2 Dihedral angle restraints: 5112 sinusoidal: 2846 harmonic: 2266 Sorted by residual: 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 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA SER A 113 " pdb=" C SER A 113 " pdb=" N VAL A 114 " pdb=" CA VAL A 114 " ideal model delta harmonic sigma weight residual 180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" N DLP B 501 " pdb=" C4 DLP B 501 " pdb=" C5 DLP B 501 " pdb=" O4P DLP B 501 " ideal model delta sinusoidal sigma weight residual 288.95 171.82 117.13 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 5109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 744 0.056 - 0.111: 113 0.111 - 0.167: 3 0.167 - 0.223: 2 0.223 - 0.278: 2 Chirality restraints: 864 Sorted by residual: chirality pdb=" C2 DLP A 501 " pdb=" C1 DLP A 501 " pdb=" C3 DLP A 501 " pdb=" O2 DLP A 501 " both_signs ideal model delta sigma weight residual False -2.35 -2.63 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C2 DLP B 501 " pdb=" C1 DLP B 501 " pdb=" C3 DLP B 501 " pdb=" O2 DLP B 501 " both_signs ideal model delta sigma weight residual False -2.35 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C2 DLP B 502 " pdb=" C1 DLP B 502 " pdb=" C3 DLP B 502 " pdb=" O2 DLP B 502 " both_signs ideal model delta sigma weight residual False -2.35 -2.57 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 861 not shown) Planarity restraints: 1482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 145 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C GLN A 145 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN A 145 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A 146 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 145 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.81e+00 pdb=" C GLN B 145 " 0.023 2.00e-02 2.50e+03 pdb=" O GLN B 145 " -0.009 2.00e-02 2.50e+03 pdb=" N SER B 146 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 15 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO B 16 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 16 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 16 " 0.016 5.00e-02 4.00e+02 ... (remaining 1479 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 949 2.22 - 2.82: 24217 2.82 - 3.41: 31679 3.41 - 4.01: 43766 4.01 - 4.60: 67832 Nonbonded interactions: 168443 Sorted by model distance: nonbonded pdb=" HD1 HIS A 237 " pdb=" O TRP A 242 " model vdw 1.629 1.850 nonbonded pdb=" OE1 GLN A 57 " pdb=" HG SER A 256 " model vdw 1.638 1.850 nonbonded pdb=" HD1 HIS B 237 " pdb=" O TRP B 242 " model vdw 1.645 1.850 nonbonded pdb=" O SER B 74 " pdb=" HG SER B 303 " model vdw 1.703 1.850 nonbonded pdb=" O SER A 74 " pdb=" HG SER A 303 " model vdw 1.716 1.850 ... (remaining 168438 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' 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: 0.010 Normalize map: mean=0, sd=1: 3.240 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: 0.160 Extract box with map and model: 15.810 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 40.160 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:10.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 0.054 5410 Z= 0.273 Angle : 0.627 11.603 7308 Z= 0.274 Chirality : 0.039 0.278 864 Planarity : 0.003 0.028 862 Dihedral : 15.528 117.129 2018 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.00 (0.35), residues: 646 helix: 1.94 (0.24), residues: 526 sheet: None (None), residues: 0 loop : -1.49 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 233 HIS 0.001 0.000 HIS A 237 PHE 0.016 0.001 PHE B 330 TYR 0.005 0.001 TYR A 130 ARG 0.001 0.000 ARG A 163 *********************** 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 71 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.846 Fit side-chains REVERT: A 277 ILE cc_start: 0.8899 (tt) cc_final: 0.8654 (tp) REVERT: B 249 ASP cc_start: 0.8063 (t0) cc_final: 0.7807 (t0) REVERT: B 277 ILE cc_start: 0.8903 (tt) cc_final: 0.8662 (tp) outliers start: 0 outliers final: 1 residues processed: 71 average time/residue: 2.2063 time to fit residues: 165.5866 Evaluate side-chains 61 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 25 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5410 Z= 0.187 Angle : 0.479 4.429 7308 Z= 0.241 Chirality : 0.036 0.126 864 Planarity : 0.003 0.029 862 Dihedral : 15.266 120.579 856 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.36 % Allowed : 7.22 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.34), residues: 646 helix: 1.99 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.50 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.000 HIS A 237 PHE 0.015 0.001 PHE A 330 TYR 0.005 0.001 TYR A 130 ARG 0.001 0.000 ARG B 91 *********************** 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 62 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.837 Fit side-chains REVERT: A 228 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7672 (tt) REVERT: A 277 ILE cc_start: 0.8898 (tt) cc_final: 0.8627 (tp) REVERT: B 249 ASP cc_start: 0.8059 (t0) cc_final: 0.7782 (t0) REVERT: B 277 ILE cc_start: 0.8908 (tt) cc_final: 0.8668 (tp) outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 2.3687 time to fit residues: 155.3097 Evaluate side-chains 60 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5410 Z= 0.232 Angle : 0.486 4.450 7308 Z= 0.248 Chirality : 0.036 0.125 864 Planarity : 0.004 0.032 862 Dihedral : 14.585 122.959 854 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.54 % Allowed : 7.04 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.34), residues: 646 helix: 2.06 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.47 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.002 0.001 HIS B 30 PHE 0.016 0.002 PHE B 330 TYR 0.005 0.001 TYR B 361 ARG 0.001 0.000 ARG A 163 *********************** 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 64 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.891 Fit side-chains REVERT: A 228 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7688 (tt) REVERT: A 250 LYS cc_start: 0.8129 (mttm) cc_final: 0.7915 (mmpt) REVERT: A 277 ILE cc_start: 0.8905 (tt) cc_final: 0.8673 (tp) REVERT: B 91 ARG cc_start: 0.7098 (ttt90) cc_final: 0.6780 (mtp85) REVERT: B 249 ASP cc_start: 0.8201 (t0) cc_final: 0.7890 (t0) REVERT: B 277 ILE cc_start: 0.8904 (tt) cc_final: 0.8649 (tp) outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 2.2691 time to fit residues: 151.1833 Evaluate side-chains 63 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5410 Z= 0.225 Angle : 0.481 4.390 7308 Z= 0.246 Chirality : 0.036 0.124 864 Planarity : 0.004 0.034 862 Dihedral : 14.496 124.290 854 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.54 % Allowed : 7.40 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.34), residues: 646 helix: 1.97 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.52 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.002 0.001 HIS A 30 PHE 0.017 0.002 PHE B 330 TYR 0.006 0.001 TYR A 130 ARG 0.001 0.000 ARG B 91 *********************** 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 64 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.850 Fit side-chains REVERT: A 228 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7687 (tt) REVERT: A 277 ILE cc_start: 0.8906 (tt) cc_final: 0.8669 (tp) REVERT: B 249 ASP cc_start: 0.8163 (t0) cc_final: 0.7880 (t0) REVERT: B 277 ILE cc_start: 0.8900 (tt) cc_final: 0.8644 (tp) outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 2.2677 time to fit residues: 150.7696 Evaluate side-chains 63 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5410 Z= 0.291 Angle : 0.506 4.435 7308 Z= 0.260 Chirality : 0.037 0.126 864 Planarity : 0.004 0.036 862 Dihedral : 14.658 126.082 854 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.72 % Allowed : 7.76 % 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: 1.81 (0.34), residues: 646 helix: 1.88 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.56 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.002 0.001 HIS B 30 PHE 0.018 0.002 PHE A 330 TYR 0.006 0.001 TYR B 361 ARG 0.002 0.000 ARG B 91 *********************** 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 65 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.875 Fit side-chains REVERT: A 277 ILE cc_start: 0.8927 (tt) cc_final: 0.8683 (tp) REVERT: B 249 ASP cc_start: 0.8190 (t0) cc_final: 0.7907 (t0) REVERT: B 277 ILE cc_start: 0.8896 (tt) cc_final: 0.8659 (tp) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 2.3686 time to fit residues: 159.7973 Evaluate side-chains 63 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 228 LEU 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: 0.9990 chunk 61 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 59 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5410 Z= 0.150 Angle : 0.456 4.240 7308 Z= 0.234 Chirality : 0.035 0.124 864 Planarity : 0.004 0.034 862 Dihedral : 14.355 122.681 854 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.54 % Allowed : 8.48 % Favored : 90.97 % 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: 2.09 (0.34), residues: 646 helix: 2.05 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.43 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 233 HIS 0.001 0.000 HIS B 30 PHE 0.014 0.001 PHE B 330 TYR 0.006 0.001 TYR A 130 ARG 0.002 0.000 ARG A 91 *********************** 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 65 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.824 Fit side-chains REVERT: A 277 ILE cc_start: 0.8918 (tt) cc_final: 0.8676 (tp) REVERT: B 249 ASP cc_start: 0.8034 (t0) cc_final: 0.7786 (t0) REVERT: B 277 ILE cc_start: 0.8891 (tt) cc_final: 0.8641 (tp) outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 2.3603 time to fit residues: 159.2176 Evaluate side-chains 63 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5410 Z= 0.201 Angle : 0.472 4.349 7308 Z= 0.241 Chirality : 0.036 0.125 864 Planarity : 0.004 0.035 862 Dihedral : 14.344 122.131 854 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.54 % Allowed : 8.66 % 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: 2.07 (0.34), residues: 646 helix: 2.05 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.45 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 233 HIS 0.002 0.000 HIS B 30 PHE 0.016 0.001 PHE B 330 TYR 0.006 0.001 TYR A 130 ARG 0.001 0.000 ARG A 91 *********************** 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 62 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.871 Fit side-chains REVERT: A 277 ILE cc_start: 0.8920 (tt) cc_final: 0.8675 (tp) REVERT: B 249 ASP cc_start: 0.8156 (t0) cc_final: 0.7888 (t0) REVERT: B 277 ILE cc_start: 0.8887 (tt) cc_final: 0.8644 (tp) outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 2.3062 time to fit residues: 148.3158 Evaluate side-chains 62 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 5 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5410 Z= 0.162 Angle : 0.457 4.538 7308 Z= 0.233 Chirality : 0.035 0.125 864 Planarity : 0.004 0.034 862 Dihedral : 14.175 119.519 854 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.90 % Allowed : 9.03 % 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: 2.18 (0.34), residues: 646 helix: 2.14 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.47 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.001 0.000 HIS A 30 PHE 0.015 0.001 PHE A 330 TYR 0.006 0.001 TYR A 130 ARG 0.001 0.000 ARG A 91 *********************** 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 66 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.853 Fit side-chains REVERT: A 88 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7296 (mmm) REVERT: A 277 ILE cc_start: 0.8915 (tt) cc_final: 0.8673 (tp) REVERT: B 249 ASP cc_start: 0.8126 (t0) cc_final: 0.7861 (t0) REVERT: B 277 ILE cc_start: 0.8873 (tt) cc_final: 0.8647 (tp) outliers start: 5 outliers final: 2 residues processed: 63 average time/residue: 2.3685 time to fit residues: 157.5538 Evaluate side-chains 63 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP 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: 0.3980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 57 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 chunk 28 optimal weight: 0.4980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5410 Z= 0.155 Angle : 0.450 4.282 7308 Z= 0.229 Chirality : 0.035 0.137 864 Planarity : 0.004 0.032 862 Dihedral : 13.988 117.147 854 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.54 % Allowed : 9.21 % 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: 2.27 (0.34), residues: 646 helix: 2.17 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.41 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.001 0.000 HIS A 30 PHE 0.014 0.001 PHE A 330 TYR 0.006 0.001 TYR A 130 ARG 0.001 0.000 ARG A 91 *********************** 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 62 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.872 Fit side-chains REVERT: A 277 ILE cc_start: 0.8911 (tt) cc_final: 0.8671 (tp) REVERT: B 249 ASP cc_start: 0.8125 (t0) cc_final: 0.7875 (t0) REVERT: B 277 ILE cc_start: 0.8880 (tt) cc_final: 0.8645 (tp) outliers start: 3 outliers final: 2 residues processed: 61 average time/residue: 2.3282 time to fit residues: 149.9105 Evaluate side-chains 61 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.0570 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5410 Z= 0.212 Angle : 0.477 5.163 7308 Z= 0.242 Chirality : 0.036 0.141 864 Planarity : 0.004 0.034 862 Dihedral : 14.057 117.221 854 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.72 % Allowed : 9.39 % 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: 2.09 (0.34), residues: 646 helix: 2.04 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.44 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.000 HIS A 30 PHE 0.016 0.001 PHE A 330 TYR 0.006 0.001 TYR A 130 ARG 0.001 0.000 ARG A 308 ********************** 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 63 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.806 Fit side-chains REVERT: A 88 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7311 (mmm) REVERT: A 277 ILE cc_start: 0.8912 (tt) cc_final: 0.8671 (tp) REVERT: B 249 ASP cc_start: 0.8143 (t0) cc_final: 0.7880 (t0) REVERT: B 277 ILE cc_start: 0.8879 (tt) cc_final: 0.8645 (tp) outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 2.3312 time to fit residues: 150.0869 Evaluate side-chains 63 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.106174 restraints weight = 17083.229| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.68 r_work: 0.3192 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5410 Z= 0.239 Angle : 0.491 5.485 7308 Z= 0.250 Chirality : 0.036 0.139 864 Planarity : 0.004 0.035 862 Dihedral : 14.167 118.242 854 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.72 % Allowed : 9.39 % 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: 1.97 (0.34), residues: 646 helix: 2.03 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -1.64 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.002 0.001 HIS A 30 PHE 0.016 0.002 PHE A 330 TYR 0.006 0.001 TYR A 130 ARG 0.001 0.000 ARG A 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4620.34 seconds wall clock time: 82 minutes 50.11 seconds (4970.11 seconds total)