Starting phenix.real_space_refine on Wed Feb 14 17:26:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6z_13860/02_2024/7q6z_13860_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6z_13860/02_2024/7q6z_13860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6z_13860/02_2024/7q6z_13860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6z_13860/02_2024/7q6z_13860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6z_13860/02_2024/7q6z_13860_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6z_13860/02_2024/7q6z_13860_trim_updated.pdb" } resolution = 3.59 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= 0.068 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 Fe 1 7.16 5 S 36 5.16 5 C 3291 2.51 5 N 802 2.21 5 O 840 1.98 5 H 4784 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9754 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7919 Classifications: {'peptide': 485} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1722 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain breaks: 1 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'9V3': 1, 'CLR': 1, 'HEM': 1, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5233 SG CYS A 324 40.122 50.446 63.748 1.00 36.18 S Time building chain proxies: 4.99, per 1000 atoms: 0.51 Number of scatterers: 9754 At special positions: 0 Unit cell: (83.1, 84.208, 98.612, 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) Fe 1 26.01 S 36 16.00 O 840 8.00 N 802 7.00 C 3291 6.00 H 4784 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 816 " - pdb=" SG CYS B 889 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.90 Conformation dependent library (CDL) restraints added in 993.4 milliseconds 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 3 sheets defined 63.5% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 4 through 31 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 71 through 88 Processing helix chain 'A' and resid 90 through 109 Proline residue: A 94 - end of helix removed outlier: 3.508A pdb=" N VAL A 108 " --> pdb=" O CYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 130 removed outlier: 6.159A pdb=" N MET A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 130 " --> pdb=" O CYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 148 Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.714A pdb=" N TRP A 159 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 187 removed outlier: 3.846A pdb=" N LEU A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 237 through 264 Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 282 through 313 removed outlier: 3.836A pdb=" N PHE A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 360 through 378 Processing helix chain 'A' and resid 383 through 407 Processing helix chain 'A' and resid 409 through 418 Processing helix chain 'A' and resid 421 through 448 removed outlier: 3.729A pdb=" N ARG A 426 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 468 through 487 Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 881 through 883 No H-bonds generated for 'chain 'B' and resid 881 through 883' Processing sheet with id= A, first strand: chain 'B' and resid 908 through 910 removed outlier: 3.510A pdb=" N ALA B 843 " --> pdb=" O TRP B 830 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG B 832 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU B 841 " --> pdb=" O ARG B 832 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 862 through 866 Processing sheet with id= C, first strand: chain 'B' and resid 890 through 892 removed outlier: 3.562A pdb=" N ALA B 891 " --> pdb=" O TYR B 903 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 792 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: 3.56 Time building geometry restraints manager: 8.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.09: 4771 1.09 - 1.34: 1451 1.34 - 1.58: 3635 1.58 - 1.83: 55 1.83 - 2.08: 5 Bond restraints: 9917 Sorted by residual: bond pdb=" C8 9V3 A 603 " pdb=" S 9V3 A 603 " ideal model delta sigma weight residual 1.720 1.967 -0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C8 9V3 A 603 " pdb=" C9 9V3 A 603 " ideal model delta sigma weight residual 1.359 1.549 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" C10 9V3 A 603 " pdb=" C11 9V3 A 603 " ideal model delta sigma weight residual 1.358 1.229 0.129 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C5 9V3 A 603 " pdb=" N1 9V3 A 603 " ideal model delta sigma weight residual 1.358 1.475 -0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" C7 9V3 A 603 " pdb=" C8 9V3 A 603 " ideal model delta sigma weight residual 1.489 1.394 0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 9912 not shown) Histogram of bond angle deviations from ideal: 74.03 - 94.27: 11 94.27 - 114.51: 11596 114.51 - 134.75: 6171 134.75 - 154.99: 1 154.99 - 175.22: 2 Bond angle restraints: 17781 Sorted by residual: angle pdb=" N MET A 1 " pdb=" CA MET A 1 " pdb=" HA MET A 1 " ideal model delta sigma weight residual 110.00 74.23 35.77 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C MET A 1 " pdb=" CA MET A 1 " pdb=" HA MET A 1 " ideal model delta sigma weight residual 110.00 74.41 35.59 3.00e+00 1.11e-01 1.41e+02 angle pdb=" CB THR A 332 " pdb=" CA THR A 332 " pdb=" HA THR A 332 " ideal model delta sigma weight residual 109.00 74.03 34.97 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N THR A 332 " pdb=" CA THR A 332 " pdb=" HA THR A 332 " ideal model delta sigma weight residual 110.00 75.32 34.68 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C THR A 332 " pdb=" CA THR A 332 " pdb=" HA THR A 332 " ideal model delta sigma weight residual 109.00 74.95 34.05 3.00e+00 1.11e-01 1.29e+02 ... (remaining 17776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4288 17.96 - 35.92: 319 35.92 - 53.88: 105 53.88 - 71.84: 20 71.84 - 89.80: 6 Dihedral angle restraints: 4738 sinusoidal: 2490 harmonic: 2248 Sorted by residual: dihedral pdb=" C2B HEM A 602 " pdb=" C3B HEM A 602 " pdb=" CAB HEM A 602 " pdb=" CBB HEM A 602 " ideal model delta sinusoidal sigma weight residual 0.00 46.64 -46.64 2 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CA MET A 334 " pdb=" C MET A 334 " pdb=" N TRP A 335 " pdb=" CA TRP A 335 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TYR A 300 " pdb=" C TYR A 300 " pdb=" N LEU A 301 " pdb=" CA LEU A 301 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 4735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 727 0.093 - 0.186: 21 0.186 - 0.279: 0 0.279 - 0.372: 2 0.372 - 0.465: 1 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA MET A 1 " pdb=" N MET A 1 " pdb=" C MET A 1 " pdb=" CB MET A 1 " both_signs ideal model delta sigma weight residual False 2.57 2.10 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA THR A 332 " pdb=" N THR A 332 " pdb=" C THR A 332 " pdb=" CB THR A 332 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C12 9V3 A 603 " pdb=" C13 9V3 A 603 " pdb=" C9 9V3 A 603 " pdb=" N1 9V3 A 603 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 748 not shown) Planarity restraints: 1413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 113 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.15e+00 pdb=" C GLY A 113 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY A 113 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 114 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 306 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 307 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 17 " -0.012 2.00e-02 2.50e+03 6.51e-03 1.27e+00 pdb=" CG PHE A 17 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 17 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 17 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 17 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 17 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 17 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 17 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 17 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 17 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE A 17 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 17 " -0.001 2.00e-02 2.50e+03 ... (remaining 1410 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 420 2.18 - 2.78: 18766 2.78 - 3.39: 27695 3.39 - 3.99: 34717 3.99 - 4.60: 54275 Nonbonded interactions: 135873 Sorted by model distance: nonbonded pdb=" O TYR A 349 " pdb=" H TYR A 351 " model vdw 1.569 1.850 nonbonded pdb=" O TRP A 106 " pdb=" H GLY A 110 " model vdw 1.582 1.850 nonbonded pdb=" O SER A 14 " pdb=" HD1 HIS A 18 " model vdw 1.662 1.850 nonbonded pdb=" OE1 GLU B 882 " pdb=" H GLU B 882 " model vdw 1.663 1.850 nonbonded pdb=" HA MET A 1 " pdb=" HB2 MET A 1 " model vdw 1.688 1.952 ... (remaining 135868 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.140 Extract box with map and model: 5.820 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 35.670 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 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 : 0.008 0.247 5133 Z= 0.512 Angle : 0.688 13.229 7004 Z= 0.345 Chirality : 0.043 0.465 751 Planarity : 0.003 0.033 839 Dihedral : 14.584 89.798 1837 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.64 (0.36), residues: 589 helix: 2.24 (0.27), residues: 381 sheet: -1.00 (0.83), residues: 52 loop : -1.10 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 388 HIS 0.006 0.001 HIS A 18 PHE 0.012 0.002 PHE A 17 TYR 0.014 0.002 TYR A 166 ARG 0.003 0.000 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7902 (tp) cc_final: 0.7305 (mt) REVERT: A 334 MET cc_start: 0.7452 (tmm) cc_final: 0.7142 (tmm) REVERT: A 370 MET cc_start: 0.6733 (tpp) cc_final: 0.5853 (tpt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.3653 time to fit residues: 44.3284 Evaluate side-chains 82 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 28 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5133 Z= 0.257 Angle : 0.530 10.485 7004 Z= 0.272 Chirality : 0.040 0.465 751 Planarity : 0.004 0.033 839 Dihedral : 7.680 79.279 766 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.97 % Allowed : 6.78 % Favored : 92.25 % 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: 1.62 (0.36), residues: 589 helix: 2.20 (0.27), residues: 381 sheet: -1.08 (0.81), residues: 52 loop : -1.02 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.004 0.001 HIS A 343 PHE 0.020 0.001 PHE A 17 TYR 0.017 0.002 TYR A 180 ARG 0.002 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7868 (tp) cc_final: 0.7294 (mt) REVERT: A 179 TYR cc_start: 0.8563 (m-80) cc_final: 0.8283 (m-10) REVERT: A 186 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6490 (tp30) REVERT: A 334 MET cc_start: 0.7571 (tmm) cc_final: 0.7282 (tmm) REVERT: A 370 MET cc_start: 0.6761 (tpp) cc_final: 0.5902 (tpt) REVERT: B 812 LEU cc_start: 0.7924 (tp) cc_final: 0.7638 (tp) outliers start: 5 outliers final: 5 residues processed: 87 average time/residue: 0.3313 time to fit residues: 37.8546 Evaluate side-chains 88 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5133 Z= 0.229 Angle : 0.504 10.283 7004 Z= 0.256 Chirality : 0.039 0.460 751 Planarity : 0.003 0.033 839 Dihedral : 6.981 73.726 766 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.55 % Allowed : 6.78 % Favored : 91.67 % 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: 1.63 (0.36), residues: 589 helix: 2.21 (0.27), residues: 381 sheet: -1.16 (0.78), residues: 52 loop : -0.97 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 904 HIS 0.004 0.001 HIS A 343 PHE 0.016 0.001 PHE A 17 TYR 0.015 0.001 TYR A 180 ARG 0.001 0.000 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7876 (tp) cc_final: 0.7290 (mt) REVERT: A 179 TYR cc_start: 0.8542 (m-80) cc_final: 0.8291 (m-10) REVERT: A 370 MET cc_start: 0.6741 (tpp) cc_final: 0.5901 (tpt) outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 0.3421 time to fit residues: 39.2083 Evaluate side-chains 88 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.0040 chunk 57 optimal weight: 0.1980 chunk 28 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 15 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.1770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5133 Z= 0.138 Angle : 0.462 10.291 7004 Z= 0.230 Chirality : 0.038 0.458 751 Planarity : 0.003 0.029 839 Dihedral : 6.570 69.206 766 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.97 % Allowed : 8.33 % Favored : 90.70 % 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 (0.36), residues: 589 helix: 2.41 (0.27), residues: 388 sheet: -0.99 (0.78), residues: 52 loop : -0.83 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.003 0.000 HIS A 18 PHE 0.015 0.001 PHE A 17 TYR 0.018 0.001 TYR A 180 ARG 0.001 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7898 (tp) cc_final: 0.7297 (mt) REVERT: A 370 MET cc_start: 0.6683 (tpp) cc_final: 0.5858 (tpt) outliers start: 5 outliers final: 5 residues processed: 91 average time/residue: 0.3660 time to fit residues: 42.9226 Evaluate side-chains 90 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5133 Z= 0.272 Angle : 0.520 10.161 7004 Z= 0.263 Chirality : 0.039 0.457 751 Planarity : 0.003 0.030 839 Dihedral : 6.678 65.656 766 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.55 % Allowed : 8.14 % Favored : 90.31 % 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: 1.70 (0.36), residues: 589 helix: 2.28 (0.27), residues: 381 sheet: -1.28 (0.77), residues: 52 loop : -0.94 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 343 PHE 0.016 0.002 PHE A 17 TYR 0.017 0.002 TYR A 179 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7876 (tp) cc_final: 0.7293 (mt) REVERT: A 370 MET cc_start: 0.6723 (tpp) cc_final: 0.5901 (tpt) REVERT: B 865 ARG cc_start: 0.7984 (ptm160) cc_final: 0.7706 (ptm160) outliers start: 8 outliers final: 8 residues processed: 92 average time/residue: 0.3373 time to fit residues: 40.5026 Evaluate side-chains 95 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.0570 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5133 Z= 0.229 Angle : 0.507 10.305 7004 Z= 0.256 Chirality : 0.039 0.462 751 Planarity : 0.003 0.031 839 Dihedral : 6.553 61.965 766 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.13 % Allowed : 7.75 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.36), residues: 589 helix: 2.24 (0.27), residues: 389 sheet: -1.26 (0.77), residues: 52 loop : -0.95 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 18 PHE 0.016 0.001 PHE A 17 TYR 0.015 0.001 TYR A 180 ARG 0.002 0.000 ARG B 839 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.7050 (m100) cc_final: 0.6784 (m100) REVERT: A 138 LEU cc_start: 0.7867 (tp) cc_final: 0.7284 (mt) REVERT: A 172 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7758 (m) REVERT: A 370 MET cc_start: 0.6695 (tpp) cc_final: 0.5879 (tpt) REVERT: B 865 ARG cc_start: 0.7972 (ptm160) cc_final: 0.7705 (ptm160) outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.3200 time to fit residues: 39.0051 Evaluate side-chains 95 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5133 Z= 0.191 Angle : 0.491 10.257 7004 Z= 0.246 Chirality : 0.039 0.462 751 Planarity : 0.003 0.029 839 Dihedral : 6.477 57.857 766 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.13 % Allowed : 8.72 % Favored : 89.15 % 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: 1.76 (0.36), residues: 589 helix: 2.27 (0.27), residues: 389 sheet: -1.28 (0.76), residues: 52 loop : -0.93 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 18 PHE 0.015 0.001 PHE A 17 TYR 0.015 0.001 TYR A 180 ARG 0.001 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7897 (tp) cc_final: 0.7295 (mt) REVERT: A 334 MET cc_start: 0.7541 (tmm) cc_final: 0.7307 (tmm) REVERT: A 370 MET cc_start: 0.6672 (tpp) cc_final: 0.5853 (tpt) REVERT: A 481 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.7222 (t-90) REVERT: B 865 ARG cc_start: 0.7961 (ptm160) cc_final: 0.7686 (ptm160) outliers start: 11 outliers final: 9 residues processed: 91 average time/residue: 0.3300 time to fit residues: 39.6988 Evaluate side-chains 96 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5133 Z= 0.196 Angle : 0.497 10.220 7004 Z= 0.248 Chirality : 0.039 0.462 751 Planarity : 0.003 0.030 839 Dihedral : 6.393 53.999 766 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.94 % Allowed : 9.30 % Favored : 88.76 % 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: 1.76 (0.36), residues: 589 helix: 2.27 (0.26), residues: 389 sheet: -1.29 (0.76), residues: 52 loop : -0.92 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 18 PHE 0.018 0.002 PHE A 125 TYR 0.015 0.001 TYR A 180 ARG 0.001 0.000 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7896 (tp) cc_final: 0.7299 (mt) REVERT: A 334 MET cc_start: 0.7583 (tmm) cc_final: 0.7357 (tmm) REVERT: A 370 MET cc_start: 0.6668 (tpp) cc_final: 0.5851 (tpt) REVERT: A 481 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.7219 (t-90) REVERT: B 865 ARG cc_start: 0.7961 (ptm160) cc_final: 0.7689 (ptm160) outliers start: 10 outliers final: 9 residues processed: 91 average time/residue: 0.3259 time to fit residues: 39.2068 Evaluate side-chains 96 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5133 Z= 0.247 Angle : 0.522 10.365 7004 Z= 0.261 Chirality : 0.040 0.464 751 Planarity : 0.003 0.029 839 Dihedral : 6.457 53.684 766 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.74 % Allowed : 9.69 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.36), residues: 589 helix: 2.23 (0.27), residues: 383 sheet: -1.32 (0.76), residues: 52 loop : -0.89 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.004 0.001 HIS A 18 PHE 0.016 0.002 PHE A 17 TYR 0.013 0.001 TYR A 180 ARG 0.002 0.000 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7932 (tp) cc_final: 0.7329 (mt) REVERT: A 179 TYR cc_start: 0.8573 (m-80) cc_final: 0.8261 (m-80) REVERT: A 370 MET cc_start: 0.6687 (tpp) cc_final: 0.5872 (tpt) REVERT: B 865 ARG cc_start: 0.7960 (ptm160) cc_final: 0.7707 (ptm160) outliers start: 9 outliers final: 8 residues processed: 90 average time/residue: 0.3305 time to fit residues: 39.6937 Evaluate side-chains 93 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.0770 chunk 6 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5133 Z= 0.244 Angle : 0.529 10.663 7004 Z= 0.264 Chirality : 0.040 0.471 751 Planarity : 0.003 0.030 839 Dihedral : 6.517 54.441 766 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.94 % Allowed : 10.27 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.36), residues: 589 helix: 2.21 (0.27), residues: 382 sheet: -1.31 (0.76), residues: 52 loop : -0.92 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.008 0.001 HIS A 32 PHE 0.024 0.002 PHE A 331 TYR 0.014 0.001 TYR A 180 ARG 0.002 0.000 ARG B 847 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7933 (tp) cc_final: 0.7331 (mt) REVERT: A 370 MET cc_start: 0.6677 (tpp) cc_final: 0.5878 (tpt) REVERT: B 865 ARG cc_start: 0.7961 (ptm160) cc_final: 0.7709 (ptm160) outliers start: 10 outliers final: 9 residues processed: 91 average time/residue: 0.3286 time to fit residues: 40.0469 Evaluate side-chains 95 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.167804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.132340 restraints weight = 15652.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.138433 restraints weight = 9042.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.142479 restraints weight = 6385.241| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5133 Z= 0.232 Angle : 0.527 10.722 7004 Z= 0.263 Chirality : 0.040 0.471 751 Planarity : 0.003 0.030 839 Dihedral : 6.546 54.592 766 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.74 % Allowed : 11.05 % Favored : 87.21 % 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: 1.66 (0.36), residues: 589 helix: 2.27 (0.27), residues: 380 sheet: -1.31 (0.76), residues: 52 loop : -0.98 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.008 0.001 HIS A 32 PHE 0.022 0.002 PHE A 331 TYR 0.014 0.001 TYR A 180 ARG 0.001 0.000 ARG B 847 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3092.41 seconds wall clock time: 55 minutes 5.99 seconds (3305.99 seconds total)