Starting phenix.real_space_refine on Sun Mar 10 15:21:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/03_2024/6riu_4898.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/03_2024/6riu_4898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/03_2024/6riu_4898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/03_2024/6riu_4898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/03_2024/6riu_4898.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/03_2024/6riu_4898.pdb" } resolution = 3.9 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= 0.001 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: 5 Type Number sf(0) Gaussians S 4 5.16 5 C 920 2.51 5 N 250 2.21 5 O 278 1.98 5 H 1430 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2882 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1441 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "B" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1441 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Time building chain proxies: 1.70, per 1000 atoms: 0.59 Number of scatterers: 2882 At special positions: 0 Unit cell: (69.828, 47.61, 49.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 278 8.00 N 250 7.00 C 920 6.00 H 1430 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: 2.15 Conformation dependent library (CDL) restraints added in 276.0 milliseconds 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 340 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 removed outlier: 3.553A pdb=" N LYS A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 32 removed outlier: 3.757A pdb=" N ALA A 23 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 54 removed outlier: 4.196A pdb=" N TYR A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 59 Processing helix chain 'A' and resid 60 through 73 removed outlier: 3.650A pdb=" N LEU A 67 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 Proline residue: A 77 - end of helix No H-bonds generated for 'chain 'A' and resid 74 through 79' Processing helix chain 'A' and resid 80 through 90 removed outlier: 4.275A pdb=" N VAL A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.553A pdb=" N LYS B 9 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 32 removed outlier: 3.758A pdb=" N ALA B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 54 removed outlier: 4.196A pdb=" N TYR B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 59 Processing helix chain 'B' and resid 60 through 73 removed outlier: 3.650A pdb=" N LEU B 67 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 Proline residue: B 77 - end of helix No H-bonds generated for 'chain 'B' and resid 74 through 79' Processing helix chain 'B' and resid 80 through 90 removed outlier: 4.275A pdb=" N VAL B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) 75 hydrogen bonds defined for protein. 219 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: 0.92 Time building geometry restraints manager: 2.24 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: 1430 1.03 - 1.22: 3 1.22 - 1.42: 616 1.42 - 1.61: 853 1.61 - 1.80: 8 Bond restraints: 2910 Sorted by residual: bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.496 -0.045 1.60e-02 3.91e+03 7.95e+00 bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.496 -0.045 1.60e-02 3.91e+03 7.83e+00 bond pdb=" N LEU B 83 " pdb=" CA LEU B 83 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.23e-02 6.61e+03 7.01e+00 bond pdb=" N LEU A 83 " pdb=" CA LEU A 83 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.23e-02 6.61e+03 6.87e+00 bond pdb=" N LEU B 83 " pdb=" H LEU B 83 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.42e+00 ... (remaining 2905 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.51: 49 105.51 - 112.62: 3274 112.62 - 119.74: 854 119.74 - 126.86: 1054 126.86 - 133.97: 23 Bond angle restraints: 5254 Sorted by residual: angle pdb=" N GLY B 61 " pdb=" CA GLY B 61 " pdb=" C GLY B 61 " ideal model delta sigma weight residual 112.49 103.08 9.41 1.21e+00 6.83e-01 6.04e+01 angle pdb=" N GLY A 61 " pdb=" CA GLY A 61 " pdb=" C GLY A 61 " ideal model delta sigma weight residual 112.49 103.14 9.35 1.21e+00 6.83e-01 5.97e+01 angle pdb=" N LYS B 9 " pdb=" CA LYS B 9 " pdb=" C LYS B 9 " ideal model delta sigma weight residual 112.89 106.94 5.95 1.24e+00 6.50e-01 2.30e+01 angle pdb=" N GLU B 36 " pdb=" CA GLU B 36 " pdb=" C GLU B 36 " ideal model delta sigma weight residual 110.58 117.63 -7.05 1.56e+00 4.11e-01 2.04e+01 angle pdb=" N VAL B 35 " pdb=" CA VAL B 35 " pdb=" C VAL B 35 " ideal model delta sigma weight residual 111.45 115.61 -4.16 9.30e-01 1.16e+00 2.01e+01 ... (remaining 5249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 1239 17.93 - 35.87: 71 35.87 - 53.80: 30 53.80 - 71.74: 8 71.74 - 89.67: 6 Dihedral angle restraints: 1354 sinusoidal: 742 harmonic: 612 Sorted by residual: dihedral pdb=" CA LEU A 74 " pdb=" C LEU A 74 " pdb=" N SER A 75 " pdb=" CA SER A 75 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LEU B 74 " pdb=" C LEU B 74 " pdb=" N SER B 75 " pdb=" CA SER B 75 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LEU A 56 " pdb=" C LEU A 56 " pdb=" N ASP A 57 " pdb=" CA ASP A 57 " ideal model delta harmonic sigma weight residual 180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 1351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 214 0.153 - 0.306: 4 0.306 - 0.459: 0 0.459 - 0.612: 0 0.612 - 0.765: 2 Chirality restraints: 220 Sorted by residual: chirality pdb=" CG LEU A 74 " pdb=" CB LEU A 74 " pdb=" CD1 LEU A 74 " pdb=" CD2 LEU A 74 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CG LEU B 74 " pdb=" CB LEU B 74 " pdb=" CD1 LEU B 74 " pdb=" CD2 LEU B 74 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CA ALA A 34 " pdb=" N ALA A 34 " pdb=" C ALA A 34 " pdb=" CB ALA A 34 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.89e-01 ... (remaining 217 not shown) Planarity restraints: 434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 59 " -0.018 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C MET B 59 " 0.065 2.00e-02 2.50e+03 pdb=" O MET B 59 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA B 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 59 " -0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C MET A 59 " 0.065 2.00e-02 2.50e+03 pdb=" O MET A 59 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA A 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 76 " 0.054 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO A 77 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " 0.045 5.00e-02 4.00e+02 ... (remaining 431 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.00: 34 2.00 - 2.65: 4114 2.65 - 3.30: 8622 3.30 - 3.95: 10370 3.95 - 4.60: 15836 Nonbonded interactions: 38976 Sorted by model distance: nonbonded pdb=" OG SER A 75 " pdb=" HG SER B 75 " model vdw 1.355 1.850 nonbonded pdb=" O GLY B 30 " pdb=" HG SER B 33 " model vdw 1.488 1.850 nonbonded pdb=" O GLY A 30 " pdb=" HG SER A 33 " model vdw 1.520 1.850 nonbonded pdb=" OD1 ASP B 49 " pdb=" HH TYR B 64 " model vdw 1.659 1.850 nonbonded pdb=" O ILE A 87 " pdb=" HG1 THR A 91 " model vdw 1.713 1.850 ... (remaining 38971 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 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: 1.400 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: 0.040 Extract box with map and model: 6.830 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.180 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 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 0.068 1480 Z= 0.527 Angle : 1.188 9.406 2006 Z= 0.756 Chirality : 0.089 0.765 220 Planarity : 0.011 0.081 260 Dihedral : 15.190 89.671 546 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % 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: -5.77 (0.42), residues: 178 helix: -3.50 (0.29), residues: 134 sheet: None (None), residues: 0 loop : -4.10 (0.72), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B 79 HIS 0.000 0.000 HIS A 55 PHE 0.020 0.004 PHE A 41 TYR 0.005 0.002 TYR B 90 ARG 0.004 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.4141 time to fit residues: 15.3176 Evaluate side-chains 27 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8022 ------------------------------------------------------------------------------- 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: 0.7071 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1480 Z= 0.176 Angle : 0.662 6.537 2006 Z= 0.346 Chirality : 0.036 0.101 220 Planarity : 0.007 0.060 260 Dihedral : 6.113 23.078 196 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 15.13 % Favored : 84.87 % 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: -4.22 (0.51), residues: 178 helix: -2.34 (0.37), residues: 138 sheet: None (None), residues: 0 loop : -3.72 (0.72), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 79 HIS 0.003 0.002 HIS B 55 PHE 0.007 0.001 PHE B 41 TYR 0.010 0.001 TYR B 42 ARG 0.002 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.4966 time to fit residues: 13.4042 Evaluate side-chains 23 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7069 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1480 Z= 0.149 Angle : 0.588 6.833 2006 Z= 0.304 Chirality : 0.035 0.106 220 Planarity : 0.005 0.049 260 Dihedral : 5.341 20.521 196 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.66 % Allowed : 17.11 % Favored : 82.24 % 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: -3.45 (0.56), residues: 178 helix: -1.73 (0.40), residues: 140 sheet: None (None), residues: 0 loop : -3.80 (0.83), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 79 HIS 0.001 0.000 HIS B 55 PHE 0.006 0.001 PHE B 41 TYR 0.004 0.001 TYR A 90 ARG 0.001 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.5037 time to fit residues: 13.6067 Evaluate side-chains 23 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7055 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1480 Z= 0.141 Angle : 0.567 6.788 2006 Z= 0.292 Chirality : 0.034 0.109 220 Planarity : 0.004 0.037 260 Dihedral : 4.959 17.918 196 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.66 % Allowed : 19.74 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.59), residues: 178 helix: -1.44 (0.40), residues: 148 sheet: None (None), residues: 0 loop : -3.73 (1.09), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 79 HIS 0.000 0.000 HIS A 55 PHE 0.006 0.001 PHE B 41 TYR 0.007 0.001 TYR A 90 ARG 0.001 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.4513 time to fit residues: 12.3584 Evaluate side-chains 23 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 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: 0.7062 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1480 Z= 0.139 Angle : 0.545 7.123 2006 Z= 0.281 Chirality : 0.035 0.106 220 Planarity : 0.004 0.032 260 Dihedral : 4.647 16.334 196 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.97 % Allowed : 21.71 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.62), residues: 178 helix: -1.03 (0.41), residues: 152 sheet: None (None), residues: 0 loop : -4.25 (1.15), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.001 0.000 HIS B 55 PHE 0.005 0.001 PHE B 41 TYR 0.003 0.001 TYR B 90 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.4480 time to fit residues: 11.7352 Evaluate side-chains 24 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1480 Z= 0.132 Angle : 0.584 11.768 2006 Z= 0.284 Chirality : 0.034 0.106 220 Planarity : 0.003 0.031 260 Dihedral : 4.441 15.670 196 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.32 % Allowed : 21.71 % Favored : 76.97 % 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: -2.05 (0.63), residues: 178 helix: -0.75 (0.42), residues: 152 sheet: None (None), residues: 0 loop : -4.19 (1.20), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.001 0.000 HIS B 55 PHE 0.005 0.001 PHE B 41 TYR 0.003 0.001 TYR B 90 ARG 0.001 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.4737 time to fit residues: 12.3802 Evaluate side-chains 25 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7081 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1480 Z= 0.138 Angle : 0.540 8.114 2006 Z= 0.278 Chirality : 0.034 0.103 220 Planarity : 0.003 0.030 260 Dihedral : 4.246 14.415 196 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.97 % Allowed : 21.71 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.64), residues: 178 helix: -0.50 (0.42), residues: 156 sheet: None (None), residues: 0 loop : -4.18 (1.46), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.001 0.000 HIS B 55 PHE 0.004 0.001 PHE B 41 TYR 0.004 0.001 TYR B 90 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.4337 time to fit residues: 12.8217 Evaluate side-chains 26 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.7066 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1480 Z= 0.124 Angle : 0.537 9.139 2006 Z= 0.270 Chirality : 0.034 0.105 220 Planarity : 0.003 0.030 260 Dihedral : 4.138 13.083 196 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.32 % Allowed : 23.03 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.65), residues: 178 helix: -0.24 (0.42), residues: 156 sheet: None (None), residues: 0 loop : -4.32 (1.36), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.001 0.000 HIS B 55 PHE 0.005 0.001 PHE B 41 TYR 0.003 0.001 TYR B 90 ARG 0.001 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.4596 time to fit residues: 12.4884 Evaluate side-chains 26 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1480 Z= 0.129 Angle : 0.535 8.084 2006 Z= 0.272 Chirality : 0.034 0.102 220 Planarity : 0.003 0.029 260 Dihedral : 4.071 12.491 196 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.97 % Allowed : 21.71 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.65), residues: 178 helix: -0.02 (0.42), residues: 156 sheet: None (None), residues: 0 loop : -4.39 (1.32), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 4 HIS 0.001 0.000 HIS A 55 PHE 0.004 0.001 PHE B 41 TYR 0.003 0.001 TYR B 90 ARG 0.001 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.4612 time to fit residues: 12.0626 Evaluate side-chains 27 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 84 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.1980 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7056 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1480 Z= 0.126 Angle : 0.534 8.314 2006 Z= 0.267 Chirality : 0.033 0.103 220 Planarity : 0.003 0.030 260 Dihedral : 3.992 11.243 196 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.97 % Allowed : 21.71 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.65), residues: 178 helix: 0.36 (0.43), residues: 156 sheet: None (None), residues: 0 loop : -4.73 (1.09), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 4 HIS 0.001 0.000 HIS A 55 PHE 0.004 0.001 PHE B 41 TYR 0.003 0.001 TYR A 42 ARG 0.001 0.000 ARG A 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.4535 time to fit residues: 12.4255 Evaluate side-chains 27 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.079968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.072318 restraints weight = 44645.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.074209 restraints weight = 26273.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.075513 restraints weight = 16733.823| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1480 Z= 0.120 Angle : 0.526 7.744 2006 Z= 0.262 Chirality : 0.033 0.102 220 Planarity : 0.003 0.029 260 Dihedral : 3.849 10.560 196 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.97 % Allowed : 21.71 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.66), residues: 178 helix: 0.70 (0.43), residues: 156 sheet: None (None), residues: 0 loop : -4.91 (1.01), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 79 HIS 0.001 0.000 HIS A 55 PHE 0.004 0.001 PHE B 41 TYR 0.003 0.001 TYR A 90 ARG 0.001 0.000 ARG A 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.68 seconds wall clock time: 32 minutes 52.91 seconds (1972.91 seconds total)