Starting phenix.real_space_refine on Thu Nov 14 06:55:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf2_34710/11_2024/8hf2_34710.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf2_34710/11_2024/8hf2_34710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf2_34710/11_2024/8hf2_34710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf2_34710/11_2024/8hf2_34710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf2_34710/11_2024/8hf2_34710.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf2_34710/11_2024/8hf2_34710.cif" } resolution = 4.14 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= 0.014 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3125 2.51 5 N 760 2.21 5 O 755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4660 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.38, per 1000 atoms: 0.51 Number of scatterers: 4660 At special positions: 0 Unit cell: (87.98, 85.86, 67.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 755 8.00 N 760 7.00 C 3125 6.00 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 - 3.00 Amino acid : True - 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: 1.17 Conformation dependent library (CDL) restraints added in 523.9 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 84.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 19 through 43 removed outlier: 4.149A pdb=" N THR A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.933A pdb=" N PHE A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 110 removed outlier: 3.574A pdb=" N ILE A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'B' and resid 20 through 43 Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 56 through 80 removed outlier: 3.933A pdb=" N PHE B 60 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 110 removed outlier: 3.573A pdb=" N ILE B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B 110 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 136 Processing helix chain 'C' and resid 20 through 43 Processing helix chain 'C' and resid 44 through 46 No H-bonds generated for 'chain 'C' and resid 44 through 46' Processing helix chain 'C' and resid 56 through 80 removed outlier: 3.933A pdb=" N PHE C 60 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 110 removed outlier: 3.574A pdb=" N ILE C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY C 101 " --> pdb=" O HIS C 97 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL C 110 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 136 Processing helix chain 'D' and resid 20 through 43 Processing helix chain 'D' and resid 44 through 46 No H-bonds generated for 'chain 'D' and resid 44 through 46' Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.932A pdb=" N PHE D 60 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG D 76 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 110 removed outlier: 3.575A pdb=" N ILE D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D 101 " --> pdb=" O HIS D 97 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 136 Processing helix chain 'E' and resid 20 through 43 Processing helix chain 'E' and resid 44 through 46 No H-bonds generated for 'chain 'E' and resid 44 through 46' Processing helix chain 'E' and resid 56 through 80 removed outlier: 3.934A pdb=" N PHE E 60 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL E 65 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG E 76 " --> pdb=" O VAL E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 110 removed outlier: 3.574A pdb=" N ILE E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY E 101 " --> pdb=" O HIS E 97 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL E 110 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 136 375 hydrogen bonds defined for protein. 1125 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: 1.21 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1393 1.34 - 1.46: 1172 1.46 - 1.58: 2175 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 4770 Sorted by residual: bond pdb=" CG LEU A 40 " pdb=" CD1 LEU A 40 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.44e+00 bond pdb=" CG LEU E 40 " pdb=" CD1 LEU E 40 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.37e+00 bond pdb=" CG LEU B 40 " pdb=" CD1 LEU B 40 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.36e+00 bond pdb=" CG LEU D 40 " pdb=" CD1 LEU D 40 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.30e+00 bond pdb=" CG LEU C 40 " pdb=" CD1 LEU C 40 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.29e+00 ... (remaining 4765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 6140 1.96 - 3.92: 297 3.92 - 5.88: 43 5.88 - 7.84: 10 7.84 - 9.80: 10 Bond angle restraints: 6500 Sorted by residual: angle pdb=" CA LEU E 42 " pdb=" CB LEU E 42 " pdb=" CG LEU E 42 " ideal model delta sigma weight residual 116.30 106.50 9.80 3.50e+00 8.16e-02 7.84e+00 angle pdb=" CA LEU D 42 " pdb=" CB LEU D 42 " pdb=" CG LEU D 42 " ideal model delta sigma weight residual 116.30 106.53 9.77 3.50e+00 8.16e-02 7.80e+00 angle pdb=" CA LEU C 42 " pdb=" CB LEU C 42 " pdb=" CG LEU C 42 " ideal model delta sigma weight residual 116.30 106.55 9.75 3.50e+00 8.16e-02 7.76e+00 angle pdb=" CA LEU A 42 " pdb=" CB LEU A 42 " pdb=" CG LEU A 42 " ideal model delta sigma weight residual 116.30 106.56 9.74 3.50e+00 8.16e-02 7.74e+00 angle pdb=" CA LEU B 42 " pdb=" CB LEU B 42 " pdb=" CG LEU B 42 " ideal model delta sigma weight residual 116.30 106.56 9.74 3.50e+00 8.16e-02 7.74e+00 ... (remaining 6495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.57: 2192 10.57 - 21.14: 336 21.14 - 31.71: 107 31.71 - 42.28: 90 42.28 - 52.85: 20 Dihedral angle restraints: 2745 sinusoidal: 1005 harmonic: 1740 Sorted by residual: dihedral pdb=" CA LEU C 43 " pdb=" C LEU C 43 " pdb=" N GLN C 44 " pdb=" CA GLN C 44 " 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 A 43 " pdb=" C LEU A 43 " pdb=" N GLN A 44 " pdb=" CA GLN A 44 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LEU E 43 " pdb=" C LEU E 43 " pdb=" N GLN E 44 " pdb=" CA GLN E 44 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 2742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 436 0.031 - 0.063: 244 0.063 - 0.094: 97 0.094 - 0.126: 23 0.126 - 0.157: 15 Chirality restraints: 815 Sorted by residual: chirality pdb=" CB VAL E 28 " pdb=" CA VAL E 28 " pdb=" CG1 VAL E 28 " pdb=" CG2 VAL E 28 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA LEU C 43 " pdb=" N LEU C 43 " pdb=" C LEU C 43 " pdb=" CB LEU C 43 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CB VAL B 28 " pdb=" CA VAL B 28 " pdb=" CG1 VAL B 28 " pdb=" CG2 VAL B 28 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 812 not shown) Planarity restraints: 770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 24 " 0.014 2.00e-02 2.50e+03 7.98e-03 1.27e+00 pdb=" CG TYR E 24 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR E 24 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR E 24 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 24 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 24 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 24 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 24 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 36 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" CG ASN C 36 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 36 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 36 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 24 " 0.014 2.00e-02 2.50e+03 7.94e-03 1.26e+00 pdb=" CG TYR D 24 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR D 24 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 24 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 24 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 24 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR D 24 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 24 " 0.005 2.00e-02 2.50e+03 ... (remaining 767 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1362 2.79 - 3.32: 5357 3.32 - 3.85: 7557 3.85 - 4.37: 8194 4.37 - 4.90: 13136 Nonbonded interactions: 35606 Sorted by model distance: nonbonded pdb=" O LYS C 20 " pdb=" OG1 THR C 23 " model vdw 2.264 3.040 nonbonded pdb=" O LYS A 20 " pdb=" OG1 THR A 23 " model vdw 2.265 3.040 nonbonded pdb=" O LYS D 20 " pdb=" OG1 THR D 23 " model vdw 2.265 3.040 nonbonded pdb=" O LYS E 20 " pdb=" OG1 THR E 23 " model vdw 2.265 3.040 nonbonded pdb=" O LYS B 20 " pdb=" OG1 THR B 23 " model vdw 2.265 3.040 ... (remaining 35601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.830 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.060 Find NCS groups from input model: 0.150 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.012 0.070 4770 Z= 0.762 Angle : 1.036 9.803 6500 Z= 0.550 Chirality : 0.047 0.157 815 Planarity : 0.004 0.025 770 Dihedral : 14.202 52.847 1615 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % 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: -4.39 (0.26), residues: 590 helix: -2.42 (0.18), residues: 470 sheet: None (None), residues: 0 loop : -4.02 (0.48), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 126 HIS 0.002 0.001 HIS E 56 PHE 0.011 0.002 PHE E 120 TYR 0.017 0.004 TYR E 24 ARG 0.003 0.001 ARG E 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.545 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 ASN cc_start: 0.8097 (p0) cc_final: 0.7781 (p0) REVERT: C 44 GLN cc_start: 0.8039 (mt0) cc_final: 0.7525 (tt0) REVERT: C 132 TYR cc_start: 0.8429 (t80) cc_final: 0.8192 (t80) REVERT: D 43 LEU cc_start: 0.9300 (pp) cc_final: 0.9035 (tt) REVERT: D 44 GLN cc_start: 0.8146 (mt0) cc_final: 0.7552 (tt0) REVERT: D 136 ASN cc_start: 0.8198 (p0) cc_final: 0.7674 (p0) REVERT: E 63 PHE cc_start: 0.8584 (t80) cc_final: 0.8311 (t80) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.1749 time to fit residues: 58.4086 Evaluate side-chains 166 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.0070 chunk 30 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4770 Z= 0.196 Angle : 0.693 10.318 6500 Z= 0.334 Chirality : 0.036 0.144 815 Planarity : 0.004 0.042 770 Dihedral : 5.200 16.756 630 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % 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: -1.00 (0.32), residues: 590 helix: 0.05 (0.23), residues: 475 sheet: None (None), residues: 0 loop : -3.41 (0.36), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 126 HIS 0.007 0.002 HIS E 29 PHE 0.014 0.001 PHE D 63 TYR 0.009 0.002 TYR E 132 ARG 0.003 0.001 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.547 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 revert: symmetry clash revert: symmetry clash REVERT: A 97 HIS cc_start: 0.8837 (m170) cc_final: 0.8496 (m90) REVERT: B 94 HIS cc_start: 0.8319 (m90) cc_final: 0.7825 (m-70) REVERT: B 107 LEU cc_start: 0.8976 (mt) cc_final: 0.8750 (mt) REVERT: B 136 ASN cc_start: 0.7965 (p0) cc_final: 0.7697 (p0) REVERT: C 44 GLN cc_start: 0.7846 (mt0) cc_final: 0.7359 (tt0) REVERT: C 97 HIS cc_start: 0.8827 (m170) cc_final: 0.8567 (m90) REVERT: C 132 TYR cc_start: 0.8336 (t80) cc_final: 0.8062 (t80) REVERT: D 44 GLN cc_start: 0.7968 (mt0) cc_final: 0.7287 (tt0) REVERT: D 97 HIS cc_start: 0.8601 (m170) cc_final: 0.8250 (m170) REVERT: D 136 ASN cc_start: 0.8000 (p0) cc_final: 0.7731 (p0) REVERT: E 97 HIS cc_start: 0.8778 (m-70) cc_final: 0.8511 (m-70) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1883 time to fit residues: 51.3014 Evaluate side-chains 175 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 15 optimal weight: 6.9990 chunk 54 optimal weight: 0.0470 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS E 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4770 Z= 0.173 Angle : 0.640 10.247 6500 Z= 0.304 Chirality : 0.033 0.108 815 Planarity : 0.004 0.028 770 Dihedral : 4.556 15.149 630 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % 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: 0.32 (0.34), residues: 590 helix: 1.02 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -3.16 (0.38), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 123 HIS 0.018 0.003 HIS E 97 PHE 0.015 0.001 PHE A 63 TYR 0.008 0.001 TYR A 132 ARG 0.003 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.520 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 revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.8121 (tt0) cc_final: 0.7465 (tt0) REVERT: A 94 HIS cc_start: 0.8211 (m90) cc_final: 0.7861 (m90) REVERT: A 97 HIS cc_start: 0.8793 (m-70) cc_final: 0.8479 (m-70) REVERT: A 102 LEU cc_start: 0.8323 (tt) cc_final: 0.8101 (tp) REVERT: B 97 HIS cc_start: 0.8718 (m170) cc_final: 0.8390 (m90) REVERT: B 132 TYR cc_start: 0.8074 (t80) cc_final: 0.7874 (t80) REVERT: B 136 ASN cc_start: 0.8028 (p0) cc_final: 0.7800 (p0) REVERT: C 44 GLN cc_start: 0.7632 (mt0) cc_final: 0.7266 (tt0) REVERT: C 80 ASP cc_start: 0.7522 (t0) cc_final: 0.7100 (t0) REVERT: C 91 LEU cc_start: 0.8396 (mp) cc_final: 0.7917 (tt) REVERT: C 94 HIS cc_start: 0.8151 (m90) cc_final: 0.7951 (m90) REVERT: C 97 HIS cc_start: 0.8869 (m170) cc_final: 0.8626 (m-70) REVERT: C 132 TYR cc_start: 0.8221 (t80) cc_final: 0.8017 (t80) REVERT: D 63 PHE cc_start: 0.8203 (t80) cc_final: 0.7996 (t80) REVERT: D 97 HIS cc_start: 0.8642 (m170) cc_final: 0.8284 (m90) REVERT: D 136 ASN cc_start: 0.7943 (p0) cc_final: 0.7704 (p0) REVERT: E 80 ASP cc_start: 0.7113 (t0) cc_final: 0.6899 (t0) REVERT: E 91 LEU cc_start: 0.8382 (mp) cc_final: 0.7861 (tt) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1732 time to fit residues: 49.6651 Evaluate side-chains 186 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4770 Z= 0.173 Angle : 0.605 10.861 6500 Z= 0.297 Chirality : 0.033 0.116 815 Planarity : 0.004 0.037 770 Dihedral : 4.343 13.790 630 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % 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: 0.68 (0.34), residues: 590 helix: 1.26 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -3.04 (0.40), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 123 HIS 0.008 0.001 HIS A 29 PHE 0.023 0.002 PHE B 63 TYR 0.013 0.002 TYR E 70 ARG 0.007 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.527 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 REVERT: A 44 GLN cc_start: 0.7838 (tt0) cc_final: 0.7555 (tt0) REVERT: A 94 HIS cc_start: 0.8034 (m90) cc_final: 0.7761 (m90) REVERT: A 97 HIS cc_start: 0.8842 (m-70) cc_final: 0.8548 (m-70) REVERT: B 53 LEU cc_start: 0.8421 (pt) cc_final: 0.8082 (pp) REVERT: B 97 HIS cc_start: 0.8650 (m170) cc_final: 0.8440 (m90) REVERT: B 132 TYR cc_start: 0.8071 (t80) cc_final: 0.7801 (t80) REVERT: C 44 GLN cc_start: 0.7704 (mt0) cc_final: 0.7379 (tt0) REVERT: C 80 ASP cc_start: 0.7173 (t0) cc_final: 0.6857 (t0) REVERT: C 97 HIS cc_start: 0.8814 (m170) cc_final: 0.8421 (m90) REVERT: C 132 TYR cc_start: 0.8193 (t80) cc_final: 0.7992 (t80) REVERT: D 91 LEU cc_start: 0.8596 (mp) cc_final: 0.7915 (tt) REVERT: D 92 ILE cc_start: 0.9053 (mm) cc_final: 0.8816 (mm) REVERT: D 94 HIS cc_start: 0.8195 (m90) cc_final: 0.7807 (m90) REVERT: E 80 ASP cc_start: 0.6960 (t0) cc_final: 0.6727 (t0) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1579 time to fit residues: 43.1764 Evaluate side-chains 185 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 94 HIS D 97 HIS ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4770 Z= 0.217 Angle : 0.630 12.177 6500 Z= 0.318 Chirality : 0.034 0.114 815 Planarity : 0.004 0.035 770 Dihedral : 4.328 13.592 630 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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: 0.75 (0.34), residues: 590 helix: 1.30 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -2.98 (0.40), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 126 HIS 0.023 0.003 HIS A 97 PHE 0.021 0.002 PHE D 66 TYR 0.012 0.002 TYR B 70 ARG 0.005 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.523 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: A 44 GLN cc_start: 0.8255 (tt0) cc_final: 0.8023 (tt0) REVERT: A 97 HIS cc_start: 0.8721 (m90) cc_final: 0.8089 (m90) REVERT: B 53 LEU cc_start: 0.8448 (pt) cc_final: 0.8032 (pp) REVERT: B 132 TYR cc_start: 0.8150 (t80) cc_final: 0.7616 (t80) REVERT: C 44 GLN cc_start: 0.7708 (mt0) cc_final: 0.7373 (tt0) REVERT: C 76 ARG cc_start: 0.8650 (mmm160) cc_final: 0.8259 (mmm160) REVERT: C 97 HIS cc_start: 0.8798 (m170) cc_final: 0.8426 (m90) REVERT: C 132 TYR cc_start: 0.8239 (t80) cc_final: 0.8001 (t80) REVERT: D 76 ARG cc_start: 0.8323 (mmm160) cc_final: 0.7711 (mmm160) REVERT: D 80 ASP cc_start: 0.7999 (m-30) cc_final: 0.7779 (m-30) REVERT: D 94 HIS cc_start: 0.8303 (m90) cc_final: 0.8096 (m90) REVERT: E 80 ASP cc_start: 0.7058 (t0) cc_final: 0.6807 (t0) REVERT: E 97 HIS cc_start: 0.8862 (m-70) cc_final: 0.8270 (m-70) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1679 time to fit residues: 44.1746 Evaluate side-chains 176 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.7123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4770 Z= 0.189 Angle : 0.640 11.258 6500 Z= 0.312 Chirality : 0.034 0.118 815 Planarity : 0.004 0.034 770 Dihedral : 4.281 13.683 630 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: 0.64 (0.34), residues: 590 helix: 1.19 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -2.78 (0.42), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 123 HIS 0.028 0.003 HIS B 97 PHE 0.020 0.002 PHE C 66 TYR 0.024 0.002 TYR D 24 ARG 0.005 0.001 ARG E 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.532 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: A 92 ILE cc_start: 0.9262 (mp) cc_final: 0.9019 (mp) REVERT: A 97 HIS cc_start: 0.8697 (m90) cc_final: 0.8029 (m90) REVERT: A 136 ASN cc_start: 0.8210 (p0) cc_final: 0.7988 (p0) REVERT: B 53 LEU cc_start: 0.8420 (pt) cc_final: 0.8083 (pp) REVERT: B 94 HIS cc_start: 0.8027 (m90) cc_final: 0.7557 (m-70) REVERT: B 132 TYR cc_start: 0.8096 (t80) cc_final: 0.7587 (t80) REVERT: C 76 ARG cc_start: 0.8502 (mmm160) cc_final: 0.8118 (mmm160) REVERT: C 94 HIS cc_start: 0.8132 (m90) cc_final: 0.7789 (m-70) REVERT: C 132 TYR cc_start: 0.8192 (t80) cc_final: 0.7935 (t80) REVERT: D 91 LEU cc_start: 0.8330 (mp) cc_final: 0.7704 (tt) REVERT: D 94 HIS cc_start: 0.7881 (m90) cc_final: 0.7566 (m90) REVERT: E 44 GLN cc_start: 0.8102 (tt0) cc_final: 0.7667 (tm-30) REVERT: E 76 ARG cc_start: 0.8641 (mmm160) cc_final: 0.8265 (mmm160) REVERT: E 97 HIS cc_start: 0.8848 (m-70) cc_final: 0.8229 (m-70) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1632 time to fit residues: 44.7600 Evaluate side-chains 181 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.0570 chunk 36 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.7433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4770 Z= 0.176 Angle : 0.639 12.071 6500 Z= 0.309 Chirality : 0.033 0.135 815 Planarity : 0.004 0.040 770 Dihedral : 4.215 12.526 630 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.20 % Allowed : 2.75 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.34), residues: 590 helix: 1.33 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -2.68 (0.43), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 123 HIS 0.014 0.002 HIS C 97 PHE 0.057 0.002 PHE E 66 TYR 0.020 0.002 TYR B 24 ARG 0.002 0.000 ARG E 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.513 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: A 97 HIS cc_start: 0.8777 (m90) cc_final: 0.8498 (m-70) REVERT: B 44 GLN cc_start: 0.7387 (pp30) cc_final: 0.6861 (pp30) REVERT: B 94 HIS cc_start: 0.7786 (m90) cc_final: 0.7378 (m-70) REVERT: B 132 TYR cc_start: 0.7949 (t80) cc_final: 0.7527 (t80) REVERT: C 44 GLN cc_start: 0.7601 (mt0) cc_final: 0.7338 (tt0) REVERT: C 132 TYR cc_start: 0.8269 (t80) cc_final: 0.7885 (t80) REVERT: D 44 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7572 (tm-30) REVERT: D 76 ARG cc_start: 0.8515 (mmm160) cc_final: 0.8271 (tpp80) REVERT: D 91 LEU cc_start: 0.8141 (mp) cc_final: 0.7600 (tt) REVERT: E 44 GLN cc_start: 0.7973 (tt0) cc_final: 0.7464 (tm-30) REVERT: E 97 HIS cc_start: 0.8801 (m-70) cc_final: 0.8512 (m-70) outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.1634 time to fit residues: 44.7470 Evaluate side-chains 187 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.7548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4770 Z= 0.192 Angle : 0.681 12.974 6500 Z= 0.332 Chirality : 0.035 0.126 815 Planarity : 0.005 0.039 770 Dihedral : 4.139 12.707 630 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.33), residues: 590 helix: 1.12 (0.23), residues: 475 sheet: None (None), residues: 0 loop : -2.61 (0.43), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 123 HIS 0.021 0.003 HIS C 97 PHE 0.045 0.002 PHE E 66 TYR 0.005 0.001 TYR C 70 ARG 0.004 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.549 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: A 94 HIS cc_start: 0.8054 (m90) cc_final: 0.7802 (m-70) REVERT: B 44 GLN cc_start: 0.7552 (pp30) cc_final: 0.7013 (pp30) REVERT: B 132 TYR cc_start: 0.7956 (t80) cc_final: 0.7571 (t80) REVERT: C 44 GLN cc_start: 0.7621 (mt0) cc_final: 0.7294 (tt0) REVERT: C 132 TYR cc_start: 0.8223 (t80) cc_final: 0.7806 (t80) REVERT: D 44 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7511 (tm-30) REVERT: E 76 ARG cc_start: 0.8145 (tpm170) cc_final: 0.7927 (mmm160) REVERT: E 97 HIS cc_start: 0.8794 (m-70) cc_final: 0.8535 (m-70) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1518 time to fit residues: 41.6705 Evaluate side-chains 177 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.0670 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 55 optimal weight: 0.0770 chunk 47 optimal weight: 8.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.7733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4770 Z= 0.190 Angle : 0.673 12.903 6500 Z= 0.325 Chirality : 0.035 0.140 815 Planarity : 0.005 0.040 770 Dihedral : 4.095 12.019 630 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: 0.43 (0.33), residues: 590 helix: 0.97 (0.23), residues: 475 sheet: None (None), residues: 0 loop : -2.52 (0.43), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 123 HIS 0.025 0.003 HIS A 97 PHE 0.042 0.002 PHE E 66 TYR 0.016 0.001 TYR B 70 ARG 0.003 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.532 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: A 44 GLN cc_start: 0.8107 (tp-100) cc_final: 0.6791 (mm-40) REVERT: B 44 GLN cc_start: 0.7560 (pp30) cc_final: 0.7015 (pp30) REVERT: B 132 TYR cc_start: 0.8060 (t80) cc_final: 0.7580 (t80) REVERT: C 44 GLN cc_start: 0.7612 (mt0) cc_final: 0.7234 (tt0) REVERT: C 94 HIS cc_start: 0.7774 (m90) cc_final: 0.7475 (m-70) REVERT: C 102 LEU cc_start: 0.8601 (mm) cc_final: 0.8178 (mm) REVERT: C 132 TYR cc_start: 0.8247 (t80) cc_final: 0.7823 (t80) REVERT: E 97 HIS cc_start: 0.8787 (m-70) cc_final: 0.8231 (m-70) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1519 time to fit residues: 41.6189 Evaluate side-chains 185 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 50 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 0.0020 chunk 19 optimal weight: 2.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.8069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4770 Z= 0.197 Angle : 0.693 13.393 6500 Z= 0.336 Chirality : 0.036 0.140 815 Planarity : 0.005 0.039 770 Dihedral : 4.194 12.386 630 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.34 (0.32), residues: 590 helix: 0.89 (0.23), residues: 475 sheet: None (None), residues: 0 loop : -2.47 (0.42), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 123 HIS 0.025 0.004 HIS E 97 PHE 0.041 0.002 PHE E 66 TYR 0.016 0.001 TYR C 70 ARG 0.007 0.000 ARG C 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.635 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: B 132 TYR cc_start: 0.8000 (t80) cc_final: 0.7732 (t80) REVERT: C 91 LEU cc_start: 0.7908 (mp) cc_final: 0.7369 (tt) REVERT: C 132 TYR cc_start: 0.8188 (t80) cc_final: 0.7790 (t80) REVERT: E 97 HIS cc_start: 0.8593 (m-70) cc_final: 0.7725 (m90) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1430 time to fit residues: 39.8610 Evaluate side-chains 185 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 0.0370 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.083616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.065106 restraints weight = 18404.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.067239 restraints weight = 11697.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.068649 restraints weight = 8494.787| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.8276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4770 Z= 0.201 Angle : 0.705 13.527 6500 Z= 0.344 Chirality : 0.037 0.147 815 Planarity : 0.005 0.039 770 Dihedral : 4.136 11.930 630 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.32), residues: 590 helix: 0.90 (0.23), residues: 475 sheet: None (None), residues: 0 loop : -2.42 (0.42), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 123 HIS 0.021 0.003 HIS A 97 PHE 0.039 0.002 PHE E 66 TYR 0.015 0.001 TYR B 70 ARG 0.008 0.001 ARG C 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1422.57 seconds wall clock time: 26 minutes 29.93 seconds (1589.93 seconds total)