Starting phenix.real_space_refine on Fri Dec 27 17:11:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ug5_42214/12_2024/8ug5_42214.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ug5_42214/12_2024/8ug5_42214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ug5_42214/12_2024/8ug5_42214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ug5_42214/12_2024/8ug5_42214.map" model { file = "/net/cci-nas-00/data/ceres_data/8ug5_42214/12_2024/8ug5_42214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ug5_42214/12_2024/8ug5_42214.cif" } resolution = 2.91 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= 0.004 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 40 5.16 5 C 4150 2.51 5 N 978 2.21 5 O 992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6160 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3080 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 8, 'TRANS': 373} Chain breaks: 6 Restraints were copied for chains: B Time building chain proxies: 5.68, per 1000 atoms: 0.92 Number of scatterers: 6160 At special positions: 0 Unit cell: (97.11, 87.15, 76.36, 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 40 16.00 O 992 8.00 N 978 7.00 C 4150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 189 " distance=2.03 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: 1.54 Conformation dependent library (CDL) restraints added in 960.5 milliseconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 82.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 53 through 56 Processing helix chain 'A' and resid 57 through 86 removed outlier: 3.565A pdb=" N PHE A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 119 Processing helix chain 'A' and resid 122 through 135 Processing helix chain 'A' and resid 158 through 185 Processing helix chain 'A' and resid 190 through 213 removed outlier: 3.616A pdb=" N LYS A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 244 removed outlier: 3.550A pdb=" N PHE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 340 Processing helix chain 'A' and resid 398 through 424 removed outlier: 4.336A pdb=" N GLY A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 435 through 464 removed outlier: 3.924A pdb=" N ASP A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 498 Processing helix chain 'A' and resid 504 through 511 Processing helix chain 'A' and resid 513 through 533 Processing helix chain 'A' and resid 551 through 579 Proline residue: A 559 - end of helix removed outlier: 3.907A pdb=" N VAL A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 56 Processing helix chain 'B' and resid 57 through 86 removed outlier: 3.565A pdb=" N PHE B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 119 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 158 through 185 Processing helix chain 'B' and resid 190 through 213 removed outlier: 3.616A pdb=" N LYS B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 244 removed outlier: 3.550A pdb=" N PHE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 340 Processing helix chain 'B' and resid 398 through 424 removed outlier: 4.337A pdb=" N GLY B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 435 through 464 removed outlier: 3.924A pdb=" N ASP B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 498 Processing helix chain 'B' and resid 504 through 511 Processing helix chain 'B' and resid 513 through 533 Processing helix chain 'B' and resid 551 through 579 Proline residue: B 559 - end of helix removed outlier: 3.907A pdb=" N VAL B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 429 Processing sheet with id=AA2, first strand: chain 'B' and resid 428 through 429 502 hydrogen bonds defined for protein. 1494 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: 1.81 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 973 1.32 - 1.44: 1801 1.44 - 1.57: 3486 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6320 Sorted by residual: bond pdb=" CA SER A 86 " pdb=" CB SER A 86 " ideal model delta sigma weight residual 1.528 1.470 0.057 1.40e-02 5.10e+03 1.68e+01 bond pdb=" CA SER B 86 " pdb=" CB SER B 86 " ideal model delta sigma weight residual 1.528 1.470 0.057 1.40e-02 5.10e+03 1.67e+01 bond pdb=" N LYS A 511 " pdb=" CA LYS A 511 " ideal model delta sigma weight residual 1.460 1.488 -0.028 7.10e-03 1.98e+04 1.53e+01 bond pdb=" N LYS B 511 " pdb=" CA LYS B 511 " ideal model delta sigma weight residual 1.460 1.487 -0.027 7.10e-03 1.98e+04 1.45e+01 bond pdb=" CA SER A 221 " pdb=" CB SER A 221 " ideal model delta sigma weight residual 1.535 1.478 0.056 1.58e-02 4.01e+03 1.28e+01 ... (remaining 6315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 7430 1.61 - 3.22: 899 3.22 - 4.83: 195 4.83 - 6.45: 30 6.45 - 8.06: 10 Bond angle restraints: 8564 Sorted by residual: angle pdb=" N VAL B 85 " pdb=" CA VAL B 85 " pdb=" C VAL B 85 " ideal model delta sigma weight residual 113.10 106.94 6.16 9.70e-01 1.06e+00 4.04e+01 angle pdb=" N VAL A 85 " pdb=" CA VAL A 85 " pdb=" C VAL A 85 " ideal model delta sigma weight residual 113.10 106.95 6.15 9.70e-01 1.06e+00 4.02e+01 angle pdb=" N ILE A 129 " pdb=" CA ILE A 129 " pdb=" C ILE A 129 " ideal model delta sigma weight residual 110.42 104.54 5.88 9.60e-01 1.09e+00 3.76e+01 angle pdb=" N ILE B 129 " pdb=" CA ILE B 129 " pdb=" C ILE B 129 " ideal model delta sigma weight residual 110.42 104.54 5.88 9.60e-01 1.09e+00 3.75e+01 angle pdb=" N ASN A 551 " pdb=" CA ASN A 551 " pdb=" C ASN A 551 " ideal model delta sigma weight residual 114.39 106.33 8.06 1.45e+00 4.76e-01 3.09e+01 ... (remaining 8559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 3162 14.14 - 28.27: 305 28.27 - 42.41: 99 42.41 - 56.54: 26 56.54 - 70.68: 9 Dihedral angle restraints: 3601 sinusoidal: 1383 harmonic: 2218 Sorted by residual: dihedral pdb=" CD ARG A 133 " pdb=" NE ARG A 133 " pdb=" CZ ARG A 133 " pdb=" NH1 ARG A 133 " ideal model delta sinusoidal sigma weight residual 0.00 60.43 -60.43 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CD ARG B 133 " pdb=" NE ARG B 133 " pdb=" CZ ARG B 133 " pdb=" NH1 ARG B 133 " ideal model delta sinusoidal sigma weight residual 0.00 60.43 -60.43 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CD ARG B 59 " pdb=" NE ARG B 59 " pdb=" CZ ARG B 59 " pdb=" NH1 ARG B 59 " ideal model delta sinusoidal sigma weight residual 0.00 39.61 -39.61 1 1.00e+01 1.00e-02 2.20e+01 ... (remaining 3598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 718 0.061 - 0.121: 160 0.121 - 0.182: 83 0.182 - 0.242: 27 0.242 - 0.303: 12 Chirality restraints: 1000 Sorted by residual: chirality pdb=" CA ILE A 129 " pdb=" N ILE A 129 " pdb=" C ILE A 129 " pdb=" CB ILE A 129 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ILE B 129 " pdb=" N ILE B 129 " pdb=" C ILE B 129 " pdb=" CB ILE B 129 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA GLU A 185 " pdb=" N GLU A 185 " pdb=" C GLU A 185 " pdb=" CB GLU A 185 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 997 not shown) Planarity restraints: 1012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 133 " -0.956 9.50e-02 1.11e+02 4.29e-01 1.11e+02 pdb=" NE ARG A 133 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 133 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 133 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 133 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 133 " 0.956 9.50e-02 1.11e+02 4.28e-01 1.11e+02 pdb=" NE ARG B 133 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG B 133 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 133 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 133 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 59 " -0.692 9.50e-02 1.11e+02 3.10e-01 5.86e+01 pdb=" NE ARG A 59 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG A 59 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 59 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 59 " -0.021 2.00e-02 2.50e+03 ... (remaining 1009 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 45 2.60 - 3.18: 5579 3.18 - 3.75: 10030 3.75 - 4.33: 13651 4.33 - 4.90: 22369 Nonbonded interactions: 51674 Sorted by model distance: nonbonded pdb=" SG CYS B 183 " pdb=" SG CYS B 189 " model vdw 2.029 3.760 nonbonded pdb=" O ILE B 99 " pdb=" OG SER B 103 " model vdw 2.335 3.040 nonbonded pdb=" O ILE A 99 " pdb=" OG SER A 103 " model vdw 2.335 3.040 nonbonded pdb=" NE2 GLN A 486 " pdb=" OE1 GLN A 490 " model vdw 2.370 3.120 nonbonded pdb=" NE2 GLN B 486 " pdb=" OE1 GLN B 490 " model vdw 2.370 3.120 ... (remaining 51669 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.640 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:14.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 0.071 6320 Z= 0.515 Angle : 1.132 8.056 8564 Z= 0.833 Chirality : 0.075 0.303 1000 Planarity : 0.024 0.429 1012 Dihedral : 13.475 70.676 2170 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % 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: 0.42 (0.31), residues: 736 helix: 0.90 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -2.28 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 54 HIS 0.009 0.001 HIS B 567 PHE 0.010 0.002 PHE A 335 TYR 0.020 0.002 TYR B 101 ARG 0.003 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.815 Fit side-chains REVERT: A 51 ARG cc_start: 0.6445 (ptp-170) cc_final: 0.5950 (ptp-170) REVERT: A 147 MET cc_start: 0.5972 (mmm) cc_final: 0.5424 (mmp) REVERT: A 506 TYR cc_start: 0.6069 (t80) cc_final: 0.5838 (t80) REVERT: A 514 LYS cc_start: 0.6884 (tttt) cc_final: 0.6413 (ttpp) REVERT: B 147 MET cc_start: 0.5940 (mmm) cc_final: 0.5446 (mmp) REVERT: B 506 TYR cc_start: 0.6040 (t80) cc_final: 0.5797 (t80) outliers start: 0 outliers final: 2 residues processed: 174 average time/residue: 1.1954 time to fit residues: 218.3876 Evaluate side-chains 96 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 445 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 126 ASN A 531 HIS B 62 ASN B 126 ASN B 531 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6320 Z= 0.203 Angle : 0.571 7.844 8564 Z= 0.300 Chirality : 0.039 0.202 1000 Planarity : 0.005 0.069 1012 Dihedral : 3.909 21.610 824 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.33 % Allowed : 15.91 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.31), residues: 736 helix: 1.74 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -1.55 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 144 HIS 0.006 0.001 HIS A 567 PHE 0.015 0.001 PHE A 181 TYR 0.018 0.002 TYR B 510 ARG 0.006 0.001 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.728 Fit side-chains REVERT: A 51 ARG cc_start: 0.6337 (ptp-170) cc_final: 0.6051 (ptp-170) REVERT: A 52 ARG cc_start: 0.7629 (ptp90) cc_final: 0.7179 (ptp-170) REVERT: A 110 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8455 (tm) REVERT: A 133 ARG cc_start: 0.4279 (OUTLIER) cc_final: 0.3971 (mmm160) REVERT: A 334 MET cc_start: 0.8540 (mmt) cc_final: 0.8220 (mmp) REVERT: A 514 LYS cc_start: 0.6897 (tttt) cc_final: 0.6441 (ttpp) REVERT: B 52 ARG cc_start: 0.7603 (ptp90) cc_final: 0.7262 (ptp-170) REVERT: B 110 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8455 (tm) REVERT: B 133 ARG cc_start: 0.4295 (OUTLIER) cc_final: 0.4019 (mmm160) REVERT: B 179 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6518 (mp0) REVERT: B 334 MET cc_start: 0.8490 (mmt) cc_final: 0.8230 (mmp) outliers start: 22 outliers final: 2 residues processed: 109 average time/residue: 0.8834 time to fit residues: 102.9470 Evaluate side-chains 99 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 320 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 151 HIS B 62 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6320 Z= 0.212 Angle : 0.527 7.345 8564 Z= 0.275 Chirality : 0.037 0.123 1000 Planarity : 0.004 0.040 1012 Dihedral : 3.563 16.413 820 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 5.15 % Allowed : 15.91 % Favored : 78.94 % 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: 2.22 (0.30), residues: 736 helix: 2.02 (0.20), residues: 602 sheet: None (None), residues: 0 loop : -1.11 (0.58), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 54 HIS 0.006 0.001 HIS B 567 PHE 0.010 0.001 PHE B 335 TYR 0.020 0.002 TYR A 101 ARG 0.005 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.735 Fit side-chains REVERT: A 51 ARG cc_start: 0.6391 (ptp-170) cc_final: 0.6074 (ptp-170) REVERT: A 104 MET cc_start: 0.8584 (mmm) cc_final: 0.8362 (mtp) REVERT: A 110 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8435 (tm) REVERT: A 194 ILE cc_start: 0.8433 (mp) cc_final: 0.7983 (mp) REVERT: A 334 MET cc_start: 0.8527 (mmt) cc_final: 0.8131 (mmp) REVERT: A 514 LYS cc_start: 0.6993 (tttt) cc_final: 0.6747 (ttpp) REVERT: B 52 ARG cc_start: 0.7614 (ptp90) cc_final: 0.7289 (ptp-170) REVERT: B 57 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6034 (tm-30) REVERT: B 59 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6910 (ptm-80) REVERT: B 110 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8446 (tm) REVERT: B 127 GLN cc_start: 0.5855 (mp10) cc_final: 0.5504 (mt0) REVERT: B 194 ILE cc_start: 0.8377 (mp) cc_final: 0.8093 (mp) REVERT: B 334 MET cc_start: 0.8511 (mmt) cc_final: 0.8150 (mmp) REVERT: B 463 THR cc_start: 0.7705 (t) cc_final: 0.7459 (t) outliers start: 34 outliers final: 7 residues processed: 113 average time/residue: 0.9880 time to fit residues: 118.3750 Evaluate side-chains 95 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 406 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 151 HIS B 62 ASN B 126 ASN B 151 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6320 Z= 0.182 Angle : 0.486 5.860 8564 Z= 0.254 Chirality : 0.037 0.114 1000 Planarity : 0.003 0.033 1012 Dihedral : 3.489 15.056 820 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 5.30 % Allowed : 15.76 % Favored : 78.94 % 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: 2.53 (0.30), residues: 736 helix: 2.17 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -0.72 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 239 HIS 0.006 0.001 HIS B 151 PHE 0.021 0.001 PHE A 181 TYR 0.019 0.001 TYR A 101 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.738 Fit side-chains REVERT: A 51 ARG cc_start: 0.6384 (ptp-170) cc_final: 0.6054 (ptp-170) REVERT: A 110 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8469 (tm) REVERT: A 127 GLN cc_start: 0.5919 (mp10) cc_final: 0.5553 (mt0) REVERT: A 179 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: A 194 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8041 (mp) REVERT: A 334 MET cc_start: 0.8526 (mmt) cc_final: 0.8129 (mmp) REVERT: A 463 THR cc_start: 0.7725 (t) cc_final: 0.7476 (t) REVERT: A 514 LYS cc_start: 0.7003 (tttt) cc_final: 0.6720 (ttpp) REVERT: B 52 ARG cc_start: 0.7648 (ptp90) cc_final: 0.7331 (ptp-170) REVERT: B 59 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6912 (ptm-80) REVERT: B 110 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8443 (tm) REVERT: B 127 GLN cc_start: 0.5897 (mp10) cc_final: 0.5536 (mt0) REVERT: B 144 TRP cc_start: 0.4869 (OUTLIER) cc_final: 0.2947 (t60) REVERT: B 179 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: B 334 MET cc_start: 0.8531 (mmt) cc_final: 0.8135 (mmp) REVERT: B 462 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7314 (mm) REVERT: B 463 THR cc_start: 0.7737 (t) cc_final: 0.7481 (t) outliers start: 35 outliers final: 9 residues processed: 117 average time/residue: 0.9247 time to fit residues: 115.0945 Evaluate side-chains 102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 144 TRP Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 144 TRP Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 462 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 151 HIS B 62 ASN B 151 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6320 Z= 0.195 Angle : 0.507 6.390 8564 Z= 0.264 Chirality : 0.037 0.128 1000 Planarity : 0.003 0.034 1012 Dihedral : 3.471 15.230 820 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 5.15 % Allowed : 15.91 % Favored : 78.94 % 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: 2.55 (0.30), residues: 736 helix: 2.17 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -0.65 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 239 HIS 0.006 0.001 HIS B 151 PHE 0.012 0.001 PHE A 212 TYR 0.019 0.001 TYR A 101 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.765 Fit side-chains REVERT: A 51 ARG cc_start: 0.6333 (ptp-170) cc_final: 0.6081 (ptp-170) REVERT: A 110 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8486 (tm) REVERT: A 127 GLN cc_start: 0.5879 (OUTLIER) cc_final: 0.5409 (mt0) REVERT: A 179 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: A 334 MET cc_start: 0.8500 (mmt) cc_final: 0.8144 (mmp) REVERT: A 463 THR cc_start: 0.7727 (t) cc_final: 0.7501 (t) REVERT: A 514 LYS cc_start: 0.6982 (tttt) cc_final: 0.6740 (ttpp) REVERT: B 57 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6138 (tm-30) REVERT: B 59 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6905 (ptm-80) REVERT: B 95 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6407 (pt) REVERT: B 110 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8469 (tm) REVERT: B 127 GLN cc_start: 0.5889 (OUTLIER) cc_final: 0.5416 (mt0) REVERT: B 144 TRP cc_start: 0.4823 (OUTLIER) cc_final: 0.2918 (t60) REVERT: B 179 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: B 334 MET cc_start: 0.8514 (mmt) cc_final: 0.8151 (mmp) REVERT: B 462 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7313 (mm) REVERT: B 463 THR cc_start: 0.7759 (t) cc_final: 0.7505 (t) outliers start: 34 outliers final: 9 residues processed: 101 average time/residue: 0.9320 time to fit residues: 100.2766 Evaluate side-chains 93 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 144 TRP Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 144 TRP Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 462 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS A 207 GLN A 237 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS B 207 GLN B 237 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 6320 Z= 0.456 Angle : 0.645 5.633 8564 Z= 0.344 Chirality : 0.044 0.138 1000 Planarity : 0.005 0.039 1012 Dihedral : 3.966 15.787 820 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.30 % Allowed : 16.52 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.30), residues: 736 helix: 1.64 (0.20), residues: 598 sheet: None (None), residues: 0 loop : -0.64 (0.61), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 94 HIS 0.007 0.002 HIS A 567 PHE 0.020 0.003 PHE B 566 TYR 0.030 0.003 TYR A 101 ARG 0.005 0.001 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.772 Fit side-chains REVERT: A 51 ARG cc_start: 0.6594 (ptp-170) cc_final: 0.6222 (ptp-170) REVERT: A 104 MET cc_start: 0.8841 (mmm) cc_final: 0.8598 (mtp) REVERT: A 110 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8502 (tm) REVERT: A 127 GLN cc_start: 0.6125 (OUTLIER) cc_final: 0.5708 (mt0) REVERT: A 128 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7072 (tt) REVERT: A 179 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: A 462 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7574 (mm) REVERT: A 463 THR cc_start: 0.7732 (t) cc_final: 0.7503 (t) REVERT: A 514 LYS cc_start: 0.6933 (tttt) cc_final: 0.6664 (ttpp) REVERT: B 57 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6258 (tm-30) REVERT: B 59 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6982 (ptm-80) REVERT: B 104 MET cc_start: 0.8817 (mmm) cc_final: 0.8590 (mtp) REVERT: B 110 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8493 (tm) REVERT: B 127 GLN cc_start: 0.6159 (OUTLIER) cc_final: 0.5724 (mt0) REVERT: B 179 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: B 462 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7597 (mm) REVERT: B 463 THR cc_start: 0.7746 (t) cc_final: 0.7525 (t) outliers start: 35 outliers final: 15 residues processed: 104 average time/residue: 0.9877 time to fit residues: 109.4946 Evaluate side-chains 101 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 207 GLN B 62 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6320 Z= 0.215 Angle : 0.515 7.057 8564 Z= 0.273 Chirality : 0.037 0.116 1000 Planarity : 0.003 0.039 1012 Dihedral : 3.707 15.136 820 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.61 % Allowed : 16.21 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.30), residues: 736 helix: 1.95 (0.20), residues: 602 sheet: None (None), residues: 0 loop : -0.89 (0.59), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 54 HIS 0.004 0.001 HIS A 567 PHE 0.009 0.001 PHE B 335 TYR 0.018 0.001 TYR A 101 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 0.782 Fit side-chains REVERT: A 51 ARG cc_start: 0.6507 (ptp-170) cc_final: 0.6154 (ptp-170) REVERT: A 110 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8523 (tm) REVERT: A 127 GLN cc_start: 0.6040 (OUTLIER) cc_final: 0.5547 (mt0) REVERT: A 128 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7017 (tt) REVERT: A 179 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: A 334 MET cc_start: 0.8427 (mmt) cc_final: 0.8162 (mmp) REVERT: A 462 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7297 (mm) REVERT: A 463 THR cc_start: 0.7764 (t) cc_final: 0.7516 (t) REVERT: A 514 LYS cc_start: 0.7001 (tttt) cc_final: 0.6689 (ttpp) REVERT: A 552 TYR cc_start: 0.7164 (m-80) cc_final: 0.6777 (m-80) REVERT: B 59 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6909 (ptm-80) REVERT: B 110 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8511 (tm) REVERT: B 127 GLN cc_start: 0.5977 (OUTLIER) cc_final: 0.5497 (mt0) REVERT: B 144 TRP cc_start: 0.4846 (OUTLIER) cc_final: 0.3541 (p90) REVERT: B 179 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6349 (mp0) REVERT: B 334 MET cc_start: 0.8473 (mmt) cc_final: 0.8168 (mmp) REVERT: B 462 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7307 (mm) REVERT: B 463 THR cc_start: 0.7765 (t) cc_final: 0.7523 (t) REVERT: B 552 TYR cc_start: 0.7171 (m-80) cc_final: 0.6787 (m-80) outliers start: 37 outliers final: 11 residues processed: 108 average time/residue: 0.9461 time to fit residues: 108.9764 Evaluate side-chains 97 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 144 TRP Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 70 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6320 Z= 0.264 Angle : 0.542 6.364 8564 Z= 0.288 Chirality : 0.039 0.112 1000 Planarity : 0.004 0.038 1012 Dihedral : 3.729 15.182 820 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.39 % Allowed : 17.58 % Favored : 78.03 % 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: 2.14 (0.30), residues: 736 helix: 1.88 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.70 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 54 HIS 0.004 0.001 HIS B 567 PHE 0.012 0.002 PHE B 335 TYR 0.021 0.002 TYR A 101 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 1.008 Fit side-chains REVERT: A 51 ARG cc_start: 0.6555 (ptp-170) cc_final: 0.6163 (ptp-170) REVERT: A 110 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8538 (tm) REVERT: A 127 GLN cc_start: 0.6054 (OUTLIER) cc_final: 0.5556 (mt0) REVERT: A 128 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6989 (tt) REVERT: A 179 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6545 (mp0) REVERT: A 462 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7297 (mm) REVERT: A 463 THR cc_start: 0.7745 (t) cc_final: 0.7505 (t) REVERT: A 514 LYS cc_start: 0.6985 (tttt) cc_final: 0.6681 (ttpp) REVERT: B 59 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6935 (ptm-80) REVERT: B 110 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8517 (tm) REVERT: B 127 GLN cc_start: 0.6053 (OUTLIER) cc_final: 0.5545 (mt0) REVERT: B 179 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: B 462 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7291 (mm) REVERT: B 463 THR cc_start: 0.7765 (t) cc_final: 0.7529 (t) outliers start: 29 outliers final: 14 residues processed: 100 average time/residue: 0.9241 time to fit residues: 98.4959 Evaluate side-chains 98 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 207 GLN B 62 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6320 Z= 0.183 Angle : 0.508 7.020 8564 Z= 0.266 Chirality : 0.037 0.114 1000 Planarity : 0.003 0.037 1012 Dihedral : 3.558 14.905 820 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.85 % Allowed : 17.58 % Favored : 77.58 % 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: 2.41 (0.30), residues: 736 helix: 2.08 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.67 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 239 HIS 0.003 0.001 HIS B 567 PHE 0.008 0.001 PHE B 563 TYR 0.017 0.001 TYR A 101 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.789 Fit side-chains REVERT: A 51 ARG cc_start: 0.6546 (ptp-170) cc_final: 0.6157 (ptp-170) REVERT: A 62 ASN cc_start: 0.7517 (OUTLIER) cc_final: 0.7219 (t0) REVERT: A 104 MET cc_start: 0.8647 (mmm) cc_final: 0.8187 (mtp) REVERT: A 110 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8520 (tm) REVERT: A 127 GLN cc_start: 0.5965 (OUTLIER) cc_final: 0.5487 (mt0) REVERT: A 128 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6965 (tt) REVERT: A 144 TRP cc_start: 0.4622 (OUTLIER) cc_final: 0.3876 (p90) REVERT: A 179 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: A 462 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7237 (mm) REVERT: A 463 THR cc_start: 0.7747 (t) cc_final: 0.7510 (t) REVERT: A 514 LYS cc_start: 0.7006 (tttt) cc_final: 0.6706 (ttpp) REVERT: B 62 ASN cc_start: 0.7549 (OUTLIER) cc_final: 0.7256 (t0) REVERT: B 104 MET cc_start: 0.8613 (mmm) cc_final: 0.8355 (mtp) REVERT: B 110 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8525 (tm) REVERT: B 127 GLN cc_start: 0.5967 (OUTLIER) cc_final: 0.5482 (mt0) REVERT: B 179 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: B 191 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6108 (mttm) REVERT: B 462 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7296 (mm) REVERT: B 463 THR cc_start: 0.7744 (t) cc_final: 0.7512 (t) outliers start: 32 outliers final: 9 residues processed: 102 average time/residue: 0.9110 time to fit residues: 98.7630 Evaluate side-chains 98 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 144 TRP Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 207 GLN B 62 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6320 Z= 0.199 Angle : 0.513 6.457 8564 Z= 0.271 Chirality : 0.037 0.111 1000 Planarity : 0.003 0.037 1012 Dihedral : 3.542 15.052 820 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.79 % Allowed : 18.79 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.30), residues: 736 helix: 2.13 (0.20), residues: 602 sheet: None (None), residues: 0 loop : -0.71 (0.59), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 54 HIS 0.004 0.001 HIS B 567 PHE 0.019 0.001 PHE A 181 TYR 0.017 0.001 TYR A 101 ARG 0.001 0.000 ARG A 430 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.727 Fit side-chains REVERT: A 51 ARG cc_start: 0.6527 (ptp-170) cc_final: 0.6138 (ptp-170) REVERT: A 62 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.7157 (t0) REVERT: A 104 MET cc_start: 0.8656 (mmm) cc_final: 0.8225 (mtp) REVERT: A 110 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8521 (tm) REVERT: A 127 GLN cc_start: 0.5996 (OUTLIER) cc_final: 0.5514 (mt0) REVERT: A 128 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6966 (tt) REVERT: A 144 TRP cc_start: 0.4627 (OUTLIER) cc_final: 0.3876 (p90) REVERT: A 179 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: A 462 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7231 (mm) REVERT: A 463 THR cc_start: 0.7710 (t) cc_final: 0.7475 (t) REVERT: A 514 LYS cc_start: 0.7002 (tttt) cc_final: 0.6708 (ttpp) REVERT: B 62 ASN cc_start: 0.7481 (OUTLIER) cc_final: 0.7202 (t0) REVERT: B 104 MET cc_start: 0.8669 (mmm) cc_final: 0.8399 (mtp) REVERT: B 110 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8509 (tm) REVERT: B 127 GLN cc_start: 0.5987 (OUTLIER) cc_final: 0.5501 (mt0) REVERT: B 144 TRP cc_start: 0.4723 (OUTLIER) cc_final: 0.3450 (p90) REVERT: B 179 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: B 191 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6082 (mttm) REVERT: B 334 MET cc_start: 0.8482 (mmt) cc_final: 0.8128 (mmp) REVERT: B 462 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7258 (mm) REVERT: B 463 THR cc_start: 0.7741 (t) cc_final: 0.7508 (t) outliers start: 25 outliers final: 9 residues processed: 95 average time/residue: 0.9035 time to fit residues: 91.8063 Evaluate side-chains 96 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 144 TRP Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 144 TRP Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 53 optimal weight: 0.0070 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 207 GLN B 62 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103479 restraints weight = 9268.179| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.02 r_work: 0.3152 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6320 Z= 0.224 Angle : 0.521 6.222 8564 Z= 0.277 Chirality : 0.038 0.123 1000 Planarity : 0.003 0.037 1012 Dihedral : 3.559 15.376 820 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.94 % Allowed : 18.64 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.30), residues: 736 helix: 2.09 (0.20), residues: 602 sheet: None (None), residues: 0 loop : -0.73 (0.59), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 54 HIS 0.004 0.001 HIS B 567 PHE 0.010 0.001 PHE B 335 TYR 0.018 0.001 TYR A 101 ARG 0.002 0.000 ARG A 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2366.50 seconds wall clock time: 44 minutes 40.26 seconds (2680.26 seconds total)