Starting phenix.real_space_refine on Tue Feb 11 15:25:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7urd_26709/02_2025/7urd_26709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7urd_26709/02_2025/7urd_26709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7urd_26709/02_2025/7urd_26709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7urd_26709/02_2025/7urd_26709.map" model { file = "/net/cci-nas-00/data/ceres_data/7urd_26709/02_2025/7urd_26709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7urd_26709/02_2025/7urd_26709.cif" } resolution = 2.92 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= 0.007 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 35 5.16 5 C 3642 2.51 5 N 897 2.21 5 O 959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5534 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3449 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 158 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 172 Unusual residues: {' ZN': 1, 'AJP': 1, 'CLR': 2, 'O50': 1, 'OLA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 9 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2833 SG CYS A 370 56.521 29.274 19.732 1.00108.35 S ATOM 2880 SG CYS A 376 55.636 28.723 23.034 1.00118.02 S ATOM 2908 SG CYS A 380 59.361 29.098 21.112 1.00127.74 S Time building chain proxies: 4.04, per 1000 atoms: 0.73 Number of scatterers: 5534 At special positions: 0 Unit cell: (98.77, 69.72, 93.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 35 16.00 O 959 8.00 N 897 7.00 C 3642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " 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: 1.70 Conformation dependent library (CDL) restraints added in 870.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 506 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 370 " pdb="ZN ZN A 506 " - pdb=" ND1 HIS A 382 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 376 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 380 " Number of angles added : 3 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1254 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 7 sheets defined 51.5% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 5 through 28 removed outlier: 4.921A pdb=" N LEU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Proline residue: A 20 - end of helix Processing helix chain 'A' and resid 29 through 43 Processing helix chain 'A' and resid 48 through 68 Processing helix chain 'A' and resid 72 through 89 removed outlier: 3.952A pdb=" N LEU A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 111 Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.686A pdb=" N HIS A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 143 removed outlier: 3.570A pdb=" N ILE A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.842A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 removed outlier: 3.870A pdb=" N LEU A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 264 removed outlier: 3.654A pdb=" N VAL A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 292 through 301 removed outlier: 4.359A pdb=" N ASN A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 320 through 336 Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.610A pdb=" N ALA A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 410 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 439 through 455 removed outlier: 3.713A pdb=" N PHE A 446 " --> pdb=" O HIS A 442 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 103 removed outlier: 3.891A pdb=" N PHE L 103 " --> pdb=" O PRO L 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 51 removed outlier: 4.201A pdb=" N TYR H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.740A pdb=" N SER H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 206 Processing sheet with id=AA3, first strand: chain 'L' and resid 24 through 27 removed outlier: 5.677A pdb=" N THR L 89 " --> pdb=" O THR L 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.863A pdb=" N LEU L 31 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP L 55 " --> pdb=" O LEU L 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.573A pdb=" N GLU H 29 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TRP H 66 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.573A pdb=" N GLU H 29 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 849 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: 1.58 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.19: 4 1.19 - 1.39: 2353 1.39 - 1.59: 3288 1.59 - 1.78: 10 1.78 - 1.98: 50 Bond restraints: 5705 Sorted by residual: bond pdb=" C07 AJP A 504 " pdb=" C08 AJP A 504 " ideal model delta sigma weight residual 1.550 1.980 -0.430 2.00e-02 2.50e+03 4.62e+02 bond pdb=" C01 AJP A 504 " pdb=" C02 AJP A 504 " ideal model delta sigma weight residual 1.521 1.947 -0.426 2.00e-02 2.50e+03 4.55e+02 bond pdb=" C08 AJP A 504 " pdb=" O09 AJP A 504 " ideal model delta sigma weight residual 1.410 0.998 0.412 2.00e-02 2.50e+03 4.24e+02 bond pdb=" C02 AJP A 504 " pdb=" C03 AJP A 504 " ideal model delta sigma weight residual 1.525 1.133 0.392 2.00e-02 2.50e+03 3.85e+02 bond pdb=" C05 AJP A 504 " pdb=" O09 AJP A 504 " ideal model delta sigma weight residual 1.407 1.784 -0.377 2.00e-02 2.50e+03 3.55e+02 ... (remaining 5700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 7706 4.20 - 8.40: 54 8.40 - 12.60: 7 12.60 - 16.80: 4 16.80 - 20.99: 1 Bond angle restraints: 7772 Sorted by residual: angle pdb=" C06 AJP A 504 " pdb=" C07 AJP A 504 " pdb=" C12 AJP A 504 " ideal model delta sigma weight residual 120.30 141.29 -20.99 3.00e+00 1.11e-01 4.90e+01 angle pdb=" C11 AJP A 504 " pdb=" C12 AJP A 504 " pdb=" C81 AJP A 504 " ideal model delta sigma weight residual 114.35 98.09 16.26 3.00e+00 1.11e-01 2.94e+01 angle pdb=" C07 AJP A 504 " pdb=" C12 AJP A 504 " pdb=" C13 AJP A 504 " ideal model delta sigma weight residual 114.18 129.16 -14.98 3.00e+00 1.11e-01 2.49e+01 angle pdb=" C07 AJP A 504 " pdb=" C08 AJP A 504 " pdb=" C10 AJP A 504 " ideal model delta sigma weight residual 107.39 93.44 13.95 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C PRO A 377 " pdb=" N PRO A 378 " pdb=" CA PRO A 378 " ideal model delta sigma weight residual 119.47 124.77 -5.30 1.16e+00 7.43e-01 2.09e+01 ... (remaining 7767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 3322 34.55 - 69.10: 79 69.10 - 103.65: 34 103.65 - 138.20: 37 138.20 - 172.75: 14 Dihedral angle restraints: 3486 sinusoidal: 1524 harmonic: 1962 Sorted by residual: dihedral pdb=" CA TYR H 74 " pdb=" C TYR H 74 " pdb=" N VAL H 75 " pdb=" CA VAL H 75 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" C06 AJP A 504 " pdb=" C07 AJP A 504 " pdb=" C12 AJP A 504 " pdb=" C13 AJP A 504 " ideal model delta sinusoidal sigma weight residual 109.15 -63.60 172.75 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C12 AJP A 504 " pdb=" C10 AJP A 504 " pdb=" C11 AJP A 504 " pdb=" O82 AJP A 504 " ideal model delta sinusoidal sigma weight residual 287.38 117.68 169.70 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 3483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.107: 849 1.107 - 2.213: 0 2.213 - 3.320: 0 3.320 - 4.426: 1 4.426 - 5.533: 24 Chirality restraints: 874 Sorted by residual: chirality pdb=" C15 AJP A 504 " pdb=" C14 AJP A 504 " pdb=" C16 AJP A 504 " pdb=" C20 AJP A 504 " both_signs ideal model delta sigma weight residual False -2.42 3.11 -5.53 2.00e-01 2.50e+01 7.65e+02 chirality pdb=" C16 AJP A 504 " pdb=" C11 AJP A 504 " pdb=" C15 AJP A 504 " pdb=" C17 AJP A 504 " both_signs ideal model delta sigma weight residual False -2.70 2.76 -5.46 2.00e-01 2.50e+01 7.45e+02 chirality pdb=" C20 AJP A 504 " pdb=" C15 AJP A 504 " pdb=" C19 AJP A 504 " pdb=" C21 AJP A 504 " both_signs ideal model delta sigma weight residual False 2.96 -2.42 5.38 2.00e-01 2.50e+01 7.23e+02 ... (remaining 871 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 215 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 216 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 219 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 220 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 14 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C LEU A 14 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 14 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 15 " -0.009 2.00e-02 2.50e+03 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 267 2.72 - 3.27: 5456 3.27 - 3.81: 9026 3.81 - 4.36: 11401 4.36 - 4.90: 19866 Nonbonded interactions: 46016 Sorted by model distance: nonbonded pdb=" OG SER A 242 " pdb=" OD1 ASP A 413 " model vdw 2.177 3.040 nonbonded pdb=" NH1 ARG A 360 " pdb=" O VAL A 371 " model vdw 2.196 3.120 nonbonded pdb=" OG SER H 26 " pdb=" OG SER H 40 " model vdw 2.251 3.040 nonbonded pdb=" OG SER L 27 " pdb=" OG1 THR L 42 " model vdw 2.266 3.040 nonbonded pdb=" OG SER A 79 " pdb=" OH TYR A 160 " model vdw 2.280 3.040 ... (remaining 46011 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.050 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.940 Find NCS groups from input model: 0.060 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:14.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.017 0.430 5705 Z= 1.120 Angle : 0.954 20.994 7772 Z= 0.412 Chirality : 0.833 5.533 874 Planarity : 0.004 0.043 924 Dihedral : 26.242 172.752 2217 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -2.44 (0.28), residues: 666 helix: -0.91 (0.25), residues: 324 sheet: -1.58 (0.42), residues: 129 loop : -2.50 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.006 0.001 HIS A 94 PHE 0.018 0.001 PHE A 403 TYR 0.013 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7350 (mmt180) cc_final: 0.6938 (mtm180) REVERT: A 361 LYS cc_start: 0.7957 (tttt) cc_final: 0.7605 (ttpt) REVERT: A 432 HIS cc_start: 0.8143 (t-90) cc_final: 0.7735 (t70) REVERT: L 23 HIS cc_start: 0.8141 (m-70) cc_final: 0.7933 (m-70) REVERT: H 101 GLN cc_start: 0.8481 (tt0) cc_final: 0.8253 (tt0) REVERT: H 119 TYR cc_start: 0.6625 (t80) cc_final: 0.6393 (t80) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 1.1959 time to fit residues: 126.3270 Evaluate side-chains 73 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 24 GLN A 66 HIS A 91 HIS A 94 HIS A 174 HIS A 247 HIS L 111 HIS H 52 ASN H 78 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.092066 restraints weight = 6250.320| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.27 r_work: 0.2839 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5705 Z= 0.181 Angle : 1.095 32.247 7772 Z= 0.414 Chirality : 0.118 2.107 874 Planarity : 0.004 0.040 924 Dihedral : 20.285 179.650 1059 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.73 % Allowed : 9.71 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.65 (0.32), residues: 666 helix: 0.62 (0.27), residues: 329 sheet: -1.03 (0.43), residues: 129 loop : -1.58 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.005 0.001 HIS A 53 PHE 0.015 0.001 PHE A 403 TYR 0.018 0.001 TYR A 83 ARG 0.005 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7084 (mmt) cc_final: 0.6372 (mtm) REVERT: A 124 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7168 (mtm-85) REVERT: A 142 ASP cc_start: 0.8505 (m-30) cc_final: 0.8194 (m-30) REVERT: A 154 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: A 235 ARG cc_start: 0.7444 (mmt180) cc_final: 0.6639 (mtm180) REVERT: A 270 GLU cc_start: 0.8296 (pt0) cc_final: 0.7999 (pt0) REVERT: A 361 LYS cc_start: 0.7647 (tttt) cc_final: 0.7366 (ttpt) REVERT: A 375 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7799 (mtt-85) REVERT: A 432 HIS cc_start: 0.7878 (t-90) cc_final: 0.7429 (t70) REVERT: L 23 HIS cc_start: 0.8292 (m-70) cc_final: 0.7994 (m-70) REVERT: H 101 GLN cc_start: 0.8217 (tt0) cc_final: 0.7951 (tt0) REVERT: H 119 TYR cc_start: 0.6777 (t80) cc_final: 0.6417 (t80) outliers start: 10 outliers final: 2 residues processed: 94 average time/residue: 1.2363 time to fit residues: 121.5575 Evaluate side-chains 88 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 375 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.091477 restraints weight = 6269.608| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.26 r_work: 0.2827 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5705 Z= 0.192 Angle : 1.076 31.573 7772 Z= 0.405 Chirality : 0.118 2.112 874 Planarity : 0.004 0.040 924 Dihedral : 20.153 179.594 1059 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.91 % Allowed : 13.69 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.17 (0.33), residues: 666 helix: 1.32 (0.28), residues: 329 sheet: -0.76 (0.43), residues: 129 loop : -1.17 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.004 0.001 HIS A 53 PHE 0.014 0.001 PHE A 403 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7746 (ptt) REVERT: A 109 MET cc_start: 0.7023 (mmt) cc_final: 0.6262 (mtm) REVERT: A 112 MET cc_start: 0.7890 (mtp) cc_final: 0.7677 (mtp) REVERT: A 124 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7226 (mtm-85) REVERT: A 142 ASP cc_start: 0.8492 (m-30) cc_final: 0.8285 (m-30) REVERT: A 154 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: A 235 ARG cc_start: 0.7435 (mmt180) cc_final: 0.6659 (mtm180) REVERT: A 270 GLU cc_start: 0.8169 (pt0) cc_final: 0.7960 (pt0) REVERT: A 375 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7804 (mtt-85) REVERT: A 432 HIS cc_start: 0.7839 (t-90) cc_final: 0.7499 (t-170) REVERT: L 81 ARG cc_start: 0.7866 (ptp90) cc_final: 0.7639 (ptp-170) REVERT: H 101 GLN cc_start: 0.8214 (tt0) cc_final: 0.7958 (tt0) REVERT: H 119 TYR cc_start: 0.6758 (t80) cc_final: 0.6400 (t80) outliers start: 11 outliers final: 1 residues processed: 89 average time/residue: 1.3320 time to fit residues: 123.7430 Evaluate side-chains 85 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 375 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.130517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.093923 restraints weight = 6263.356| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.34 r_work: 0.2888 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5705 Z= 0.167 Angle : 1.067 31.587 7772 Z= 0.399 Chirality : 0.118 2.116 874 Planarity : 0.004 0.039 924 Dihedral : 20.080 179.936 1059 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.60 % Allowed : 14.90 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 666 helix: 1.68 (0.29), residues: 330 sheet: -0.53 (0.44), residues: 128 loop : -0.82 (0.47), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.003 0.001 HIS A 53 PHE 0.013 0.001 PHE A 403 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7674 (ptt) REVERT: A 109 MET cc_start: 0.6982 (mmt) cc_final: 0.6270 (mtm) REVERT: A 112 MET cc_start: 0.7818 (mtp) cc_final: 0.7444 (mtt) REVERT: A 124 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7089 (mtt-85) REVERT: A 154 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: A 235 ARG cc_start: 0.7308 (mmt180) cc_final: 0.6584 (mtm180) REVERT: A 338 PHE cc_start: 0.7332 (t80) cc_final: 0.6395 (m-80) REVERT: A 375 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7844 (mtt-85) REVERT: A 432 HIS cc_start: 0.7833 (t-90) cc_final: 0.7462 (t-170) REVERT: L 89 THR cc_start: 0.8860 (p) cc_final: 0.8191 (m) REVERT: H 101 GLN cc_start: 0.8171 (tt0) cc_final: 0.7889 (tt0) REVERT: H 119 TYR cc_start: 0.6743 (t80) cc_final: 0.6406 (t80) outliers start: 15 outliers final: 3 residues processed: 94 average time/residue: 1.3024 time to fit residues: 128.0259 Evaluate side-chains 84 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 388 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.094173 restraints weight = 6242.415| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.32 r_work: 0.2886 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5705 Z= 0.169 Angle : 1.065 31.352 7772 Z= 0.398 Chirality : 0.118 2.109 874 Planarity : 0.004 0.039 924 Dihedral : 20.041 179.654 1059 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.39 % Allowed : 16.81 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 666 helix: 1.83 (0.29), residues: 331 sheet: -0.30 (0.45), residues: 127 loop : -0.88 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 128 HIS 0.003 0.001 HIS A 53 PHE 0.013 0.001 PHE A 403 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.6973 (mmt) cc_final: 0.6245 (mtm) REVERT: A 112 MET cc_start: 0.7757 (mtp) cc_final: 0.7544 (mtp) REVERT: A 124 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7166 (mtm-85) REVERT: A 154 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: A 235 ARG cc_start: 0.7320 (mmt180) cc_final: 0.6605 (mtm180) REVERT: A 338 PHE cc_start: 0.7363 (t80) cc_final: 0.6400 (m-80) REVERT: A 432 HIS cc_start: 0.7810 (t-90) cc_final: 0.7435 (t-170) REVERT: L 89 THR cc_start: 0.8817 (p) cc_final: 0.8182 (m) REVERT: H 29 GLU cc_start: 0.6821 (mt-10) cc_final: 0.5804 (mm-30) REVERT: H 101 GLN cc_start: 0.8099 (tt0) cc_final: 0.7836 (tt0) REVERT: H 119 TYR cc_start: 0.6758 (t80) cc_final: 0.6399 (t80) outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 1.2910 time to fit residues: 113.2859 Evaluate side-chains 86 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 388 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.091896 restraints weight = 6196.483| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.32 r_work: 0.2856 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5705 Z= 0.246 Angle : 1.085 31.479 7772 Z= 0.411 Chirality : 0.118 2.109 874 Planarity : 0.004 0.039 924 Dihedral : 20.092 179.699 1059 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.56 % Allowed : 17.68 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.83 (0.34), residues: 666 helix: 1.79 (0.29), residues: 331 sheet: -0.23 (0.45), residues: 129 loop : -0.93 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.003 0.001 HIS A 336 PHE 0.017 0.001 PHE A 403 TYR 0.018 0.001 TYR A 83 ARG 0.002 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.6980 (mmt) cc_final: 0.6220 (mtp) REVERT: A 122 LYS cc_start: 0.8175 (tttm) cc_final: 0.7948 (tttp) REVERT: A 124 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7186 (mtm-85) REVERT: A 154 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: A 235 ARG cc_start: 0.7312 (mmt180) cc_final: 0.6609 (mtm180) REVERT: A 432 HIS cc_start: 0.7759 (t-90) cc_final: 0.7348 (t70) REVERT: L 23 HIS cc_start: 0.8274 (m-70) cc_final: 0.7952 (m-70) REVERT: L 89 THR cc_start: 0.8816 (p) cc_final: 0.8140 (m) REVERT: H 30 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8176 (tm) REVERT: H 101 GLN cc_start: 0.8076 (tt0) cc_final: 0.7825 (tt0) REVERT: H 119 TYR cc_start: 0.6855 (t80) cc_final: 0.6455 (t80) outliers start: 9 outliers final: 3 residues processed: 85 average time/residue: 1.2969 time to fit residues: 115.0990 Evaluate side-chains 88 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain H residue 30 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.091692 restraints weight = 6251.089| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.35 r_work: 0.2855 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5705 Z= 0.232 Angle : 1.081 31.481 7772 Z= 0.408 Chirality : 0.118 2.107 874 Planarity : 0.004 0.040 924 Dihedral : 20.067 179.550 1059 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.91 % Allowed : 16.98 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.92 (0.34), residues: 666 helix: 1.81 (0.29), residues: 330 sheet: -0.13 (0.46), residues: 129 loop : -0.81 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.003 0.001 HIS A 336 PHE 0.016 0.001 PHE A 403 TYR 0.018 0.001 TYR A 83 ARG 0.001 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.6939 (mmt) cc_final: 0.6175 (mtm) REVERT: A 112 MET cc_start: 0.7803 (mtp) cc_final: 0.7410 (mtt) REVERT: A 124 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7177 (mtm-85) REVERT: A 154 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: A 235 ARG cc_start: 0.7302 (mmt180) cc_final: 0.6580 (mtm180) REVERT: A 432 HIS cc_start: 0.7757 (t-90) cc_final: 0.7339 (t70) REVERT: L 23 HIS cc_start: 0.8244 (m-70) cc_final: 0.7929 (m-70) REVERT: L 89 THR cc_start: 0.8804 (p) cc_final: 0.8181 (m) REVERT: H 32 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7556 (mtmm) REVERT: H 74 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.6869 (p90) REVERT: H 101 GLN cc_start: 0.8071 (tt0) cc_final: 0.7867 (tt0) REVERT: H 119 TYR cc_start: 0.6953 (t80) cc_final: 0.6617 (t80) outliers start: 11 outliers final: 3 residues processed: 84 average time/residue: 1.3378 time to fit residues: 117.2263 Evaluate side-chains 86 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 9 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.093292 restraints weight = 6137.287| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.33 r_work: 0.2901 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5705 Z= 0.189 Angle : 1.074 31.422 7772 Z= 0.403 Chirality : 0.118 2.106 874 Planarity : 0.004 0.040 924 Dihedral : 20.029 179.531 1059 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.91 % Allowed : 16.98 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.99 (0.34), residues: 666 helix: 1.89 (0.29), residues: 331 sheet: -0.13 (0.46), residues: 129 loop : -0.80 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.001 PHE A 403 TYR 0.018 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: A 72 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7641 (ptt) REVERT: A 109 MET cc_start: 0.6951 (mmt) cc_final: 0.6187 (mtm) REVERT: A 112 MET cc_start: 0.7768 (mtp) cc_final: 0.7353 (mtt) REVERT: A 124 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7089 (mtm-85) REVERT: A 154 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: A 235 ARG cc_start: 0.7345 (mmt180) cc_final: 0.6594 (mtm180) REVERT: A 432 HIS cc_start: 0.7759 (t-90) cc_final: 0.7507 (t-170) REVERT: L 23 HIS cc_start: 0.8227 (m-70) cc_final: 0.7887 (m-70) REVERT: L 89 THR cc_start: 0.8803 (p) cc_final: 0.8225 (m) REVERT: H 32 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7472 (mtmm) REVERT: H 74 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.6900 (p90) REVERT: H 119 TYR cc_start: 0.6923 (t80) cc_final: 0.6579 (t80) outliers start: 11 outliers final: 4 residues processed: 84 average time/residue: 1.2861 time to fit residues: 112.8467 Evaluate side-chains 87 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 0.0970 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.094313 restraints weight = 6186.308| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.34 r_work: 0.2896 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5705 Z= 0.158 Angle : 1.065 31.373 7772 Z= 0.397 Chirality : 0.118 2.104 874 Planarity : 0.004 0.040 924 Dihedral : 19.981 179.556 1059 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.56 % Allowed : 17.85 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.08 (0.34), residues: 666 helix: 1.94 (0.29), residues: 331 sheet: -0.11 (0.46), residues: 128 loop : -0.70 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 74 HIS 0.003 0.001 HIS A 53 PHE 0.012 0.001 PHE A 403 TYR 0.018 0.001 TYR A 83 ARG 0.002 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: A 109 MET cc_start: 0.6889 (mmt) cc_final: 0.6127 (mtm) REVERT: A 112 MET cc_start: 0.7723 (mtp) cc_final: 0.7314 (mtt) REVERT: A 124 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7097 (mtm-85) REVERT: A 154 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: A 235 ARG cc_start: 0.7356 (mmt180) cc_final: 0.6611 (mtm180) REVERT: A 432 HIS cc_start: 0.7862 (t-90) cc_final: 0.7443 (t70) REVERT: L 23 HIS cc_start: 0.8196 (m-70) cc_final: 0.7679 (m-70) REVERT: L 89 THR cc_start: 0.8782 (p) cc_final: 0.8280 (m) REVERT: H 74 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.6961 (p90) REVERT: H 119 TYR cc_start: 0.6894 (t80) cc_final: 0.6533 (t80) outliers start: 9 outliers final: 3 residues processed: 84 average time/residue: 1.2855 time to fit residues: 112.6097 Evaluate side-chains 83 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.094167 restraints weight = 6225.194| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.35 r_work: 0.2888 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5705 Z= 0.176 Angle : 1.071 31.445 7772 Z= 0.401 Chirality : 0.118 2.102 874 Planarity : 0.004 0.040 924 Dihedral : 19.987 179.783 1059 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.91 % Allowed : 18.02 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.18 (0.34), residues: 666 helix: 2.00 (0.29), residues: 331 sheet: -0.14 (0.45), residues: 137 loop : -0.55 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 128 HIS 0.003 0.001 HIS A 53 PHE 0.014 0.001 PHE A 62 TYR 0.018 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: A 72 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7574 (ptt) REVERT: A 109 MET cc_start: 0.6890 (mmt) cc_final: 0.6131 (mtm) REVERT: A 112 MET cc_start: 0.7733 (mtp) cc_final: 0.7326 (mtt) REVERT: A 124 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7097 (mtm-85) REVERT: A 154 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: A 235 ARG cc_start: 0.7352 (mmt180) cc_final: 0.6588 (mtm180) REVERT: A 432 HIS cc_start: 0.7836 (t-90) cc_final: 0.7421 (t70) REVERT: L 23 HIS cc_start: 0.8234 (m-70) cc_final: 0.7736 (m-70) REVERT: L 85 SER cc_start: 0.8288 (t) cc_final: 0.8055 (p) REVERT: L 89 THR cc_start: 0.8776 (p) cc_final: 0.8301 (m) REVERT: H 30 LEU cc_start: 0.8672 (tp) cc_final: 0.8418 (tm) REVERT: H 74 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.6985 (p90) REVERT: H 119 TYR cc_start: 0.6911 (t80) cc_final: 0.6559 (t80) outliers start: 11 outliers final: 3 residues processed: 84 average time/residue: 1.2679 time to fit residues: 111.5559 Evaluate side-chains 86 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 34 optimal weight: 0.0770 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.093574 restraints weight = 6272.368| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.36 r_work: 0.2885 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5705 Z= 0.187 Angle : 1.075 31.492 7772 Z= 0.404 Chirality : 0.118 2.101 874 Planarity : 0.004 0.040 924 Dihedral : 19.989 179.885 1059 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.73 % Allowed : 18.02 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.17 (0.34), residues: 666 helix: 1.98 (0.29), residues: 331 sheet: -0.11 (0.45), residues: 137 loop : -0.54 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 128 HIS 0.003 0.001 HIS A 336 PHE 0.014 0.001 PHE A 403 TYR 0.018 0.001 TYR A 83 ARG 0.002 0.000 ARG A 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4221.33 seconds wall clock time: 75 minutes 10.06 seconds (4510.06 seconds total)