Starting phenix.real_space_refine on Fri Dec 27 06:22:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ex8_28654/12_2024/8ex8_28654.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ex8_28654/12_2024/8ex8_28654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ex8_28654/12_2024/8ex8_28654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ex8_28654/12_2024/8ex8_28654.map" model { file = "/net/cci-nas-00/data/ceres_data/8ex8_28654/12_2024/8ex8_28654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ex8_28654/12_2024/8ex8_28654.cif" } resolution = 4.17 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= 0.011 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 17 5.16 5 C 2090 2.51 5 N 524 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3177 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3177 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 12, 'TRANS': 401} Chain breaks: 2 Time building chain proxies: 3.23, per 1000 atoms: 1.02 Number of scatterers: 3177 At special positions: 0 Unit cell: (72.688, 62.304, 75.284, 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 17 16.00 O 546 8.00 N 524 7.00 C 2090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 388.2 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 91.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 99 through 121 removed outlier: 3.876A pdb=" N ALA A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 136 through 160 removed outlier: 3.909A pdb=" N ALA A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE A 148 " --> pdb=" O GLN A 144 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 166 through 186 removed outlier: 3.900A pdb=" N ILE A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 removed outlier: 3.930A pdb=" N VAL A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TYR A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 223 through 256 removed outlier: 4.777A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.540A pdb=" N TYR A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.534A pdb=" N TRP A 261 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 280 removed outlier: 4.282A pdb=" N VAL A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 removed outlier: 3.522A pdb=" N ARG A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 347 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 361 through 390 removed outlier: 4.510A pdb=" N LEU A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 422 removed outlier: 4.557A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.632A pdb=" N VAL A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 455 through 470 Processing helix chain 'A' and resid 474 through 490 removed outlier: 3.755A pdb=" N THR A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 539 removed outlier: 3.810A pdb=" N PHE A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 780 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.85 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 970 1.34 - 1.46: 709 1.46 - 1.58: 1546 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3251 Sorted by residual: bond pdb=" N VAL A 181 " pdb=" CA VAL A 181 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.14e-02 7.69e+03 7.09e+00 bond pdb=" N ILE A 175 " pdb=" CA ILE A 175 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.17e-02 7.31e+03 6.60e+00 bond pdb=" N PHE A 177 " pdb=" CA PHE A 177 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.92e+00 bond pdb=" N SER A 179 " pdb=" CA SER A 179 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.33e+00 bond pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.26e+00 ... (remaining 3246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 4229 2.12 - 4.23: 154 4.23 - 6.35: 28 6.35 - 8.47: 3 8.47 - 10.58: 2 Bond angle restraints: 4416 Sorted by residual: angle pdb=" N PHE A 236 " pdb=" CA PHE A 236 " pdb=" C PHE A 236 " ideal model delta sigma weight residual 112.38 107.11 5.27 1.22e+00 6.72e-01 1.87e+01 angle pdb=" CA VAL A 181 " pdb=" C VAL A 181 " pdb=" O VAL A 181 " ideal model delta sigma weight residual 121.27 117.28 3.99 1.04e+00 9.25e-01 1.47e+01 angle pdb=" N ILE A 175 " pdb=" CA ILE A 175 " pdb=" C ILE A 175 " ideal model delta sigma weight residual 110.42 107.37 3.05 9.60e-01 1.09e+00 1.01e+01 angle pdb=" CA TYR A 116 " pdb=" CB TYR A 116 " pdb=" CG TYR A 116 " ideal model delta sigma weight residual 113.90 108.27 5.63 1.80e+00 3.09e-01 9.80e+00 angle pdb=" CA CYS A 173 " pdb=" C CYS A 173 " pdb=" O CYS A 173 " ideal model delta sigma weight residual 120.82 117.54 3.28 1.05e+00 9.07e-01 9.76e+00 ... (remaining 4411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 1642 15.20 - 30.41: 166 30.41 - 45.61: 55 45.61 - 60.81: 7 60.81 - 76.01: 2 Dihedral angle restraints: 1872 sinusoidal: 692 harmonic: 1180 Sorted by residual: dihedral pdb=" CA MET A 334 " pdb=" C MET A 334 " pdb=" N TRP A 335 " pdb=" CA TRP A 335 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU A 364 " pdb=" C LEU A 364 " pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA THR A 223 " pdb=" C THR A 223 " pdb=" N LYS A 224 " pdb=" CA LYS A 224 " ideal model delta harmonic sigma weight residual -180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 1869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 360 0.049 - 0.098: 124 0.098 - 0.147: 35 0.147 - 0.197: 0 0.197 - 0.246: 2 Chirality restraints: 521 Sorted by residual: chirality pdb=" CA TRP A 178 " pdb=" N TRP A 178 " pdb=" C TRP A 178 " pdb=" CB TRP A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE A 175 " pdb=" N ILE A 175 " pdb=" C ILE A 175 " pdb=" CB ILE A 175 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL A 513 " pdb=" CA VAL A 513 " pdb=" CG1 VAL A 513 " pdb=" CG2 VAL A 513 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 518 not shown) Planarity restraints: 539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 238 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A 239 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 116 " -0.016 2.00e-02 2.50e+03 1.50e-02 4.50e+00 pdb=" CG TYR A 116 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 116 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 116 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 116 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 116 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 116 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 481 " -0.014 2.00e-02 2.50e+03 1.34e-02 3.14e+00 pdb=" CG PHE A 481 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 481 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 481 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 481 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 481 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 481 " -0.001 2.00e-02 2.50e+03 ... (remaining 536 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 92 2.69 - 3.24: 3787 3.24 - 3.79: 5401 3.79 - 4.35: 6672 4.35 - 4.90: 10236 Nonbonded interactions: 26188 Sorted by model distance: nonbonded pdb=" OG SER A 145 " pdb=" OH TYR A 477 " model vdw 2.138 3.040 nonbonded pdb=" O ILE A 486 " pdb=" OG SER A 489 " model vdw 2.155 3.040 nonbonded pdb=" O LEU A 320 " pdb=" OG SER A 323 " model vdw 2.194 3.040 nonbonded pdb=" O PRO A 239 " pdb=" OG SER A 242 " model vdw 2.226 3.040 nonbonded pdb=" O ASP A 118 " pdb=" NH2 ARG A 200 " model vdw 2.231 3.120 ... (remaining 26183 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.130 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.007 0.052 3251 Z= 0.459 Angle : 0.963 10.583 4416 Z= 0.561 Chirality : 0.052 0.246 521 Planarity : 0.006 0.055 539 Dihedral : 13.999 76.014 1116 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.41), residues: 408 helix: -0.32 (0.27), residues: 335 sheet: None (None), residues: 0 loop : -0.39 (0.91), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 440 HIS 0.006 0.002 HIS A 341 PHE 0.031 0.003 PHE A 481 TYR 0.036 0.004 TYR A 116 ARG 0.006 0.001 ARG A 530 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 514 LEU cc_start: 0.8583 (mm) cc_final: 0.8376 (mm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1403 time to fit residues: 9.5575 Evaluate side-chains 41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3251 Z= 0.195 Angle : 0.630 6.656 4416 Z= 0.341 Chirality : 0.043 0.152 521 Planarity : 0.005 0.041 539 Dihedral : 5.079 20.448 444 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % 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: 0.13 (0.43), residues: 408 helix: 0.25 (0.27), residues: 356 sheet: None (None), residues: 0 loop : -0.07 (1.11), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 178 HIS 0.003 0.002 HIS A 260 PHE 0.018 0.002 PHE A 366 TYR 0.027 0.002 TYR A 116 ARG 0.001 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 514 LEU cc_start: 0.8549 (mm) cc_final: 0.8332 (mm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1270 time to fit residues: 10.6437 Evaluate side-chains 50 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3251 Z= 0.184 Angle : 0.630 8.129 4416 Z= 0.335 Chirality : 0.043 0.153 521 Planarity : 0.005 0.042 539 Dihedral : 4.889 20.892 444 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.30 % Allowed : 3.58 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.44), residues: 408 helix: 0.65 (0.28), residues: 352 sheet: None (None), residues: 0 loop : 0.45 (1.08), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS A 132 PHE 0.020 0.001 PHE A 366 TYR 0.018 0.002 TYR A 235 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7422 (tp) REVERT: A 387 TRP cc_start: 0.6026 (t-100) cc_final: 0.5503 (t60) REVERT: A 514 LEU cc_start: 0.8660 (mm) cc_final: 0.8458 (mm) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1426 time to fit residues: 13.0688 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3251 Z= 0.201 Angle : 0.629 6.504 4416 Z= 0.335 Chirality : 0.044 0.161 521 Planarity : 0.005 0.040 539 Dihedral : 4.828 21.137 444 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % 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: 0.84 (0.44), residues: 408 helix: 0.70 (0.28), residues: 352 sheet: None (None), residues: 0 loop : 0.38 (1.07), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.021 0.001 PHE A 366 TYR 0.016 0.002 TYR A 116 ARG 0.003 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.317 Fit side-chains REVERT: A 466 THR cc_start: 0.8738 (p) cc_final: 0.8325 (t) REVERT: A 510 PHE cc_start: 0.7619 (m-10) cc_final: 0.7240 (m-10) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1171 time to fit residues: 10.7292 Evaluate side-chains 52 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3251 Z= 0.185 Angle : 0.613 6.404 4416 Z= 0.325 Chirality : 0.043 0.148 521 Planarity : 0.005 0.038 539 Dihedral : 4.748 21.246 444 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: 0.88 (0.44), residues: 408 helix: 0.71 (0.28), residues: 358 sheet: None (None), residues: 0 loop : 0.53 (1.22), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 496 HIS 0.002 0.001 HIS A 341 PHE 0.019 0.001 PHE A 366 TYR 0.013 0.001 TYR A 116 ARG 0.003 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.354 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1116 time to fit residues: 10.0676 Evaluate side-chains 55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.0040 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3251 Z= 0.172 Angle : 0.625 6.296 4416 Z= 0.326 Chirality : 0.043 0.147 521 Planarity : 0.005 0.038 539 Dihedral : 4.704 22.731 444 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.44), residues: 408 helix: 0.77 (0.28), residues: 356 sheet: None (None), residues: 0 loop : 0.28 (1.16), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 178 HIS 0.002 0.001 HIS A 341 PHE 0.023 0.001 PHE A 498 TYR 0.013 0.001 TYR A 116 ARG 0.002 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8301 (tt0) cc_final: 0.7058 (tt0) REVERT: A 221 LEU cc_start: 0.7640 (tp) cc_final: 0.7096 (tt) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1155 time to fit residues: 10.4981 Evaluate side-chains 55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3251 Z= 0.173 Angle : 0.613 6.338 4416 Z= 0.320 Chirality : 0.042 0.147 521 Planarity : 0.005 0.037 539 Dihedral : 4.643 21.324 444 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: 0.99 (0.44), residues: 408 helix: 0.79 (0.28), residues: 357 sheet: None (None), residues: 0 loop : 0.48 (1.18), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 496 HIS 0.001 0.001 HIS A 468 PHE 0.020 0.001 PHE A 498 TYR 0.012 0.001 TYR A 116 ARG 0.003 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.331 Fit side-chains REVERT: A 334 MET cc_start: 0.7737 (ttm) cc_final: 0.7362 (tmm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1099 time to fit residues: 9.1088 Evaluate side-chains 55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3251 Z= 0.195 Angle : 0.630 6.334 4416 Z= 0.330 Chirality : 0.043 0.146 521 Planarity : 0.005 0.043 539 Dihedral : 4.725 23.319 444 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.44), residues: 408 helix: 0.80 (0.28), residues: 356 sheet: None (None), residues: 0 loop : 0.63 (1.15), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 178 HIS 0.002 0.001 HIS A 341 PHE 0.019 0.001 PHE A 498 TYR 0.015 0.001 TYR A 116 ARG 0.003 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.344 Fit side-chains REVERT: A 221 LEU cc_start: 0.7790 (tp) cc_final: 0.7536 (tt) REVERT: A 334 MET cc_start: 0.7786 (ttm) cc_final: 0.7473 (tmm) REVERT: A 404 MET cc_start: 0.7335 (mmp) cc_final: 0.7124 (mmp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0977 time to fit residues: 8.4373 Evaluate side-chains 55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3251 Z= 0.197 Angle : 0.628 6.289 4416 Z= 0.330 Chirality : 0.043 0.146 521 Planarity : 0.005 0.040 539 Dihedral : 4.737 24.258 444 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: 0.92 (0.44), residues: 408 helix: 0.72 (0.28), residues: 356 sheet: None (None), residues: 0 loop : 0.68 (1.14), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 440 HIS 0.002 0.001 HIS A 341 PHE 0.017 0.001 PHE A 366 TYR 0.018 0.001 TYR A 116 ARG 0.003 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.354 Fit side-chains REVERT: A 116 TYR cc_start: 0.8448 (m-80) cc_final: 0.8038 (m-80) REVERT: A 221 LEU cc_start: 0.7807 (tp) cc_final: 0.7422 (tt) REVERT: A 238 ILE cc_start: 0.8344 (mt) cc_final: 0.8140 (mt) REVERT: A 334 MET cc_start: 0.7772 (ttm) cc_final: 0.7415 (tmm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1085 time to fit residues: 9.0103 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0070 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3251 Z= 0.206 Angle : 0.640 6.284 4416 Z= 0.338 Chirality : 0.044 0.146 521 Planarity : 0.005 0.039 539 Dihedral : 4.786 23.517 444 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.44), residues: 408 helix: 0.68 (0.28), residues: 359 sheet: None (None), residues: 0 loop : 0.34 (1.19), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 496 HIS 0.002 0.001 HIS A 341 PHE 0.023 0.001 PHE A 498 TYR 0.012 0.002 TYR A 116 ARG 0.003 0.000 ARG A 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.317 Fit side-chains REVERT: A 116 TYR cc_start: 0.8453 (m-80) cc_final: 0.8154 (m-10) REVERT: A 334 MET cc_start: 0.7779 (ttm) cc_final: 0.7389 (tmm) REVERT: A 404 MET cc_start: 0.7380 (mmp) cc_final: 0.7162 (mmp) REVERT: A 526 PHE cc_start: 0.4681 (t80) cc_final: 0.4452 (t80) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1074 time to fit residues: 8.5506 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 40 optimal weight: 8.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 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 = 0.4228 r_free = 0.4228 target = 0.183569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.150775 restraints weight = 5038.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150699 restraints weight = 5026.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.152028 restraints weight = 4094.707| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3251 Z= 0.174 Angle : 0.618 6.261 4416 Z= 0.323 Chirality : 0.043 0.145 521 Planarity : 0.005 0.039 539 Dihedral : 4.725 22.917 444 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.44), residues: 408 helix: 0.81 (0.28), residues: 355 sheet: None (None), residues: 0 loop : 0.47 (1.11), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 496 HIS 0.001 0.001 HIS A 341 PHE 0.023 0.001 PHE A 498 TYR 0.016 0.001 TYR A 116 ARG 0.003 0.000 ARG A 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1039.01 seconds wall clock time: 19 minutes 45.38 seconds (1185.38 seconds total)