Starting phenix.real_space_refine on Fri Dec 27 06:56:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cuj_27001/12_2024/8cuj_27001.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cuj_27001/12_2024/8cuj_27001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cuj_27001/12_2024/8cuj_27001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cuj_27001/12_2024/8cuj_27001.map" model { file = "/net/cci-nas-00/data/ceres_data/8cuj_27001/12_2024/8cuj_27001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cuj_27001/12_2024/8cuj_27001.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2153 2.51 5 N 526 2.21 5 O 593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3293 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3292 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.76, per 1000 atoms: 0.84 Number of scatterers: 3293 At special positions: 0 Unit cell: (73.272, 66.456, 79.236, 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 21 16.00 O 593 8.00 N 526 7.00 C 2153 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: 0.92 Conformation dependent library (CDL) restraints added in 444.2 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 800 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 83.6% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 18 through 41 Processing helix chain 'A' and resid 45 through 81 removed outlier: 3.675A pdb=" N LYS A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Proline residue: A 55 - end of helix removed outlier: 3.898A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 83 through 117 Processing helix chain 'A' and resid 117 through 122 removed outlier: 4.781A pdb=" N THR A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 122' Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.728A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.824A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 272 removed outlier: 3.735A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.569A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 282 through 309 removed outlier: 3.503A pdb=" N MET A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.660A pdb=" N GLY A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 365 Proline residue: A 360 - end of helix removed outlier: 3.824A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 385 Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.672A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.527A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.911A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 436 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 438 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 4.605A pdb=" N LEU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 removed outlier: 3.567A pdb=" N LEU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 245 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1033 1.34 - 1.46: 659 1.46 - 1.58: 1610 1.58 - 1.70: 0 1.70 - 1.81: 39 Bond restraints: 3341 Sorted by residual: bond pdb=" CG1 ILE A 330 " pdb=" CD1 ILE A 330 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.35e+00 bond pdb=" CA PHE A 54 " pdb=" C PHE A 54 " ideal model delta sigma weight residual 1.521 1.531 -0.010 1.17e-02 7.31e+03 7.45e-01 bond pdb=" C ILE A 254 " pdb=" O ILE A 254 " ideal model delta sigma weight residual 1.237 1.248 -0.010 1.29e-02 6.01e+03 6.56e-01 bond pdb=" CA MET A 258 " pdb=" C MET A 258 " ideal model delta sigma weight residual 1.521 1.531 -0.009 1.17e-02 7.31e+03 6.55e-01 bond pdb=" N ILE A 67 " pdb=" CA ILE A 67 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.25e-02 6.40e+03 5.12e-01 ... (remaining 3336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 4472 1.71 - 3.41: 48 3.41 - 5.12: 11 5.12 - 6.82: 4 6.82 - 8.53: 1 Bond angle restraints: 4536 Sorted by residual: angle pdb=" N ILE A 67 " pdb=" CA ILE A 67 " pdb=" C ILE A 67 " ideal model delta sigma weight residual 109.34 116.03 -6.69 2.08e+00 2.31e-01 1.03e+01 angle pdb=" CA LEU A 103 " pdb=" CB LEU A 103 " pdb=" CG LEU A 103 " ideal model delta sigma weight residual 116.30 124.83 -8.53 3.50e+00 8.16e-02 5.93e+00 angle pdb=" C LEU A 328 " pdb=" N MET A 329 " pdb=" CA MET A 329 " ideal model delta sigma weight residual 121.80 117.05 4.75 2.16e+00 2.14e-01 4.84e+00 angle pdb=" CB MET A 60 " pdb=" CG MET A 60 " pdb=" SD MET A 60 " ideal model delta sigma weight residual 112.70 119.16 -6.46 3.00e+00 1.11e-01 4.64e+00 angle pdb=" CA GLU A 374 " pdb=" CB GLU A 374 " pdb=" CG GLU A 374 " ideal model delta sigma weight residual 114.10 118.38 -4.28 2.00e+00 2.50e-01 4.59e+00 ... (remaining 4531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 1716 15.33 - 30.65: 208 30.65 - 45.98: 67 45.98 - 61.30: 9 61.30 - 76.62: 1 Dihedral angle restraints: 2001 sinusoidal: 760 harmonic: 1241 Sorted by residual: dihedral pdb=" CA VAL A 299 " pdb=" C VAL A 299 " pdb=" N ILE A 300 " pdb=" CA ILE A 300 " ideal model delta harmonic sigma weight residual -180.00 -161.72 -18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" N ARG A 166 " pdb=" CA ARG A 166 " pdb=" CB ARG A 166 " pdb=" CG ARG A 166 " ideal model delta sinusoidal sigma weight residual -180.00 -122.23 -57.77 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CB MET A 255 " pdb=" CG MET A 255 " pdb=" SD MET A 255 " pdb=" CE MET A 255 " ideal model delta sinusoidal sigma weight residual 60.00 112.27 -52.27 3 1.50e+01 4.44e-03 9.10e+00 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 342 0.025 - 0.049: 126 0.049 - 0.074: 73 0.074 - 0.098: 24 0.098 - 0.123: 10 Chirality restraints: 575 Sorted by residual: chirality pdb=" CA LEU A 337 " pdb=" N LEU A 337 " pdb=" C LEU A 337 " pdb=" CB LEU A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CB THR A 326 " pdb=" CA THR A 326 " pdb=" OG1 THR A 326 " pdb=" CG2 THR A 326 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 572 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 296 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C HIS A 296 " 0.027 2.00e-02 2.50e+03 pdb=" O HIS A 296 " -0.010 2.00e-02 2.50e+03 pdb=" N SER A 297 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 374 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" CD GLU A 374 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU A 374 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU A 374 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 411 " 0.021 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 412 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.018 5.00e-02 4.00e+02 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 795 2.80 - 3.33: 3329 3.33 - 3.85: 5304 3.85 - 4.38: 5710 4.38 - 4.90: 10348 Nonbonded interactions: 25486 Sorted by model distance: nonbonded pdb=" OG1 THR A 101 " pdb=" O HOH A 601 " model vdw 2.276 3.040 nonbonded pdb=" O PRO A 69 " pdb=" OG SER A 73 " model vdw 2.380 3.040 nonbonded pdb=" ND2 ASN A 366 " pdb=" OD1 ASP A 455 " model vdw 2.386 3.120 nonbonded pdb=" O ALA A 414 " pdb=" OG1 THR A 418 " model vdw 2.396 3.040 nonbonded pdb=" OD1 ASN A 366 " pdb=" O HOH A 601 " model vdw 2.462 3.040 ... (remaining 25481 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 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: 1.370 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.240 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.002 0.045 3341 Z= 0.165 Angle : 0.531 8.526 4536 Z= 0.278 Chirality : 0.036 0.123 575 Planarity : 0.003 0.033 555 Dihedral : 14.734 76.625 1201 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 21.61 % Favored : 78.39 % 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: 1.48 (0.40), residues: 429 helix: 1.76 (0.28), residues: 337 sheet: -0.35 (1.12), residues: 18 loop : -2.37 (0.58), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.010 0.001 PHE A 239 TYR 0.018 0.002 TYR A 305 ARG 0.001 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.344 Fit side-chains REVERT: A 329 MET cc_start: 0.4939 (mpp) cc_final: 0.4656 (mpp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1858 time to fit residues: 10.2227 Evaluate side-chains 42 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 0.0050 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3341 Z= 0.131 Angle : 0.458 6.042 4536 Z= 0.237 Chirality : 0.035 0.115 575 Planarity : 0.003 0.031 555 Dihedral : 3.496 18.037 455 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.05 % Allowed : 17.73 % Favored : 79.22 % 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: 1.96 (0.40), residues: 429 helix: 2.06 (0.28), residues: 341 sheet: 0.40 (1.09), residues: 16 loop : -2.35 (0.59), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.008 0.001 PHE A 218 TYR 0.011 0.001 TYR A 305 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.379 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 0.1555 time to fit residues: 10.8266 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 441 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3341 Z= 0.153 Angle : 0.477 8.793 4536 Z= 0.243 Chirality : 0.036 0.111 575 Planarity : 0.003 0.029 555 Dihedral : 3.509 18.237 455 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.32 % Allowed : 19.39 % Favored : 77.29 % 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: 1.95 (0.40), residues: 429 helix: 2.12 (0.28), residues: 339 sheet: -0.00 (1.07), residues: 16 loop : -2.51 (0.55), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 PHE 0.010 0.001 PHE A 240 TYR 0.012 0.001 TYR A 305 ARG 0.001 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.393 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 55 average time/residue: 0.1385 time to fit residues: 9.7335 Evaluate side-chains 45 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.0370 chunk 34 optimal weight: 3.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3341 Z= 0.160 Angle : 0.472 6.723 4536 Z= 0.244 Chirality : 0.036 0.110 575 Planarity : 0.003 0.029 555 Dihedral : 3.537 18.219 455 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.88 % Allowed : 18.84 % Favored : 77.29 % 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: 1.87 (0.40), residues: 429 helix: 2.07 (0.28), residues: 339 sheet: -0.11 (1.06), residues: 16 loop : -2.53 (0.56), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 PHE 0.010 0.001 PHE A 240 TYR 0.012 0.001 TYR A 305 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.367 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 53 average time/residue: 0.1375 time to fit residues: 9.3380 Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3341 Z= 0.151 Angle : 0.478 9.366 4536 Z= 0.242 Chirality : 0.036 0.113 575 Planarity : 0.003 0.028 555 Dihedral : 3.519 18.278 455 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.60 % Allowed : 20.78 % Favored : 75.62 % 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: 1.88 (0.40), residues: 429 helix: 2.08 (0.28), residues: 339 sheet: -0.19 (1.03), residues: 16 loop : -2.55 (0.56), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 PHE 0.010 0.001 PHE A 240 TYR 0.011 0.001 TYR A 305 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.466 Fit side-chains REVERT: A 472 GLN cc_start: 0.7064 (tm-30) cc_final: 0.6686 (pp30) outliers start: 13 outliers final: 12 residues processed: 52 average time/residue: 0.1477 time to fit residues: 9.9643 Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3341 Z= 0.272 Angle : 0.566 8.161 4536 Z= 0.294 Chirality : 0.039 0.114 575 Planarity : 0.004 0.030 555 Dihedral : 3.890 19.347 455 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.16 % Allowed : 20.78 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.39), residues: 429 helix: 1.67 (0.27), residues: 337 sheet: -0.46 (1.01), residues: 16 loop : -2.80 (0.50), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.017 0.002 PHE A 240 TYR 0.015 0.002 TYR A 305 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.411 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 53 average time/residue: 0.1427 time to fit residues: 9.7177 Evaluate side-chains 53 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3341 Z= 0.182 Angle : 0.514 9.548 4536 Z= 0.264 Chirality : 0.036 0.108 575 Planarity : 0.003 0.029 555 Dihedral : 3.724 18.820 455 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.88 % Allowed : 21.05 % Favored : 75.07 % 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: 1.39 (0.39), residues: 429 helix: 1.74 (0.28), residues: 339 sheet: -0.47 (1.01), residues: 16 loop : -2.72 (0.53), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.011 0.001 PHE A 240 TYR 0.012 0.002 TYR A 305 ARG 0.001 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.378 Fit side-chains REVERT: A 149 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8403 (mtm) REVERT: A 345 GLU cc_start: 0.5862 (mt-10) cc_final: 0.5534 (mt-10) outliers start: 14 outliers final: 11 residues processed: 52 average time/residue: 0.1411 time to fit residues: 9.4641 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 0.0050 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3341 Z= 0.212 Angle : 0.537 9.278 4536 Z= 0.276 Chirality : 0.037 0.110 575 Planarity : 0.003 0.028 555 Dihedral : 3.792 18.533 455 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.16 % Allowed : 21.33 % Favored : 74.52 % 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: 1.27 (0.39), residues: 429 helix: 1.66 (0.27), residues: 339 sheet: -0.54 (0.99), residues: 16 loop : -2.72 (0.54), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.013 0.002 PHE A 240 TYR 0.013 0.002 TYR A 373 ARG 0.002 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.338 Fit side-chains REVERT: A 149 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8431 (mtm) outliers start: 15 outliers final: 11 residues processed: 51 average time/residue: 0.1493 time to fit residues: 9.5709 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3341 Z= 0.188 Angle : 0.536 9.226 4536 Z= 0.272 Chirality : 0.037 0.118 575 Planarity : 0.003 0.028 555 Dihedral : 3.739 18.309 455 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.16 % Allowed : 21.33 % Favored : 74.52 % 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: 1.35 (0.40), residues: 429 helix: 1.72 (0.28), residues: 339 sheet: -0.63 (1.00), residues: 16 loop : -2.71 (0.54), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.011 0.001 PHE A 240 TYR 0.014 0.002 TYR A 373 ARG 0.002 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.471 Fit side-chains REVERT: A 149 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8428 (mtm) outliers start: 15 outliers final: 12 residues processed: 50 average time/residue: 0.1444 time to fit residues: 9.2937 Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 0.0370 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3341 Z= 0.154 Angle : 0.521 9.633 4536 Z= 0.259 Chirality : 0.036 0.112 575 Planarity : 0.003 0.028 555 Dihedral : 3.589 17.506 455 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.05 % Allowed : 22.44 % Favored : 74.52 % 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: 1.56 (0.40), residues: 429 helix: 1.88 (0.28), residues: 339 sheet: -0.56 (1.01), residues: 16 loop : -2.69 (0.54), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 PHE 0.008 0.001 PHE A 218 TYR 0.014 0.001 TYR A 373 ARG 0.002 0.000 ARG A 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.387 Fit side-chains REVERT: A 149 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8394 (mtm) outliers start: 11 outliers final: 10 residues processed: 45 average time/residue: 0.1448 time to fit residues: 8.3180 Evaluate side-chains 47 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 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 = 0.4068 r_free = 0.4068 target = 0.183570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133813 restraints weight = 3953.443| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.11 r_work: 0.3372 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3341 Z= 0.159 Angle : 0.528 9.800 4536 Z= 0.262 Chirality : 0.036 0.116 575 Planarity : 0.003 0.028 555 Dihedral : 3.568 17.472 455 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.88 % Allowed : 21.88 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.40), residues: 429 helix: 1.91 (0.28), residues: 338 sheet: -0.50 (1.00), residues: 16 loop : -2.78 (0.55), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 PHE 0.009 0.001 PHE A 240 TYR 0.013 0.002 TYR A 373 ARG 0.002 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1093.72 seconds wall clock time: 20 minutes 52.55 seconds (1252.55 seconds total)