Starting phenix.real_space_refine on Fri Dec 27 06:53:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cud_26998/12_2024/8cud_26998.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cud_26998/12_2024/8cud_26998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cud_26998/12_2024/8cud_26998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cud_26998/12_2024/8cud_26998.map" model { file = "/net/cci-nas-00/data/ceres_data/8cud_26998/12_2024/8cud_26998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cud_26998/12_2024/8cud_26998.cif" } resolution = 2.94 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 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 3294 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.92, per 1000 atoms: 0.89 Number of scatterers: 3294 At special positions: 0 Unit cell: (71.568, 66.456, 80.088, 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 594 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: 0.85 Conformation dependent library (CDL) restraints added in 404.1 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: 24 helices and 1 sheets defined 81.5% alpha, 3.2% 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 19 through 42 removed outlier: 3.604A pdb=" N ILE A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.520A pdb=" N PHE A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.888A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 117 removed outlier: 3.673A pdb=" N GLY A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.551A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 228 removed outlier: 3.659A pdb=" N LYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.616A pdb=" N LYS A 232 " --> pdb=" O MET A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 270 removed outlier: 3.596A pdb=" N VAL A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.644A pdb=" N GLY A 268 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 319 removed outlier: 4.157A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.517A pdb=" N ASN A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 removed outlier: 4.179A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 4.032A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.796A pdb=" N ILE A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.648A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 removed outlier: 3.678A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.623A pdb=" N ILE A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 433 through 438' Processing helix chain 'A' and resid 442 through 466 removed outlier: 3.802A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 229 hydrogen bonds defined for protein. 681 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: 0.91 Time building geometry restraints manager: 0.99 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: 936 1.34 - 1.45: 415 1.45 - 1.57: 1951 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 3341 Sorted by residual: bond pdb=" N VAL A 113 " pdb=" CA VAL A 113 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.47e+00 bond pdb=" N MET A 367 " pdb=" CA MET A 367 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.37e+00 bond pdb=" N ILE A 210 " pdb=" CA ILE A 210 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.27e-02 6.20e+03 9.33e+00 bond pdb=" N ILE A 116 " pdb=" CA ILE A 116 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.16e+00 bond pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 8.98e+00 ... (remaining 3336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 4143 0.99 - 1.98: 248 1.98 - 2.97: 106 2.97 - 3.96: 27 3.96 - 4.95: 12 Bond angle restraints: 4536 Sorted by residual: angle pdb=" CA ASP A 368 " pdb=" C ASP A 368 " pdb=" O ASP A 368 " ideal model delta sigma weight residual 121.07 116.89 4.18 1.10e+00 8.26e-01 1.44e+01 angle pdb=" CA ILE A 116 " pdb=" C ILE A 116 " pdb=" O ILE A 116 " ideal model delta sigma weight residual 120.95 117.14 3.81 1.04e+00 9.25e-01 1.34e+01 angle pdb=" CA THR A 448 " pdb=" C THR A 448 " pdb=" O THR A 448 " ideal model delta sigma weight residual 120.82 117.18 3.64 1.05e+00 9.07e-01 1.21e+01 angle pdb=" N ARG A 315 " pdb=" CA ARG A 315 " pdb=" C ARG A 315 " ideal model delta sigma weight residual 111.36 107.59 3.77 1.09e+00 8.42e-01 1.20e+01 angle pdb=" C GLY A 369 " pdb=" N THR A 370 " pdb=" CA THR A 370 " ideal model delta sigma weight residual 120.54 125.06 -4.52 1.35e+00 5.49e-01 1.12e+01 ... (remaining 4531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 1765 17.91 - 35.83: 182 35.83 - 53.74: 44 53.74 - 71.65: 6 71.65 - 89.57: 4 Dihedral angle restraints: 2001 sinusoidal: 760 harmonic: 1241 Sorted by residual: dihedral pdb=" CA GLU A 40 " pdb=" C GLU A 40 " pdb=" N HIS A 41 " pdb=" CA HIS A 41 " ideal model delta harmonic sigma weight residual 180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A 463 " pdb=" CG GLU A 463 " pdb=" CD GLU A 463 " pdb=" OE1 GLU A 463 " ideal model delta sinusoidal sigma weight residual 0.00 -89.57 89.57 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" C ASP A 368 " pdb=" N ASP A 368 " pdb=" CA ASP A 368 " pdb=" CB ASP A 368 " ideal model delta harmonic sigma weight residual -122.60 -130.60 8.00 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 405 0.042 - 0.083: 111 0.083 - 0.125: 40 0.125 - 0.166: 14 0.166 - 0.208: 5 Chirality restraints: 575 Sorted by residual: chirality pdb=" CA ASP A 368 " pdb=" N ASP A 368 " pdb=" C ASP A 368 " pdb=" CB ASP A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL A 113 " pdb=" CA VAL A 113 " pdb=" CG1 VAL A 113 " pdb=" CG2 VAL A 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA MET A 318 " pdb=" N MET A 318 " pdb=" C MET A 318 " pdb=" CB MET A 318 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 572 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 364 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C THR A 364 " 0.035 2.00e-02 2.50e+03 pdb=" O THR A 364 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 365 " -0.012 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 3.21e-02 1.65e+00 pdb=" N PRO A 412 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 66 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.31e+00 pdb=" C ILE A 66 " -0.020 2.00e-02 2.50e+03 pdb=" O ILE A 66 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE A 67 " 0.007 2.00e-02 2.50e+03 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 1340 2.93 - 3.42: 3473 3.42 - 3.91: 5224 3.91 - 4.41: 5551 4.41 - 4.90: 9805 Nonbonded interactions: 25393 Sorted by model distance: nonbonded pdb=" O PRO A 69 " pdb=" OG SER A 73 " model vdw 2.433 3.040 nonbonded pdb=" OE2 GLU A 345 " pdb=" NH1 ARG A 356 " model vdw 2.437 3.120 nonbonded pdb=" O SER A 331 " pdb=" OG SER A 331 " model vdw 2.535 3.040 nonbonded pdb=" OD1 ASN A 312 " pdb=" N PHE A 314 " model vdw 2.547 3.120 nonbonded pdb=" OH TYR A 373 " pdb=" OD1 ASP A 440 " model vdw 2.554 3.040 ... (remaining 25388 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: 1.130 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.810 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.005 0.072 3341 Z= 0.294 Angle : 0.667 4.948 4536 Z= 0.466 Chirality : 0.049 0.208 575 Planarity : 0.004 0.032 555 Dihedral : 15.611 89.566 1201 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 22.99 % Favored : 77.01 % 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: 1.42 (0.42), residues: 429 helix: 1.51 (0.31), residues: 320 sheet: 1.60 (1.19), residues: 16 loop : -1.08 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.002 0.001 HIS A 41 PHE 0.011 0.001 PHE A 457 TYR 0.010 0.001 TYR A 97 ARG 0.002 0.000 ARG A 447 *********************** 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 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.368 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 1.1507 time to fit residues: 68.8593 Evaluate side-chains 47 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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: 6.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3341 Z= 0.162 Angle : 0.475 5.244 4536 Z= 0.251 Chirality : 0.038 0.138 575 Planarity : 0.003 0.030 555 Dihedral : 3.468 14.518 455 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.60 % Allowed : 22.16 % 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: 1.84 (0.42), residues: 429 helix: 1.92 (0.31), residues: 322 sheet: 1.98 (1.22), residues: 16 loop : -1.53 (0.57), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.002 0.001 HIS A 296 PHE 0.012 0.001 PHE A 341 TYR 0.010 0.001 TYR A 373 ARG 0.004 0.000 ARG A 447 *********************** 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 64 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.387 Fit side-chains REVERT: A 428 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6905 (mt) outliers start: 13 outliers final: 3 residues processed: 60 average time/residue: 0.9207 time to fit residues: 57.4209 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 13 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3341 Z= 0.261 Angle : 0.553 6.842 4536 Z= 0.289 Chirality : 0.041 0.235 575 Planarity : 0.004 0.033 555 Dihedral : 3.672 15.369 455 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.26 % Allowed : 20.78 % Favored : 73.96 % 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: 1.44 (0.42), residues: 429 helix: 1.70 (0.30), residues: 317 sheet: 1.90 (1.22), residues: 16 loop : -1.81 (0.57), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.013 0.002 PHE A 341 TYR 0.011 0.002 TYR A 98 ARG 0.004 0.001 ARG A 447 *********************** 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 64 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.363 Fit side-chains REVERT: A 200 TYR cc_start: 0.8016 (m-10) cc_final: 0.7621 (m-10) REVERT: A 231 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7288 (tp30) REVERT: A 315 ARG cc_start: 0.6962 (mtt-85) cc_final: 0.6346 (mmm-85) REVERT: A 428 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6792 (mp) outliers start: 19 outliers final: 6 residues processed: 60 average time/residue: 1.0855 time to fit residues: 67.4418 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3341 Z= 0.253 Angle : 0.535 6.753 4536 Z= 0.283 Chirality : 0.041 0.179 575 Planarity : 0.004 0.045 555 Dihedral : 3.705 15.755 455 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 6.09 % Allowed : 21.33 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.42), residues: 429 helix: 1.63 (0.30), residues: 317 sheet: 2.04 (1.36), residues: 16 loop : -1.83 (0.57), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.015 0.002 PHE A 341 TYR 0.015 0.002 TYR A 373 ARG 0.004 0.001 ARG A 447 *********************** 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 69 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.301 Fit side-chains REVERT: A 200 TYR cc_start: 0.8035 (m-10) cc_final: 0.7610 (m-10) REVERT: A 231 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7300 (tp30) REVERT: A 428 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6762 (mp) outliers start: 22 outliers final: 7 residues processed: 63 average time/residue: 0.9792 time to fit residues: 64.0313 Evaluate side-chains 53 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1733 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= 0.186 Angle : 0.495 6.106 4536 Z= 0.260 Chirality : 0.040 0.236 575 Planarity : 0.004 0.048 555 Dihedral : 3.587 15.056 455 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.43 % Allowed : 24.10 % Favored : 71.47 % 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: 1.54 (0.42), residues: 429 helix: 1.82 (0.31), residues: 314 sheet: 2.15 (1.39), residues: 16 loop : -1.89 (0.56), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.014 0.001 PHE A 341 TYR 0.014 0.001 TYR A 373 ARG 0.003 0.000 ARG A 447 *********************** 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 60 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.364 Fit side-chains REVERT: A 200 TYR cc_start: 0.8018 (m-10) cc_final: 0.7576 (m-10) REVERT: A 231 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7197 (tp30) REVERT: A 428 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6778 (mp) outliers start: 16 outliers final: 6 residues processed: 56 average time/residue: 1.0139 time to fit residues: 58.9107 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3341 Z= 0.167 Angle : 0.472 5.607 4536 Z= 0.250 Chirality : 0.039 0.174 575 Planarity : 0.004 0.050 555 Dihedral : 3.515 14.342 455 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.99 % Allowed : 23.82 % Favored : 71.19 % 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: 1.64 (0.42), residues: 429 helix: 1.91 (0.31), residues: 314 sheet: 2.29 (1.40), residues: 16 loop : -1.92 (0.55), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.013 0.001 PHE A 341 TYR 0.014 0.001 TYR A 373 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 63 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.335 Fit side-chains REVERT: A 200 TYR cc_start: 0.7990 (m-10) cc_final: 0.7537 (m-10) REVERT: A 231 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7062 (tp30) REVERT: A 428 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6702 (mp) outliers start: 18 outliers final: 6 residues processed: 58 average time/residue: 0.9811 time to fit residues: 59.1083 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3341 Z= 0.186 Angle : 0.495 6.751 4536 Z= 0.260 Chirality : 0.041 0.320 575 Planarity : 0.004 0.051 555 Dihedral : 3.542 14.660 455 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.16 % Allowed : 24.93 % Favored : 70.91 % 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: 1.59 (0.42), residues: 429 helix: 1.87 (0.30), residues: 314 sheet: 2.42 (1.40), residues: 16 loop : -1.94 (0.54), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.012 0.001 PHE A 341 TYR 0.015 0.001 TYR A 373 ARG 0.003 0.000 ARG A 447 *********************** 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 60 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.279 Fit side-chains REVERT: A 200 TYR cc_start: 0.8014 (m-10) cc_final: 0.7569 (m-10) REVERT: A 231 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7070 (tp30) REVERT: A 315 ARG cc_start: 0.7107 (mtt-85) cc_final: 0.6754 (mmm-85) REVERT: A 428 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6678 (mp) outliers start: 15 outliers final: 7 residues processed: 53 average time/residue: 1.0611 time to fit residues: 58.2143 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3341 Z= 0.167 Angle : 0.476 5.531 4536 Z= 0.251 Chirality : 0.040 0.235 575 Planarity : 0.004 0.051 555 Dihedral : 3.482 14.415 455 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.60 % Allowed : 26.32 % Favored : 70.08 % 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: 1.65 (0.42), residues: 429 helix: 1.92 (0.31), residues: 314 sheet: 2.47 (1.38), residues: 16 loop : -1.96 (0.54), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.013 0.001 PHE A 341 TYR 0.015 0.001 TYR A 373 ARG 0.003 0.000 ARG A 447 *********************** 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 59 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.380 Fit side-chains REVERT: A 200 TYR cc_start: 0.8000 (m-10) cc_final: 0.7558 (m-10) REVERT: A 231 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6990 (tp30) REVERT: A 315 ARG cc_start: 0.7072 (mtt-85) cc_final: 0.6461 (mmm-85) REVERT: A 428 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6673 (mp) outliers start: 13 outliers final: 6 residues processed: 54 average time/residue: 1.0960 time to fit residues: 61.3381 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3341 Z= 0.176 Angle : 0.482 5.752 4536 Z= 0.254 Chirality : 0.039 0.209 575 Planarity : 0.004 0.052 555 Dihedral : 3.480 14.488 455 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.60 % Allowed : 26.59 % Favored : 69.81 % 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: 1.63 (0.42), residues: 429 helix: 1.91 (0.31), residues: 314 sheet: 2.51 (1.39), residues: 16 loop : -1.98 (0.54), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.014 0.001 PHE A 341 TYR 0.017 0.001 TYR A 373 ARG 0.003 0.000 ARG A 447 *********************** 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 59 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.337 Fit side-chains REVERT: A 200 TYR cc_start: 0.8005 (m-10) cc_final: 0.7568 (m-10) REVERT: A 231 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7012 (tp30) REVERT: A 315 ARG cc_start: 0.7021 (mtt-85) cc_final: 0.6410 (mmm-85) REVERT: A 428 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6647 (mp) outliers start: 13 outliers final: 9 residues processed: 53 average time/residue: 1.0489 time to fit residues: 57.6456 Evaluate side-chains 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3341 Z= 0.198 Angle : 0.502 6.146 4536 Z= 0.264 Chirality : 0.040 0.197 575 Planarity : 0.004 0.052 555 Dihedral : 3.542 14.695 455 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.88 % Allowed : 26.04 % Favored : 70.08 % 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: 1.54 (0.42), residues: 429 helix: 1.84 (0.30), residues: 314 sheet: 2.44 (1.44), residues: 16 loop : -2.01 (0.54), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.013 0.001 PHE A 341 TYR 0.019 0.001 TYR A 373 ARG 0.004 0.000 ARG A 447 ********************** 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 59 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.407 Fit side-chains REVERT: A 200 TYR cc_start: 0.8006 (m-10) cc_final: 0.7572 (m-10) REVERT: A 231 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: A 315 ARG cc_start: 0.7035 (mtt-85) cc_final: 0.6444 (mmm-85) REVERT: A 428 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6671 (mp) outliers start: 14 outliers final: 7 residues processed: 54 average time/residue: 1.0520 time to fit residues: 58.9530 Evaluate side-chains 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.175299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.124301 restraints weight = 3828.309| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.82 r_work: 0.3200 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3341 Z= 0.184 Angle : 0.512 8.921 4536 Z= 0.266 Chirality : 0.044 0.480 575 Planarity : 0.004 0.052 555 Dihedral : 3.524 14.604 455 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.77 % Allowed : 26.59 % Favored : 70.64 % 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: 1.59 (0.42), residues: 429 helix: 1.88 (0.30), residues: 314 sheet: 2.48 (1.42), residues: 16 loop : -2.02 (0.54), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.001 HIS A 41 PHE 0.014 0.001 PHE A 341 TYR 0.018 0.001 TYR A 373 ARG 0.003 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1602.67 seconds wall clock time: 29 minutes 53.29 seconds (1793.29 seconds total)