Starting phenix.real_space_refine on Sun Mar 10 16:20:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cud_26998/03_2024/8cud_26998.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cud_26998/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cud_26998/03_2024/8cud_26998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cud_26998/03_2024/8cud_26998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cud_26998/03_2024/8cud_26998.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cud_26998/03_2024/8cud_26998.pdb" } 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 Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3294 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3294 Classifications: {'peptide': 433, 'water': 2} Link IDs: {'PTRANS': 12, 'TRANS': 420, None: 2} Not linked: pdbres="SER A 476 " pdbres="HOH A 601 " Not linked: pdbres="HOH A 601 " pdbres="HOH A 602 " Chain breaks: 1 Time building chain proxies: 2.32, per 1000 atoms: 0.70 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 821.8 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: 0.42 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: 1.05 Time building geometry restraints manager: 1.42 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: 100.22 - 107.03: 75 107.03 - 113.85: 1981 113.85 - 120.66: 1445 120.66 - 127.48: 1018 127.48 - 134.30: 17 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 2.440 nonbonded pdb=" OE2 GLU A 345 " pdb=" NH1 ARG A 356 " model vdw 2.437 2.520 nonbonded pdb=" O SER A 331 " pdb=" OG SER A 331 " model vdw 2.535 2.440 nonbonded pdb=" OD1 ASN A 312 " pdb=" N PHE A 314 " model vdw 2.547 2.520 nonbonded pdb=" OH TYR A 373 " pdb=" OD1 ASP A 440 " model vdw 2.554 2.440 ... (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: 1.220 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: 5.690 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.640 Find NCS groups from input model: 0.090 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.980 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.415 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 1.1486 time to fit residues: 68.8192 Evaluate side-chains 47 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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: 0.5980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1133 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= 0.173 Angle : 0.480 5.485 4536 Z= 0.253 Chirality : 0.038 0.132 575 Planarity : 0.004 0.031 555 Dihedral : 3.491 14.304 455 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.88 % Allowed : 22.16 % 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: 1.83 (0.42), residues: 429 helix: 1.90 (0.30), residues: 323 sheet: 1.96 (1.23), residues: 16 loop : -1.50 (0.58), residues: 90 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 0.012 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 66 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.371 Fit side-chains REVERT: A 231 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6992 (tp30) REVERT: A 315 ARG cc_start: 0.6883 (mtt-85) cc_final: 0.6220 (mmm-85) REVERT: A 352 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6597 (tppp) REVERT: A 367 MET cc_start: 0.7641 (mmt) cc_final: 0.7441 (mmp) REVERT: A 428 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6903 (mt) REVERT: A 449 MET cc_start: 0.7433 (ttm) cc_final: 0.7232 (ttp) REVERT: A 473 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6911 (ptp) outliers start: 14 outliers final: 2 residues processed: 61 average time/residue: 1.0247 time to fit residues: 64.7464 Evaluate side-chains 51 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 473 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 10 optimal weight: 0.0970 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8072 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3341 Z= 0.160 Angle : 0.463 5.515 4536 Z= 0.242 Chirality : 0.038 0.173 575 Planarity : 0.003 0.030 555 Dihedral : 3.393 14.623 455 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.71 % Allowed : 22.16 % Favored : 73.13 % 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: 1.92 (0.42), residues: 429 helix: 2.06 (0.30), residues: 318 sheet: 1.88 (1.18), residues: 16 loop : -1.68 (0.56), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR A 373 ARG 0.003 0.000 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 65 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.379 Fit side-chains REVERT: A 200 TYR cc_start: 0.7955 (m-10) cc_final: 0.7542 (m-10) REVERT: A 352 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6611 (tppp) REVERT: A 428 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6777 (mp) outliers start: 17 outliers final: 7 residues processed: 59 average time/residue: 0.8562 time to fit residues: 52.6250 Evaluate side-chains 54 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 307 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 473 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 10.0000 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3341 Z= 0.170 Angle : 0.475 6.978 4536 Z= 0.248 Chirality : 0.039 0.174 575 Planarity : 0.003 0.040 555 Dihedral : 3.394 14.358 455 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.71 % Allowed : 21.61 % Favored : 73.68 % 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: 1.79 (0.42), residues: 429 helix: 2.05 (0.31), residues: 314 sheet: 2.13 (1.23), 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 0.010 0.001 PHE A 341 TYR 0.009 0.001 TYR A 373 ARG 0.002 0.000 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 61 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 44 time to evaluate : 0.342 Fit side-chains REVERT: A 200 TYR cc_start: 0.7961 (m-10) cc_final: 0.7540 (m-10) REVERT: A 231 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6963 (tp30) REVERT: A 428 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6739 (mp) outliers start: 17 outliers final: 8 residues processed: 56 average time/residue: 0.8911 time to fit residues: 51.9639 Evaluate side-chains 52 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 411 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 473 MET 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: 0.9980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3341 Z= 0.165 Angle : 0.467 5.434 4536 Z= 0.244 Chirality : 0.039 0.171 575 Planarity : 0.004 0.045 555 Dihedral : 3.390 13.935 455 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 5.82 % Allowed : 21.61 % 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: 1.84 (0.42), residues: 429 helix: 2.04 (0.31), residues: 315 sheet: 2.20 (1.29), residues: 16 loop : -1.81 (0.55), residues: 98 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 0.011 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 66 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 45 time to evaluate : 0.386 Fit side-chains REVERT: A 200 TYR cc_start: 0.7977 (m-10) cc_final: 0.7552 (m-10) REVERT: A 231 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: A 315 ARG cc_start: 0.7103 (mtt-85) cc_final: 0.6440 (mmm-85) REVERT: A 428 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6669 (mp) outliers start: 21 outliers final: 9 residues processed: 61 average time/residue: 0.9231 time to fit residues: 58.4892 Evaluate side-chains 54 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 307 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 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: 5.9990 chunk 10 optimal weight: 0.0570 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.0050 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.0070 chunk 23 optimal weight: 0.9980 overall best weight: 0.3930 ------------------------------------------------------------------------------- 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: 0.8027 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3341 Z= 0.127 Angle : 0.440 5.050 4536 Z= 0.229 Chirality : 0.039 0.218 575 Planarity : 0.003 0.047 555 Dihedral : 3.242 14.877 455 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.60 % Allowed : 24.10 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.42), residues: 429 helix: 2.19 (0.31), residues: 319 sheet: None (None), residues: 0 loop : -1.30 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.011 0.001 PHE A 341 TYR 0.013 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 60 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.322 Fit side-chains REVERT: A 200 TYR cc_start: 0.7950 (m-10) cc_final: 0.7506 (m-10) REVERT: A 231 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6681 (tp30) REVERT: A 428 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6612 (mp) outliers start: 13 outliers final: 6 residues processed: 55 average time/residue: 0.9281 time to fit residues: 53.1623 Evaluate side-chains 53 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 473 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1686 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= 0.166 Angle : 0.464 5.378 4536 Z= 0.242 Chirality : 0.039 0.184 575 Planarity : 0.004 0.048 555 Dihedral : 3.311 13.823 455 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.60 % Allowed : 24.38 % Favored : 72.02 % 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: 1.97 (0.42), residues: 429 helix: 2.16 (0.31), residues: 314 sheet: 2.52 (1.38), residues: 16 loop : -1.87 (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 0.009 0.001 PHE A 240 TYR 0.014 0.001 TYR A 373 ARG 0.002 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 58 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.386 Fit side-chains REVERT: A 200 TYR cc_start: 0.7985 (m-10) cc_final: 0.7546 (m-10) REVERT: A 231 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6916 (tp30) REVERT: A 315 ARG cc_start: 0.7065 (mtt-85) cc_final: 0.6446 (mmm-85) REVERT: A 428 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6614 (mp) outliers start: 13 outliers final: 6 residues processed: 55 average time/residue: 0.9790 time to fit residues: 55.8811 Evaluate side-chains 51 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 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: 3.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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: 0.8064 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3341 Z= 0.157 Angle : 0.468 7.124 4536 Z= 0.243 Chirality : 0.041 0.346 575 Planarity : 0.003 0.049 555 Dihedral : 3.327 13.934 455 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.77 % Allowed : 25.48 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.42), residues: 429 helix: 2.19 (0.31), residues: 314 sheet: 2.59 (1.38), residues: 16 loop : -1.87 (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 0.011 0.001 PHE A 341 TYR 0.015 0.001 TYR A 373 ARG 0.002 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 54 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.408 Fit side-chains REVERT: A 200 TYR cc_start: 0.7984 (m-10) cc_final: 0.7541 (m-10) REVERT: A 231 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6892 (tp30) REVERT: A 428 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6567 (mp) outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 0.9243 time to fit residues: 48.1577 Evaluate side-chains 52 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 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: 0.9980 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8076 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3341 Z= 0.167 Angle : 0.471 6.030 4536 Z= 0.245 Chirality : 0.040 0.286 575 Planarity : 0.004 0.050 555 Dihedral : 3.353 14.045 455 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.77 % Allowed : 26.04 % 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: 1.96 (0.42), residues: 429 helix: 2.18 (0.31), residues: 314 sheet: 1.41 (1.48), residues: 18 loop : -1.79 (0.55), residues: 97 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 0.010 0.001 PHE A 341 TYR 0.015 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 55 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.400 Fit side-chains REVERT: A 200 TYR cc_start: 0.7989 (m-10) cc_final: 0.7536 (m-10) REVERT: A 231 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6953 (tp30) REVERT: A 315 ARG cc_start: 0.7013 (mtt-85) cc_final: 0.6407 (mmm-85) REVERT: A 428 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6591 (mp) outliers start: 10 outliers final: 6 residues processed: 51 average time/residue: 0.9563 time to fit residues: 50.7114 Evaluate side-chains 52 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 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: 0.9990 chunk 3 optimal weight: 0.0270 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- 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: 0.8060 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3341 Z= 0.148 Angle : 0.446 5.115 4536 Z= 0.234 Chirality : 0.038 0.171 575 Planarity : 0.004 0.050 555 Dihedral : 3.305 13.921 455 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.22 % Allowed : 26.04 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.42), residues: 429 helix: 2.17 (0.30), residues: 319 sheet: 1.39 (1.49), residues: 18 loop : -1.48 (0.57), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.011 0.001 PHE A 341 TYR 0.016 0.001 TYR A 373 ARG 0.003 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 53 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.411 Fit side-chains REVERT: A 200 TYR cc_start: 0.7989 (m-10) cc_final: 0.7531 (m-10) REVERT: A 231 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6831 (tp30) REVERT: A 315 ARG cc_start: 0.7061 (mtt-85) cc_final: 0.6599 (mmm-85) REVERT: A 428 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6579 (mp) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 1.0031 time to fit residues: 52.0954 Evaluate side-chains 53 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 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: 0.9990 chunk 4 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.0270 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.0370 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.180212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131658 restraints weight = 3815.742| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.75 r_work: 0.3290 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3341 Z= 0.123 Angle : 0.427 5.084 4536 Z= 0.223 Chirality : 0.038 0.167 575 Planarity : 0.003 0.050 555 Dihedral : 3.177 14.278 455 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.05 % Allowed : 25.48 % 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: 2.21 (0.43), residues: 429 helix: 2.20 (0.30), residues: 326 sheet: 1.32 (1.48), residues: 18 loop : -1.54 (0.60), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 256 HIS 0.001 0.000 HIS A 296 PHE 0.009 0.001 PHE A 341 TYR 0.016 0.001 TYR A 373 ARG 0.002 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.31 seconds wall clock time: 29 minutes 50.79 seconds (1790.79 seconds total)