Starting phenix.real_space_refine on Sun Mar 10 16:18:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cuj_27001/03_2024/8cuj_27001.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cuj_27001/03_2024/8cuj_27001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cuj_27001/03_2024/8cuj_27001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cuj_27001/03_2024/8cuj_27001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cuj_27001/03_2024/8cuj_27001.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cuj_27001/03_2024/8cuj_27001.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2153 2.51 5 N 526 2.21 5 O 593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A GLU 463": "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: 3293 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3293 Classifications: {'peptide': 433, 'water': 1} Link IDs: {'PTRANS': 12, 'TRANS': 420, None: 1} Not linked: pdbres="SER A 476 " pdbres="HOH A 601 " Chain breaks: 1 Time building chain proxies: 2.37, per 1000 atoms: 0.72 Number of scatterers: 3293 At special positions: 0 Unit cell: (73.272, 66.456, 79.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 593 8.00 N 526 7.00 C 2153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 1.16 Conformation dependent library (CDL) restraints added in 550.4 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 800 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 83.6% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 18 through 41 Processing helix chain 'A' and resid 45 through 81 removed outlier: 3.675A pdb=" N LYS A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Proline residue: A 55 - end of helix removed outlier: 3.898A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 83 through 117 Processing helix chain 'A' and resid 117 through 122 removed outlier: 4.781A pdb=" N THR A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 122' Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.728A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.824A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 272 removed outlier: 3.735A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.569A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 282 through 309 removed outlier: 3.503A pdb=" N MET A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.660A pdb=" N GLY A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 365 Proline residue: A 360 - end of helix removed outlier: 3.824A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 385 Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.672A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.527A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.911A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 436 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 438 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 4.605A pdb=" N LEU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 removed outlier: 3.567A pdb=" N LEU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 245 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1033 1.34 - 1.46: 659 1.46 - 1.58: 1610 1.58 - 1.70: 0 1.70 - 1.81: 39 Bond restraints: 3341 Sorted by residual: bond pdb=" CG1 ILE A 330 " pdb=" CD1 ILE A 330 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.35e+00 bond pdb=" CA PHE A 54 " pdb=" C PHE A 54 " ideal model delta sigma weight residual 1.521 1.531 -0.010 1.17e-02 7.31e+03 7.45e-01 bond pdb=" C ILE A 254 " pdb=" O ILE A 254 " ideal model delta sigma weight residual 1.237 1.248 -0.010 1.29e-02 6.01e+03 6.56e-01 bond pdb=" CA MET A 258 " pdb=" C MET A 258 " ideal model delta sigma weight residual 1.521 1.531 -0.009 1.17e-02 7.31e+03 6.55e-01 bond pdb=" N ILE A 67 " pdb=" CA ILE A 67 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.25e-02 6.40e+03 5.12e-01 ... (remaining 3336 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.72: 72 106.72 - 113.54: 1953 113.54 - 120.37: 1242 120.37 - 127.19: 1250 127.19 - 134.02: 19 Bond angle restraints: 4536 Sorted by residual: angle pdb=" N ILE A 67 " pdb=" CA ILE A 67 " pdb=" C ILE A 67 " ideal model delta sigma weight residual 109.34 116.03 -6.69 2.08e+00 2.31e-01 1.03e+01 angle pdb=" CA LEU A 103 " pdb=" CB LEU A 103 " pdb=" CG LEU A 103 " ideal model delta sigma weight residual 116.30 124.83 -8.53 3.50e+00 8.16e-02 5.93e+00 angle pdb=" C LEU A 328 " pdb=" N MET A 329 " pdb=" CA MET A 329 " ideal model delta sigma weight residual 121.80 117.05 4.75 2.16e+00 2.14e-01 4.84e+00 angle pdb=" CB MET A 60 " pdb=" CG MET A 60 " pdb=" SD MET A 60 " ideal model delta sigma weight residual 112.70 119.16 -6.46 3.00e+00 1.11e-01 4.64e+00 angle pdb=" CA GLU A 374 " pdb=" CB GLU A 374 " pdb=" CG GLU A 374 " ideal model delta sigma weight residual 114.10 118.38 -4.28 2.00e+00 2.50e-01 4.59e+00 ... (remaining 4531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 1716 15.33 - 30.65: 208 30.65 - 45.98: 67 45.98 - 61.30: 9 61.30 - 76.62: 1 Dihedral angle restraints: 2001 sinusoidal: 760 harmonic: 1241 Sorted by residual: dihedral pdb=" CA VAL A 299 " pdb=" C VAL A 299 " pdb=" N ILE A 300 " pdb=" CA ILE A 300 " ideal model delta harmonic sigma weight residual -180.00 -161.72 -18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" N ARG A 166 " pdb=" CA ARG A 166 " pdb=" CB ARG A 166 " pdb=" CG ARG A 166 " ideal model delta sinusoidal sigma weight residual -180.00 -122.23 -57.77 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CB MET A 255 " pdb=" CG MET A 255 " pdb=" SD MET A 255 " pdb=" CE MET A 255 " ideal model delta sinusoidal sigma weight residual 60.00 112.27 -52.27 3 1.50e+01 4.44e-03 9.10e+00 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 342 0.025 - 0.049: 126 0.049 - 0.074: 73 0.074 - 0.098: 24 0.098 - 0.123: 10 Chirality restraints: 575 Sorted by residual: chirality pdb=" CA LEU A 337 " pdb=" N LEU A 337 " pdb=" C LEU A 337 " pdb=" CB LEU A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CB THR A 326 " pdb=" CA THR A 326 " pdb=" OG1 THR A 326 " pdb=" CG2 THR A 326 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 572 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 296 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C HIS A 296 " 0.027 2.00e-02 2.50e+03 pdb=" O HIS A 296 " -0.010 2.00e-02 2.50e+03 pdb=" N SER A 297 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 374 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" CD GLU A 374 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU A 374 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU A 374 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 411 " 0.021 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 412 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.018 5.00e-02 4.00e+02 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 795 2.80 - 3.33: 3329 3.33 - 3.85: 5304 3.85 - 4.38: 5710 4.38 - 4.90: 10348 Nonbonded interactions: 25486 Sorted by model distance: nonbonded pdb=" OG1 THR A 101 " pdb=" O HOH A 601 " model vdw 2.276 2.440 nonbonded pdb=" O PRO A 69 " pdb=" OG SER A 73 " model vdw 2.380 2.440 nonbonded pdb=" ND2 ASN A 366 " pdb=" OD1 ASP A 455 " model vdw 2.386 2.520 nonbonded pdb=" O ALA A 414 " pdb=" OG1 THR A 418 " model vdw 2.396 2.440 nonbonded pdb=" OD1 ASN A 366 " pdb=" O HOH A 601 " model vdw 2.462 2.440 ... (remaining 25481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 5.810 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.510 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 3341 Z= 0.165 Angle : 0.531 8.526 4536 Z= 0.278 Chirality : 0.036 0.123 575 Planarity : 0.003 0.033 555 Dihedral : 14.734 76.625 1201 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 21.61 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.40), residues: 429 helix: 1.76 (0.28), residues: 337 sheet: -0.35 (1.12), residues: 18 loop : -2.37 (0.58), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.010 0.001 PHE A 239 TYR 0.018 0.002 TYR A 305 ARG 0.001 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.364 Fit side-chains REVERT: A 329 MET cc_start: 0.4939 (mpp) cc_final: 0.4656 (mpp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1861 time to fit residues: 10.2039 Evaluate side-chains 42 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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: 4.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3341 Z= 0.163 Angle : 0.484 5.778 4536 Z= 0.252 Chirality : 0.036 0.116 575 Planarity : 0.003 0.031 555 Dihedral : 3.609 18.549 455 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.32 % Allowed : 19.11 % Favored : 77.56 % 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: 1.77 (0.40), residues: 429 helix: 1.92 (0.28), residues: 341 sheet: 0.38 (1.09), residues: 16 loop : -2.39 (0.57), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR A 305 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.317 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 0.1554 time to fit residues: 10.5955 Evaluate side-chains 51 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 441 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3341 Z= 0.225 Angle : 0.528 5.923 4536 Z= 0.276 Chirality : 0.038 0.112 575 Planarity : 0.003 0.030 555 Dihedral : 3.824 19.011 455 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.88 % Allowed : 19.94 % Favored : 76.18 % 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: 1.41 (0.39), residues: 429 helix: 1.68 (0.28), residues: 341 sheet: -0.03 (1.09), residues: 16 loop : -2.54 (0.53), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.014 0.002 PHE A 240 TYR 0.014 0.002 TYR A 305 ARG 0.001 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 61 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.363 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 58 average time/residue: 0.1480 time to fit residues: 10.8639 Evaluate side-chains 53 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.0870 chunk 29 optimal weight: 0.0060 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.0000 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 0.0050 chunk 34 optimal weight: 3.9990 overall best weight: 0.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1244 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= 0.126 Angle : 0.450 6.107 4536 Z= 0.232 Chirality : 0.035 0.119 575 Planarity : 0.003 0.030 555 Dihedral : 3.504 18.007 455 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.22 % Allowed : 21.88 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.40), residues: 429 helix: 2.03 (0.28), residues: 341 sheet: 0.01 (1.07), residues: 16 loop : -2.45 (0.57), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.002 0.001 HIS A 41 PHE 0.007 0.001 PHE A 239 TYR 0.010 0.001 TYR A 305 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.364 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 0.1431 time to fit residues: 9.7583 Evaluate side-chains 44 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3341 Z= 0.226 Angle : 0.530 9.323 4536 Z= 0.272 Chirality : 0.037 0.116 575 Planarity : 0.003 0.027 555 Dihedral : 3.689 18.377 455 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.43 % Allowed : 21.05 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.40), residues: 429 helix: 1.79 (0.28), residues: 339 sheet: -0.12 (1.05), residues: 16 loop : -2.64 (0.54), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.014 0.002 PHE A 240 TYR 0.014 0.002 TYR A 305 ARG 0.001 0.000 ARG A 445 *********************** 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 57 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 0.317 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 55 average time/residue: 0.1366 time to fit residues: 9.5202 Evaluate side-chains 51 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 chunk 3 optimal weight: 0.0470 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3341 Z= 0.145 Angle : 0.473 8.588 4536 Z= 0.242 Chirality : 0.036 0.112 575 Planarity : 0.003 0.028 555 Dihedral : 3.534 18.000 455 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.60 % Allowed : 22.44 % 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: 1.70 (0.40), residues: 429 helix: 1.96 (0.28), residues: 339 sheet: -0.27 (1.04), residues: 16 loop : -2.66 (0.54), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.008 0.001 PHE A 218 TYR 0.011 0.001 TYR A 305 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 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 54 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.325 Fit side-chains REVERT: A 472 GLN cc_start: 0.7050 (tm-30) cc_final: 0.6690 (pp30) outliers start: 13 outliers final: 12 residues processed: 52 average time/residue: 0.1417 time to fit residues: 9.4090 Evaluate side-chains 51 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3341 Z= 0.206 Angle : 0.516 7.794 4536 Z= 0.265 Chirality : 0.037 0.111 575 Planarity : 0.003 0.028 555 Dihedral : 3.662 18.277 455 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.71 % Allowed : 21.33 % 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: 1.45 (0.40), residues: 429 helix: 1.81 (0.28), residues: 339 sheet: -0.45 (1.02), residues: 16 loop : -2.79 (0.52), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.013 0.002 PHE A 240 TYR 0.012 0.002 TYR A 305 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 40 time to evaluate : 0.356 Fit side-chains REVERT: A 472 GLN cc_start: 0.7109 (tm-30) cc_final: 0.6727 (pp30) outliers start: 17 outliers final: 13 residues processed: 54 average time/residue: 0.1492 time to fit residues: 10.1203 Evaluate side-chains 51 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 475 VAL 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: 0.8980 chunk 3 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 0.0270 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.0770 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1376 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 : 0.502 8.004 4536 Z= 0.256 Chirality : 0.036 0.110 575 Planarity : 0.003 0.028 555 Dihedral : 3.623 18.181 455 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.88 % Allowed : 23.27 % Favored : 72.85 % 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: 1.47 (0.40), residues: 429 helix: 1.82 (0.28), residues: 339 sheet: -0.43 (1.03), residues: 16 loop : -2.80 (0.53), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 PHE 0.010 0.001 PHE A 240 TYR 0.013 0.002 TYR A 373 ARG 0.002 0.000 ARG A 353 *********************** 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 55 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.359 Fit side-chains REVERT: A 60 MET cc_start: 0.8514 (mmm) cc_final: 0.8124 (mmp) REVERT: A 416 LEU cc_start: 0.6199 (mt) cc_final: 0.5883 (mm) REVERT: A 472 GLN cc_start: 0.7113 (tm-30) cc_final: 0.6692 (pp30) outliers start: 14 outliers final: 13 residues processed: 52 average time/residue: 0.1468 time to fit residues: 9.7056 Evaluate side-chains 50 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 37 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3341 Z= 0.247 Angle : 0.554 7.309 4536 Z= 0.286 Chirality : 0.038 0.131 575 Planarity : 0.003 0.028 555 Dihedral : 3.829 18.760 455 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.71 % Allowed : 22.99 % 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: 1.15 (0.39), residues: 429 helix: 1.59 (0.28), residues: 339 sheet: -0.57 (1.02), residues: 16 loop : -2.91 (0.50), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.015 0.002 PHE A 240 TYR 0.014 0.002 TYR A 373 ARG 0.002 0.000 ARG A 353 *********************** 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 58 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 0.336 Fit side-chains REVERT: A 60 MET cc_start: 0.8571 (mmm) cc_final: 0.8215 (mmp) REVERT: A 416 LEU cc_start: 0.6162 (mt) cc_final: 0.5857 (mm) outliers start: 17 outliers final: 15 residues processed: 54 average time/residue: 0.1322 time to fit residues: 9.1435 Evaluate side-chains 54 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 10.0000 chunk 3 optimal weight: 0.0050 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1486 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= 0.179 Angle : 0.523 10.056 4536 Z= 0.265 Chirality : 0.036 0.110 575 Planarity : 0.003 0.028 555 Dihedral : 3.699 18.362 455 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.88 % Allowed : 23.27 % Favored : 72.85 % 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: 1.28 (0.40), residues: 429 helix: 1.69 (0.28), residues: 339 sheet: -0.58 (1.02), residues: 16 loop : -2.87 (0.52), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 PHE 0.010 0.001 PHE A 240 TYR 0.013 0.002 TYR A 373 ARG 0.001 0.000 ARG A 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.372 Fit side-chains REVERT: A 60 MET cc_start: 0.8483 (mmm) cc_final: 0.8132 (mmp) REVERT: A 142 MET cc_start: 0.8159 (mmm) cc_final: 0.7877 (mmm) REVERT: A 472 GLN cc_start: 0.7155 (tm-30) cc_final: 0.6952 (pp30) outliers start: 14 outliers final: 12 residues processed: 50 average time/residue: 0.1401 time to fit residues: 8.9782 Evaluate side-chains 49 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.0070 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.0770 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.185164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135892 restraints weight = 3955.198| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.13 r_work: 0.3421 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3341 Z= 0.145 Angle : 0.501 10.146 4536 Z= 0.250 Chirality : 0.036 0.110 575 Planarity : 0.003 0.028 555 Dihedral : 3.528 17.628 455 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.32 % Allowed : 23.55 % 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: 1.50 (0.40), residues: 429 helix: 1.87 (0.28), residues: 338 sheet: -0.49 (1.03), residues: 16 loop : -2.89 (0.52), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.008 0.001 PHE A 218 TYR 0.013 0.001 TYR A 373 ARG 0.004 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1096.94 seconds wall clock time: 20 minutes 37.19 seconds (1237.19 seconds total)