Starting phenix.real_space_refine on Thu Jul 18 19:34:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtt_36652/07_2024/8jtt_36652.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtt_36652/07_2024/8jtt_36652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtt_36652/07_2024/8jtt_36652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtt_36652/07_2024/8jtt_36652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtt_36652/07_2024/8jtt_36652.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtt_36652/07_2024/8jtt_36652.cif" } resolution = 3.87 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= 0.001 sd= 0.083 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 2182 2.51 5 N 534 2.21 5 O 584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3312 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 113 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.70, per 1000 atoms: 0.81 Number of scatterers: 3321 At special positions: 0 Unit cell: (85.5175, 58.455, 64.95, 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 584 8.00 N 534 7.00 C 2182 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: 1.46 Conformation dependent library (CDL) restraints added in 670.1 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 32 through 37 removed outlier: 4.023A pdb=" N CYS A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 143 through 173 removed outlier: 3.515A pdb=" N LEU A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 195 removed outlier: 3.724A pdb=" N PHE A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 255 removed outlier: 3.704A pdb=" N VAL A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 278 removed outlier: 3.907A pdb=" N LEU A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 294 through 310 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.794A pdb=" N GLU A 323 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 removed outlier: 4.146A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 338' Processing helix chain 'A' and resid 339 through 367 removed outlier: 5.596A pdb=" N LYS A 345 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 385 through 397 removed outlier: 3.749A pdb=" N GLY A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 Processing helix chain 'A' and resid 419 through 422 Processing helix chain 'A' and resid 429 through 456 removed outlier: 3.702A pdb=" N CYS A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 Processing helix chain 'A' and resid 473 through 491 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 492 through 510 removed outlier: 3.962A pdb=" N LEU A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.917A pdb=" N ALA A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 696 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: 0.83 Time building geometry restraints manager: 1.58 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: 1031 1.34 - 1.46: 712 1.46 - 1.58: 1625 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 3400 Sorted by residual: bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.439 -0.158 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C07 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.393 1.252 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C04 MF8 A 601 " pdb=" N02 MF8 A 601 " ideal model delta sigma weight residual 1.362 1.448 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C07 MF8 A 601 " pdb=" N09 MF8 A 601 " ideal model delta sigma weight residual 1.358 1.444 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C04 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.387 1.454 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 3395 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.28: 100 106.28 - 113.22: 1847 113.22 - 120.16: 1254 120.16 - 127.10: 1415 127.10 - 134.04: 45 Bond angle restraints: 4661 Sorted by residual: angle pdb=" N02 MF8 A 601 " pdb=" C04 MF8 A 601 " pdb=" N05 MF8 A 601 " ideal model delta sigma weight residual 126.24 116.62 9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" N02 MF8 A 601 " pdb=" C04 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 113.43 122.89 -9.46 3.00e+00 1.11e-01 9.93e+00 angle pdb=" N ARG A 439 " pdb=" CA ARG A 439 " pdb=" C ARG A 439 " ideal model delta sigma weight residual 111.07 107.88 3.19 1.07e+00 8.73e-01 8.88e+00 angle pdb=" N MET A 448 " pdb=" CA MET A 448 " pdb=" C MET A 448 " ideal model delta sigma weight residual 111.14 113.92 -2.78 1.08e+00 8.57e-01 6.62e+00 angle pdb=" C VAL A 212 " pdb=" CA VAL A 212 " pdb=" CB VAL A 212 " ideal model delta sigma weight residual 112.22 108.70 3.52 1.38e+00 5.25e-01 6.52e+00 ... (remaining 4656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 1766 16.55 - 33.10: 150 33.10 - 49.65: 31 49.65 - 66.20: 0 66.20 - 82.75: 1 Dihedral angle restraints: 1948 sinusoidal: 648 harmonic: 1300 Sorted by residual: dihedral pdb=" CA THR A 396 " pdb=" C THR A 396 " pdb=" N ILE A 397 " pdb=" CA ILE A 397 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU A 521 " pdb=" C LEU A 521 " pdb=" N PRO A 522 " pdb=" CA PRO A 522 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LEU A 27 " pdb=" C LEU A 27 " pdb=" N LEU A 28 " pdb=" CA LEU A 28 " ideal model delta harmonic sigma weight residual 180.00 164.52 15.48 0 5.00e+00 4.00e-02 9.59e+00 ... (remaining 1945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 414 0.048 - 0.097: 116 0.097 - 0.145: 29 0.145 - 0.193: 2 0.193 - 0.241: 4 Chirality restraints: 565 Sorted by residual: chirality pdb=" CB THR A 45 " pdb=" CA THR A 45 " pdb=" OG1 THR A 45 " pdb=" CG2 THR A 45 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB VAL A 228 " pdb=" CA VAL A 228 " pdb=" CG1 VAL A 228 " pdb=" CG2 VAL A 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL A 166 " pdb=" CA VAL A 166 " pdb=" CG1 VAL A 166 " pdb=" CG2 VAL A 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 562 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " -0.222 2.00e-02 2.50e+03 3.51e-01 2.78e+03 pdb=" C03 MF8 A 601 " -0.138 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " 0.229 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " -0.097 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " -0.043 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " 0.587 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " 0.083 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " 0.325 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " -0.723 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 271 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 282 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO A 283 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.027 5.00e-02 4.00e+02 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 752 2.78 - 3.31: 3285 3.31 - 3.84: 5585 3.84 - 4.37: 5758 4.37 - 4.90: 9929 Nonbonded interactions: 25309 Sorted by model distance: nonbonded pdb=" OG SER A 409 " pdb=" O GLY A 441 " model vdw 2.250 2.440 nonbonded pdb=" O PHE A 22 " pdb=" OH TYR A 240 " model vdw 2.252 2.440 nonbonded pdb=" O LEU A 42 " pdb=" OG SER A 133 " model vdw 2.348 2.440 nonbonded pdb=" OG1 THR A 245 " pdb=" OE1 GLU A 386 " model vdw 2.357 2.440 nonbonded pdb=" OG SER A 189 " pdb=" OE1 GLN A 209 " model vdw 2.391 2.440 ... (remaining 25304 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.490 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 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 : 0.006 0.158 3400 Z= 0.400 Angle : 0.869 9.617 4661 Z= 0.444 Chirality : 0.049 0.241 565 Planarity : 0.016 0.351 581 Dihedral : 12.926 82.753 1112 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -2.01 (0.35), residues: 450 helix: -0.51 (0.26), residues: 327 sheet: None (None), residues: 0 loop : -3.46 (0.45), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 217 HIS 0.002 0.001 HIS A 367 PHE 0.027 0.002 PHE A 482 TYR 0.015 0.001 TYR A 240 ARG 0.002 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0978 time to fit residues: 9.4249 Evaluate side-chains 54 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.0040 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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: 0.5861 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3400 Z= 0.184 Angle : 0.582 10.212 4661 Z= 0.295 Chirality : 0.039 0.142 565 Planarity : 0.005 0.049 581 Dihedral : 4.350 16.303 475 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.46 % Allowed : 9.23 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.38), residues: 450 helix: 0.35 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -3.40 (0.49), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 261 HIS 0.002 0.001 HIS A 260 PHE 0.008 0.001 PHE A 161 TYR 0.013 0.001 TYR A 199 ARG 0.002 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.334 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 58 average time/residue: 0.0882 time to fit residues: 7.2614 Evaluate side-chains 59 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 0.0670 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3400 Z= 0.163 Angle : 0.544 9.633 4661 Z= 0.274 Chirality : 0.037 0.137 565 Planarity : 0.004 0.044 581 Dihedral : 4.098 15.099 475 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.46 % Allowed : 13.85 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.40), residues: 450 helix: 0.74 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -3.12 (0.52), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 261 HIS 0.002 0.001 HIS A 260 PHE 0.009 0.001 PHE A 151 TYR 0.010 0.001 TYR A 199 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.364 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.1000 time to fit residues: 8.6879 Evaluate side-chains 62 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.0870 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.6336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3400 Z= 0.178 Angle : 0.551 9.492 4661 Z= 0.278 Chirality : 0.037 0.132 565 Planarity : 0.004 0.044 581 Dihedral : 4.078 15.044 475 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.77 % Allowed : 18.15 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.41), residues: 450 helix: 0.96 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.88 (0.52), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 261 HIS 0.003 0.001 HIS A 260 PHE 0.024 0.002 PHE A 151 TYR 0.008 0.001 TYR A 199 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.416 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.0792 time to fit residues: 7.2792 Evaluate side-chains 61 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 30 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 0.0010 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5865 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3400 Z= 0.154 Angle : 0.535 9.358 4661 Z= 0.268 Chirality : 0.036 0.124 565 Planarity : 0.004 0.044 581 Dihedral : 3.911 15.358 475 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.46 % Allowed : 19.08 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.41), residues: 450 helix: 1.10 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.82 (0.52), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 261 HIS 0.002 0.001 HIS A 260 PHE 0.015 0.001 PHE A 275 TYR 0.008 0.001 TYR A 199 ARG 0.001 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.373 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.0994 time to fit residues: 8.8454 Evaluate side-chains 62 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 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 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3400 Z= 0.204 Angle : 0.590 9.136 4661 Z= 0.295 Chirality : 0.038 0.134 565 Planarity : 0.004 0.044 581 Dihedral : 4.037 15.099 475 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.38 % Allowed : 19.69 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.41), residues: 450 helix: 1.00 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -2.82 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 261 HIS 0.003 0.002 HIS A 260 PHE 0.024 0.002 PHE A 151 TYR 0.008 0.001 TYR A 199 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.381 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 67 average time/residue: 0.0889 time to fit residues: 8.4277 Evaluate side-chains 67 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.0010 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3400 Z= 0.170 Angle : 0.565 9.157 4661 Z= 0.279 Chirality : 0.037 0.123 565 Planarity : 0.004 0.043 581 Dihedral : 3.927 15.556 475 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.38 % Allowed : 20.92 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.41), residues: 450 helix: 1.05 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -2.74 (0.55), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.015 0.001 PHE A 275 TYR 0.008 0.001 TYR A 199 ARG 0.001 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.388 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 65 average time/residue: 0.0901 time to fit residues: 8.2588 Evaluate side-chains 68 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.0070 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3400 Z= 0.202 Angle : 0.589 9.037 4661 Z= 0.294 Chirality : 0.037 0.130 565 Planarity : 0.004 0.043 581 Dihedral : 4.005 15.309 475 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.31 % Allowed : 21.54 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.41), residues: 450 helix: 1.02 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -2.70 (0.55), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.026 0.002 PHE A 151 TYR 0.007 0.001 TYR A 199 ARG 0.001 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.319 Fit side-chains REVERT: A 173 PHE cc_start: 0.4655 (OUTLIER) cc_final: 0.4155 (m-10) REVERT: A 371 THR cc_start: 0.4191 (OUTLIER) cc_final: 0.3807 (t) outliers start: 14 outliers final: 10 residues processed: 68 average time/residue: 0.0821 time to fit residues: 7.9023 Evaluate side-chains 70 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 44 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3400 Z= 0.202 Angle : 0.593 9.040 4661 Z= 0.297 Chirality : 0.037 0.125 565 Planarity : 0.004 0.043 581 Dihedral : 4.053 15.600 475 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.69 % Allowed : 23.38 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.41), residues: 450 helix: 0.99 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -2.57 (0.56), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.014 0.001 PHE A 275 TYR 0.009 0.001 TYR A 240 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.346 Fit side-chains REVERT: A 173 PHE cc_start: 0.4702 (OUTLIER) cc_final: 0.4236 (m-10) REVERT: A 371 THR cc_start: 0.4488 (OUTLIER) cc_final: 0.4130 (t) outliers start: 12 outliers final: 10 residues processed: 65 average time/residue: 0.0946 time to fit residues: 8.6928 Evaluate side-chains 68 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.0040 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3400 Z= 0.199 Angle : 0.593 8.935 4661 Z= 0.297 Chirality : 0.037 0.126 565 Planarity : 0.004 0.043 581 Dihedral : 4.011 15.680 475 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.69 % Allowed : 23.69 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.41), residues: 450 helix: 0.99 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -2.53 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.013 0.001 PHE A 275 TYR 0.007 0.001 TYR A 240 ARG 0.002 0.000 ARG A 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.365 Fit side-chains REVERT: A 173 PHE cc_start: 0.4748 (OUTLIER) cc_final: 0.4290 (m-10) REVERT: A 371 THR cc_start: 0.4522 (OUTLIER) cc_final: 0.4114 (t) REVERT: A 455 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7391 (mm-30) outliers start: 12 outliers final: 10 residues processed: 68 average time/residue: 0.0953 time to fit residues: 8.8373 Evaluate side-chains 70 residues out of total 382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.0170 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 0.0040 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** 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 = 0.5395 r_free = 0.5395 target = 0.296974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5189 r_free = 0.5189 target = 0.270553 restraints weight = 3872.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5225 r_free = 0.5225 target = 0.276032 restraints weight = 2204.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5244 r_free = 0.5244 target = 0.279143 restraints weight = 1492.100| |-----------------------------------------------------------------------------| r_work (final): 0.5243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3400 Z= 0.181 Angle : 0.580 9.083 4661 Z= 0.287 Chirality : 0.037 0.119 565 Planarity : 0.004 0.043 581 Dihedral : 3.899 15.804 475 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.69 % Allowed : 23.69 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.41), residues: 450 helix: 1.14 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -2.51 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.014 0.001 PHE A 22 TYR 0.006 0.001 TYR A 199 ARG 0.001 0.000 ARG A 439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1003.83 seconds wall clock time: 19 minutes 31.29 seconds (1171.29 seconds total)