Starting phenix.real_space_refine on Thu Nov 14 03:55:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/11_2024/8sdy_40354.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/11_2024/8sdy_40354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/11_2024/8sdy_40354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/11_2024/8sdy_40354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/11_2024/8sdy_40354.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdy_40354/11_2024/8sdy_40354.cif" } resolution = 2.79 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= 0.002 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 30 5.16 5 C 2528 2.51 5 N 653 2.21 5 O 683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3894 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3840 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3831 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 25, 'TRANS': 468} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 494, 3831 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 25, 'TRANS': 468} Chain breaks: 3 bond proxies already assigned to first conformer: 3912 Chain: "A" Number of atoms: 54 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 13, 26 Unusual residues: {'ZWD': 1} Classifications: {'undetermined': 1, 'water': 12} Link IDs: {None: 12} Conformer: "B" Number of residues, atoms: 13, 26 Unusual residues: {'ZWD': 1} Classifications: {'undetermined': 1, 'water': 12} Link IDs: {None: 12} Conformer: "C" Number of residues, atoms: 13, 26 Unusual residues: {'ZWD': 1} Classifications: {'undetermined': 1, 'water': 12} Link IDs: {None: 12} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALYS A 382 " occ=0.52 ... (16 atoms not shown) pdb=" NZ BLYS A 382 " occ=0.48 residue: pdb=" C01AZWD A 601 " occ=0.85 ... (40 atoms not shown) pdb=" O13CZWD A 601 " occ=0.14 Time building chain proxies: 4.67, per 1000 atoms: 1.20 Number of scatterers: 3894 At special positions: 0 Unit cell: (85.49, 68.89, 94.62, 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 30 16.00 O 683 8.00 N 653 7.00 C 2528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 82.0% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.786A pdb=" N GLY A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 27 through 36 removed outlier: 4.003A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 131 through 160 removed outlier: 4.204A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 Processing helix chain 'A' and resid 184 through 213 removed outlier: 3.844A pdb=" N MET A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 244 removed outlier: 3.563A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.966A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 297 through 304 removed outlier: 3.786A pdb=" N LYS A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.623A pdb=" N ARG A 331 " --> pdb=" O MET A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 358 removed outlier: 3.861A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 4.128A pdb=" N PHE A 363 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY A 364 " --> pdb=" O GLN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 377 through 392 Processing helix chain 'A' and resid 393 through 415 removed outlier: 3.500A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.684A pdb=" N TYR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 484 through 502 Proline residue: A 494 - end of helix removed outlier: 3.813A pdb=" N ALA A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 274 hydrogen bonds defined for protein. 811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 586 1.31 - 1.44: 1105 1.44 - 1.56: 2236 1.56 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 3974 Sorted by residual: bond pdb=" C07AZWD A 601 " pdb=" N09AZWD A 601 " ideal model delta sigma weight residual 1.350 1.453 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C07BZWD A 601 " pdb=" N09BZWD A 601 " ideal model delta sigma weight residual 1.350 1.451 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C07CZWD A 601 " pdb=" N09CZWD A 601 " ideal model delta sigma weight residual 1.350 1.450 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C03AZWD A 601 " pdb=" N14AZWD A 601 " ideal model delta sigma weight residual 1.379 1.451 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C03BZWD A 601 " pdb=" N14BZWD A 601 " ideal model delta sigma weight residual 1.379 1.450 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 3969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 5217 1.46 - 2.91: 121 2.91 - 4.37: 50 4.37 - 5.82: 10 5.82 - 7.28: 4 Bond angle restraints: 5402 Sorted by residual: angle pdb=" CA GLN A 289 " pdb=" CB GLN A 289 " pdb=" CG GLN A 289 " ideal model delta sigma weight residual 114.10 120.60 -6.50 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA TYR A 264 " pdb=" CB TYR A 264 " pdb=" CG TYR A 264 " ideal model delta sigma weight residual 113.90 119.00 -5.10 1.80e+00 3.09e-01 8.02e+00 angle pdb=" CG ARG A 290 " pdb=" CD ARG A 290 " pdb=" NE ARG A 290 " ideal model delta sigma weight residual 112.00 117.66 -5.66 2.20e+00 2.07e-01 6.62e+00 angle pdb=" O12AZWD A 601 " pdb=" C11AZWD A 601 " pdb=" O13AZWD A 601 " ideal model delta sigma weight residual 127.09 119.81 7.28 3.00e+00 1.11e-01 5.89e+00 angle pdb=" O12BZWD A 601 " pdb=" C11BZWD A 601 " pdb=" O13BZWD A 601 " ideal model delta sigma weight residual 127.09 120.13 6.96 3.00e+00 1.11e-01 5.39e+00 ... (remaining 5397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 2001 17.59 - 35.18: 255 35.18 - 52.77: 80 52.77 - 70.36: 9 70.36 - 87.95: 4 Dihedral angle restraints: 2349 sinusoidal: 920 harmonic: 1429 Sorted by residual: dihedral pdb=" CG ARG A 290 " pdb=" CD ARG A 290 " pdb=" NE ARG A 290 " pdb=" CZ ARG A 290 " ideal model delta sinusoidal sigma weight residual 90.00 41.14 48.86 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CG ARG A 280 " pdb=" CD ARG A 280 " pdb=" NE ARG A 280 " pdb=" CZ ARG A 280 " ideal model delta sinusoidal sigma weight residual 180.00 136.55 43.45 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG A 80 " pdb=" CD ARG A 80 " pdb=" NE ARG A 80 " pdb=" CZ ARG A 80 " ideal model delta sinusoidal sigma weight residual 90.00 133.22 -43.22 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 2346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 390 0.027 - 0.055: 149 0.055 - 0.082: 58 0.082 - 0.110: 20 0.110 - 0.137: 8 Chirality restraints: 625 Sorted by residual: chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 269 " pdb=" N ILE A 269 " pdb=" C ILE A 269 " pdb=" CB ILE A 269 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 622 not shown) Planarity restraints: 673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 290 " -0.202 9.50e-02 1.11e+02 9.10e-02 5.88e+00 pdb=" NE ARG A 290 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 290 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 290 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 290 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 395 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO A 396 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 332 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A 333 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " -0.015 5.00e-02 4.00e+02 ... (remaining 670 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 40 2.59 - 3.17: 3437 3.17 - 3.75: 6386 3.75 - 4.32: 8807 4.32 - 4.90: 14720 Nonbonded interactions: 33390 Sorted by model distance: nonbonded pdb=" OH TYR A 444 " pdb=" O PRO A 505 " model vdw 2.018 3.040 nonbonded pdb=" OG SER A 33 " pdb=" O HOH A 701 " model vdw 2.066 3.040 nonbonded pdb=" OD1 ASN A 168 " pdb=" OG SER A 201 " model vdw 2.201 3.040 nonbonded pdb=" NH2 ARG A 80 " pdb=" OE2 GLU A 103 " model vdw 2.222 3.120 nonbonded pdb=" OG1 THR A 172 " pdb=" OG SER A 198 " model vdw 2.226 3.040 ... (remaining 33385 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=0.01 max=1.00 mean=0.99 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: 0.310 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.290 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 3974 Z= 0.343 Angle : 0.660 7.279 5402 Z= 0.319 Chirality : 0.037 0.137 625 Planarity : 0.005 0.091 673 Dihedral : 16.845 87.947 1425 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.72 % Allowed : 23.50 % Favored : 75.78 % 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: 2.03 (0.38), residues: 489 helix: 1.62 (0.27), residues: 374 sheet: -2.13 (1.49), residues: 10 loop : 1.03 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.003 0.001 HIS A 217 PHE 0.013 0.001 PHE A 442 TYR 0.016 0.001 TYR A 264 ARG 0.016 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.440 Fit side-chains REVERT: A 290 ARG cc_start: 0.6347 (mtp85) cc_final: 0.6129 (mmm-85) REVERT: A 389 ILE cc_start: 0.7839 (mt) cc_final: 0.7617 (mp) REVERT: A 437 SER cc_start: 0.8553 (t) cc_final: 0.8204 (p) REVERT: A 460 MET cc_start: 0.7089 (mmm) cc_final: 0.6785 (mmm) outliers start: 3 outliers final: 3 residues processed: 52 average time/residue: 1.1149 time to fit residues: 60.2848 Evaluate side-chains 52 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 462 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 38 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 17 GLN A 289 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3974 Z= 0.204 Angle : 0.570 6.190 5402 Z= 0.289 Chirality : 0.039 0.137 625 Planarity : 0.004 0.033 673 Dihedral : 6.595 54.834 563 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.68 % Allowed : 22.06 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.39), residues: 489 helix: 1.78 (0.27), residues: 375 sheet: -1.65 (1.45), residues: 10 loop : 0.88 (0.68), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 346 HIS 0.003 0.001 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.009 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.442 Fit side-chains REVERT: A 313 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6884 (mm) REVERT: A 437 SER cc_start: 0.8556 (t) cc_final: 0.8237 (p) REVERT: A 460 MET cc_start: 0.7113 (mmm) cc_final: 0.6813 (mmm) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 1.1512 time to fit residues: 64.4930 Evaluate side-chains 54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3974 Z= 0.168 Angle : 0.528 7.061 5402 Z= 0.268 Chirality : 0.038 0.131 625 Planarity : 0.004 0.031 673 Dihedral : 5.938 53.456 561 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.64 % Allowed : 21.34 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.39), residues: 489 helix: 1.96 (0.27), residues: 374 sheet: -1.44 (1.47), residues: 10 loop : 0.90 (0.69), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 274 HIS 0.003 0.001 HIS A 217 PHE 0.015 0.001 PHE A 351 TYR 0.015 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.391 Fit side-chains REVERT: A 103 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6501 (pm20) REVERT: A 225 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7184 (tm) REVERT: A 437 SER cc_start: 0.8580 (t) cc_final: 0.8287 (p) REVERT: A 460 MET cc_start: 0.7100 (mmt) cc_final: 0.6800 (mmm) outliers start: 11 outliers final: 3 residues processed: 57 average time/residue: 1.1449 time to fit residues: 67.8252 Evaluate side-chains 54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7943 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3974 Z= 0.162 Angle : 0.520 7.102 5402 Z= 0.263 Chirality : 0.038 0.161 625 Planarity : 0.004 0.034 673 Dihedral : 5.576 52.330 561 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.60 % Allowed : 20.38 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.39), residues: 489 helix: 1.95 (0.27), residues: 373 sheet: -1.34 (1.47), residues: 10 loop : 0.90 (0.68), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 213 HIS 0.002 0.000 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.007 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.394 Fit side-chains REVERT: A 103 GLU cc_start: 0.7163 (pt0) cc_final: 0.6209 (pm20) REVERT: A 313 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6819 (mm) REVERT: A 437 SER cc_start: 0.8567 (t) cc_final: 0.8282 (p) REVERT: A 460 MET cc_start: 0.7119 (mmt) cc_final: 0.6825 (mmm) outliers start: 15 outliers final: 4 residues processed: 61 average time/residue: 1.0765 time to fit residues: 68.3277 Evaluate side-chains 53 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 27 optimal weight: 7.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3974 Z= 0.162 Angle : 0.534 7.343 5402 Z= 0.265 Chirality : 0.038 0.185 625 Planarity : 0.004 0.032 673 Dihedral : 5.267 51.244 561 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.64 % Allowed : 21.34 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.39), residues: 489 helix: 1.96 (0.27), residues: 373 sheet: -1.22 (1.49), residues: 10 loop : 0.88 (0.68), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 274 HIS 0.002 0.001 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.017 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.442 Fit side-chains REVERT: A 103 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6197 (pm20) REVERT: A 313 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6773 (mm) REVERT: A 437 SER cc_start: 0.8567 (t) cc_final: 0.8278 (p) REVERT: A 460 MET cc_start: 0.7117 (mmt) cc_final: 0.6818 (mmm) outliers start: 11 outliers final: 4 residues processed: 54 average time/residue: 1.1180 time to fit residues: 62.8432 Evaluate side-chains 54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.7897 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3974 Z= 0.143 Angle : 0.521 7.302 5402 Z= 0.258 Chirality : 0.038 0.186 625 Planarity : 0.004 0.031 673 Dihedral : 4.866 49.224 561 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.92 % Allowed : 21.34 % Favored : 76.74 % 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: 2.50 (0.39), residues: 489 helix: 2.01 (0.27), residues: 374 sheet: -1.16 (1.51), residues: 10 loop : 0.87 (0.68), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 274 HIS 0.001 0.000 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.460 Fit side-chains REVERT: A 103 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6176 (pm20) REVERT: A 313 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6776 (mm) REVERT: A 437 SER cc_start: 0.8568 (t) cc_final: 0.8297 (p) REVERT: A 460 MET cc_start: 0.7066 (mmt) cc_final: 0.6788 (mmm) outliers start: 8 outliers final: 4 residues processed: 55 average time/residue: 1.1535 time to fit residues: 65.9239 Evaluate side-chains 53 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 28 optimal weight: 0.0570 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3974 Z= 0.182 Angle : 0.555 6.747 5402 Z= 0.281 Chirality : 0.039 0.166 625 Planarity : 0.004 0.028 673 Dihedral : 4.989 48.742 561 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.40 % Allowed : 21.82 % Favored : 75.78 % 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: 2.29 (0.38), residues: 489 helix: 1.84 (0.26), residues: 373 sheet: -1.13 (1.49), residues: 10 loop : 0.84 (0.68), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 213 HIS 0.002 0.001 HIS A 48 PHE 0.012 0.001 PHE A 351 TYR 0.018 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.447 Fit side-chains REVERT: A 103 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6235 (pm20) REVERT: A 313 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6773 (mm) REVERT: A 437 SER cc_start: 0.8652 (t) cc_final: 0.8340 (p) REVERT: A 460 MET cc_start: 0.7134 (mmt) cc_final: 0.6827 (mmm) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 1.1533 time to fit residues: 68.3164 Evaluate side-chains 57 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.0070 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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: 0.7908 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3974 Z= 0.160 Angle : 0.561 7.551 5402 Z= 0.284 Chirality : 0.038 0.152 625 Planarity : 0.004 0.032 673 Dihedral : 4.831 47.703 561 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.16 % Allowed : 22.78 % Favored : 75.06 % 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: 2.32 (0.39), residues: 489 helix: 1.81 (0.27), residues: 377 sheet: -0.97 (1.51), residues: 10 loop : 1.02 (0.70), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 213 HIS 0.001 0.000 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.500 Fit side-chains REVERT: A 103 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6245 (pm20) REVERT: A 313 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6772 (mm) REVERT: A 437 SER cc_start: 0.8600 (t) cc_final: 0.8306 (p) REVERT: A 460 MET cc_start: 0.7087 (mmt) cc_final: 0.6799 (mmm) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 1.1286 time to fit residues: 65.6864 Evaluate side-chains 54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.0070 overall best weight: 0.8006 ------------------------------------------------------------------------------- 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: 0.7923 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3974 Z= 0.171 Angle : 0.563 7.346 5402 Z= 0.285 Chirality : 0.038 0.157 625 Planarity : 0.004 0.033 673 Dihedral : 4.829 47.211 561 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.16 % Allowed : 22.78 % Favored : 75.06 % 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: 2.28 (0.39), residues: 489 helix: 1.79 (0.26), residues: 377 sheet: -1.02 (1.48), residues: 10 loop : 0.97 (0.70), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 213 HIS 0.001 0.001 HIS A 48 PHE 0.013 0.001 PHE A 351 TYR 0.017 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7933 (mttt) cc_final: 0.7687 (mmtt) REVERT: A 103 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6235 (pm20) REVERT: A 313 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6682 (mm) REVERT: A 437 SER cc_start: 0.8611 (t) cc_final: 0.8309 (p) REVERT: A 460 MET cc_start: 0.7103 (mmt) cc_final: 0.6812 (mmm) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 1.1963 time to fit residues: 66.9799 Evaluate side-chains 54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.0170 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 0.0060 chunk 38 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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: 0.7878 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 3974 Z= 0.151 Angle : 0.551 7.379 5402 Z= 0.278 Chirality : 0.037 0.153 625 Planarity : 0.004 0.027 673 Dihedral : 4.684 46.072 561 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.92 % Allowed : 22.78 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.39), residues: 489 helix: 1.81 (0.27), residues: 378 sheet: -0.89 (1.54), residues: 10 loop : 1.01 (0.70), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.001 0.000 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.007 0.000 ARG A 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7884 (mttt) cc_final: 0.7675 (mmtt) REVERT: A 103 GLU cc_start: 0.7103 (pt0) cc_final: 0.6237 (pm20) REVERT: A 290 ARG cc_start: 0.6592 (mmm-85) cc_final: 0.6252 (mtm180) REVERT: A 313 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6676 (mm) REVERT: A 437 SER cc_start: 0.8621 (t) cc_final: 0.8333 (p) REVERT: A 460 MET cc_start: 0.7066 (mmt) cc_final: 0.6775 (mmm) outliers start: 8 outliers final: 6 residues processed: 57 average time/residue: 1.3478 time to fit residues: 79.6547 Evaluate side-chains 54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 444 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.187347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.143053 restraints weight = 12769.743| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.02 r_work: 0.3546 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3974 Z= 0.163 Angle : 0.557 7.311 5402 Z= 0.281 Chirality : 0.038 0.153 625 Planarity : 0.004 0.027 673 Dihedral : 4.679 46.045 561 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.16 % Allowed : 22.78 % Favored : 75.06 % 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: 2.24 (0.39), residues: 489 helix: 1.77 (0.26), residues: 377 sheet: -0.94 (1.52), residues: 10 loop : 0.95 (0.70), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 213 HIS 0.001 0.000 HIS A 48 PHE 0.013 0.001 PHE A 351 TYR 0.017 0.001 TYR A 264 ARG 0.007 0.000 ARG A 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1853.48 seconds wall clock time: 38 minutes 20.42 seconds (2300.42 seconds total)