Starting phenix.real_space_refine on Fri Apr 5 13:43:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtv_36653/04_2024/8jtv_36653_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtv_36653/04_2024/8jtv_36653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtv_36653/04_2024/8jtv_36653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtv_36653/04_2024/8jtv_36653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtv_36653/04_2024/8jtv_36653_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtv_36653/04_2024/8jtv_36653_updated.pdb" } resolution = 3.77 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= 0.107 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 27 5.16 5 C 2010 2.51 5 N 505 2.21 5 O 525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3067 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3058 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 21, 'TRANS': 415} Chain breaks: 2 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 276 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 211 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: 2.18, per 1000 atoms: 0.71 Number of scatterers: 3067 At special positions: 0 Unit cell: (70.3625, 88.765, 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 27 16.00 O 525 8.00 N 505 7.00 C 2010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 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: 1.19 Conformation dependent library (CDL) restraints added in 624.1 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 800 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 1 sheets defined 70.0% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 removed outlier: 3.671A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.556A pdb=" N GLU A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 105 through 108 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 145 through 170 Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.666A pdb=" N PHE A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 227 Processing helix chain 'A' and resid 234 through 257 Processing helix chain 'A' and resid 261 through 272 Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 341 through 371 removed outlier: 3.653A pdb=" N ARG A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 396 removed outlier: 3.737A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 404 through 422 Processing helix chain 'A' and resid 428 through 456 removed outlier: 3.701A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 487 removed outlier: 3.560A pdb=" N LEU A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 4.019A pdb=" N ARG A 486 " --> pdb=" O PHE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 512 removed outlier: 4.299A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 48 through 50 216 hydrogen bonds defined for protein. 645 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: 0.80 Time building geometry restraints manager: 1.32 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: 961 1.34 - 1.46: 688 1.46 - 1.58: 1451 1.58 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 3139 Sorted by residual: bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.451 -0.170 2.00e-02 2.50e+03 7.19e+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 4.94e+01 bond pdb=" C04 MF8 A 601 " pdb=" N02 MF8 A 601 " ideal model delta sigma weight residual 1.362 1.444 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C07 MF8 A 601 " pdb=" N09 MF8 A 601 " ideal model delta sigma weight residual 1.358 1.439 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C04 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.387 1.451 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 3134 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.53: 107 106.53 - 113.58: 1727 113.58 - 120.62: 1421 120.62 - 127.67: 1011 127.67 - 134.72: 39 Bond angle restraints: 4305 Sorted by residual: angle pdb=" N VAL A 103 " pdb=" CA VAL A 103 " pdb=" C VAL A 103 " ideal model delta sigma weight residual 111.56 104.18 7.38 8.60e-01 1.35e+00 7.37e+01 angle pdb=" C VAL A 103 " pdb=" CA VAL A 103 " pdb=" CB VAL A 103 " ideal model delta sigma weight residual 111.44 116.67 -5.23 9.50e-01 1.11e+00 3.03e+01 angle pdb=" N ASP A 104 " pdb=" CA ASP A 104 " pdb=" CB ASP A 104 " ideal model delta sigma weight residual 111.09 105.80 5.29 1.24e+00 6.50e-01 1.82e+01 angle pdb=" N02 MF8 A 601 " pdb=" C04 MF8 A 601 " pdb=" N05 MF8 A 601 " ideal model delta sigma weight residual 126.24 117.99 8.25 3.00e+00 1.11e-01 7.57e+00 angle pdb=" N ILE A 483 " pdb=" CA ILE A 483 " pdb=" C ILE A 483 " ideal model delta sigma weight residual 111.81 109.50 2.31 8.60e-01 1.35e+00 7.20e+00 ... (remaining 4300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.71: 1617 13.71 - 27.42: 127 27.42 - 41.13: 54 41.13 - 54.84: 4 54.84 - 68.56: 4 Dihedral angle restraints: 1806 sinusoidal: 560 harmonic: 1246 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual 93.00 24.44 68.56 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 160.55 -67.55 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CA LEU A 140 " pdb=" C LEU A 140 " pdb=" N VAL A 141 " pdb=" CA VAL A 141 " ideal model delta harmonic sigma weight residual -180.00 -163.67 -16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 1803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 290 0.025 - 0.050: 143 0.050 - 0.076: 56 0.076 - 0.101: 27 0.101 - 0.126: 8 Chirality restraints: 524 Sorted by residual: chirality pdb=" CB VAL A 385 " pdb=" CA VAL A 385 " pdb=" CG1 VAL A 385 " pdb=" CG2 VAL A 385 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA THR A 480 " pdb=" N THR A 480 " pdb=" C THR A 480 " pdb=" CB THR A 480 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.34e-01 chirality pdb=" CA LEU A 494 " pdb=" N LEU A 494 " pdb=" C LEU A 494 " pdb=" CB LEU A 494 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.98e-01 ... (remaining 521 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " 0.078 2.00e-02 2.50e+03 6.73e-02 1.02e+02 pdb=" C03 MF8 A 601 " 0.003 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " -0.044 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " -0.017 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " 0.014 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " -0.008 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " -0.152 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " 0.037 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 258 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO A 259 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 33 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 34 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 34 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 34 " -0.021 5.00e-02 4.00e+02 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 870 2.81 - 3.34: 3194 3.34 - 3.86: 5151 3.86 - 4.38: 5269 4.38 - 4.90: 9318 Nonbonded interactions: 23802 Sorted by model distance: nonbonded pdb=" OH TYR A 72 " pdb=" O VAL A 103 " model vdw 2.293 2.440 nonbonded pdb=" OG SER A 409 " pdb=" O GLY A 441 " model vdw 2.302 2.440 nonbonded pdb=" OD1 ASN A 186 " pdb=" NE2 GLN A 209 " model vdw 2.341 2.520 nonbonded pdb=" O CYS A 88 " pdb=" NH1 ARG A 89 " model vdw 2.350 2.520 nonbonded pdb=" O ILE A 392 " pdb=" OG1 THR A 396 " model vdw 2.369 2.440 ... (remaining 23797 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: 0.000 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: 0.010 Extract box with map and model: 1.810 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.470 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 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 0.170 3139 Z= 0.398 Angle : 0.664 8.457 4305 Z= 0.366 Chirality : 0.039 0.126 524 Planarity : 0.005 0.067 540 Dihedral : 12.161 65.075 997 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.36 % Allowed : 1.44 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.41), residues: 431 helix: 1.42 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.42 (0.51), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.003 0.001 HIS A 48 PHE 0.014 0.001 PHE A 159 TYR 0.013 0.001 TYR A 361 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.301 Fit side-chains REVERT: A 35 ILE cc_start: 0.5840 (mm) cc_final: 0.5552 (mm) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.0970 time to fit residues: 6.4469 Evaluate side-chains 36 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3139 Z= 0.199 Angle : 0.574 8.612 4305 Z= 0.280 Chirality : 0.038 0.132 524 Planarity : 0.004 0.043 540 Dihedral : 4.266 40.116 456 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.44 % Allowed : 9.03 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.42), residues: 431 helix: 1.69 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.11 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.015 0.001 PHE A 348 TYR 0.007 0.001 TYR A 361 ARG 0.002 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.237 Fit side-chains REVERT: A 35 ILE cc_start: 0.6197 (mm) cc_final: 0.5989 (mm) REVERT: A 420 MET cc_start: 0.7608 (ttm) cc_final: 0.7374 (tpp) REVERT: A 435 MET cc_start: 0.6950 (tpp) cc_final: 0.6716 (tpp) outliers start: 4 outliers final: 4 residues processed: 42 average time/residue: 0.1075 time to fit residues: 6.1211 Evaluate side-chains 42 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.0060 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3139 Z= 0.203 Angle : 0.566 8.837 4305 Z= 0.276 Chirality : 0.037 0.134 524 Planarity : 0.004 0.037 540 Dihedral : 4.159 37.703 456 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.53 % Allowed : 12.27 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.42), residues: 431 helix: 1.79 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -2.09 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 354 HIS 0.001 0.001 HIS A 48 PHE 0.014 0.001 PHE A 273 TYR 0.006 0.001 TYR A 361 ARG 0.002 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.306 Fit side-chains REVERT: A 35 ILE cc_start: 0.6273 (mm) cc_final: 0.6023 (mm) REVERT: A 258 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7510 (pp) REVERT: A 406 MET cc_start: 0.7200 (tpp) cc_final: 0.6939 (tpt) REVERT: A 420 MET cc_start: 0.7718 (ttm) cc_final: 0.7438 (tpp) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.0897 time to fit residues: 5.6265 Evaluate side-chains 44 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3139 Z= 0.203 Angle : 0.570 8.960 4305 Z= 0.277 Chirality : 0.037 0.136 524 Planarity : 0.004 0.036 540 Dihedral : 4.184 39.203 456 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.89 % Allowed : 15.52 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.42), residues: 431 helix: 1.78 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -2.01 (0.56), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.017 0.001 PHE A 273 TYR 0.005 0.001 TYR A 361 ARG 0.001 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.316 Fit side-chains REVERT: A 217 TRP cc_start: 0.6170 (t60) cc_final: 0.5918 (t60) REVERT: A 406 MET cc_start: 0.7320 (tpp) cc_final: 0.6965 (tpt) outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 0.1023 time to fit residues: 6.3143 Evaluate side-chains 44 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3139 Z= 0.199 Angle : 0.579 8.807 4305 Z= 0.279 Chirality : 0.037 0.134 524 Planarity : 0.004 0.038 540 Dihedral : 4.179 38.795 456 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.17 % Allowed : 16.97 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.42), residues: 431 helix: 1.74 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.00 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.013 0.001 PHE A 273 TYR 0.008 0.001 TYR A 256 ARG 0.001 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.310 Fit side-chains REVERT: A 217 TRP cc_start: 0.6179 (t60) cc_final: 0.5926 (t60) outliers start: 6 outliers final: 6 residues processed: 42 average time/residue: 0.0990 time to fit residues: 5.7433 Evaluate side-chains 43 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 4 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN A 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3139 Z= 0.198 Angle : 0.576 8.701 4305 Z= 0.277 Chirality : 0.037 0.132 524 Planarity : 0.003 0.033 540 Dihedral : 4.172 38.956 456 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.97 % Allowed : 18.77 % Favored : 77.26 % 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: 1.15 (0.42), residues: 431 helix: 1.72 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.02 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.011 0.001 PHE A 273 TYR 0.007 0.001 TYR A 361 ARG 0.001 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.289 Fit side-chains REVERT: A 217 TRP cc_start: 0.6233 (t60) cc_final: 0.6000 (t60) outliers start: 11 outliers final: 8 residues processed: 44 average time/residue: 0.0969 time to fit residues: 5.9039 Evaluate side-chains 44 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3139 Z= 0.193 Angle : 0.590 9.157 4305 Z= 0.279 Chirality : 0.037 0.136 524 Planarity : 0.003 0.035 540 Dihedral : 4.172 39.205 456 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.25 % Allowed : 20.22 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.42), residues: 431 helix: 1.73 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.16 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 273 TYR 0.006 0.001 TYR A 256 ARG 0.001 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.305 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 44 average time/residue: 0.0986 time to fit residues: 6.0262 Evaluate side-chains 47 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3139 Z= 0.208 Angle : 0.598 8.538 4305 Z= 0.285 Chirality : 0.037 0.130 524 Planarity : 0.003 0.033 540 Dihedral : 4.210 39.646 456 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.97 % Allowed : 19.49 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.42), residues: 431 helix: 1.76 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -2.09 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 151 TYR 0.005 0.001 TYR A 361 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.273 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 45 average time/residue: 0.0990 time to fit residues: 6.0807 Evaluate side-chains 47 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.0000 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.0870 overall best weight: 0.4162 ------------------------------------------------------------------------------- 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: 0.6258 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3139 Z= 0.179 Angle : 0.577 8.319 4305 Z= 0.273 Chirality : 0.036 0.128 524 Planarity : 0.003 0.032 540 Dihedral : 4.128 39.372 456 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.61 % Allowed : 20.58 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.42), residues: 431 helix: 1.84 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -2.05 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.020 0.001 PHE A 273 TYR 0.006 0.001 TYR A 361 ARG 0.001 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.311 Fit side-chains REVERT: A 217 TRP cc_start: 0.6239 (t60) cc_final: 0.6032 (t60) REVERT: A 387 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.6954 (tp) outliers start: 10 outliers final: 9 residues processed: 46 average time/residue: 0.1025 time to fit residues: 6.4651 Evaluate side-chains 46 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 26 optimal weight: 0.0770 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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: 0.6319 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3139 Z= 0.212 Angle : 0.614 8.396 4305 Z= 0.289 Chirality : 0.037 0.136 524 Planarity : 0.003 0.032 540 Dihedral : 4.197 39.759 456 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.61 % Allowed : 20.94 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.42), residues: 431 helix: 1.76 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -2.05 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.018 0.001 PHE A 273 TYR 0.005 0.001 TYR A 361 ARG 0.002 0.000 ARG A 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.325 Fit side-chains REVERT: A 387 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7014 (tp) REVERT: A 440 MET cc_start: 0.6771 (tmm) cc_final: 0.6472 (ttp) outliers start: 10 outliers final: 9 residues processed: 44 average time/residue: 0.0869 time to fit residues: 5.4225 Evaluate side-chains 46 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 6 optimal weight: 0.0170 chunk 29 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.221111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.196782 restraints weight = 3595.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.200292 restraints weight = 2667.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.201782 restraints weight = 2189.321| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3139 Z= 0.171 Angle : 0.581 8.061 4305 Z= 0.272 Chirality : 0.036 0.122 524 Planarity : 0.003 0.032 540 Dihedral : 4.093 39.386 456 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.61 % Allowed : 20.94 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.42), residues: 431 helix: 1.84 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -2.04 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 429 HIS 0.001 0.000 HIS A 49 PHE 0.020 0.001 PHE A 273 TYR 0.006 0.001 TYR A 361 ARG 0.001 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 991.42 seconds wall clock time: 18 minutes 42.34 seconds (1122.34 seconds total)