Starting phenix.real_space_refine on Fri Dec 27 06:19:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ju0_36658/12_2024/8ju0_36658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ju0_36658/12_2024/8ju0_36658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ju0_36658/12_2024/8ju0_36658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ju0_36658/12_2024/8ju0_36658.map" model { file = "/net/cci-nas-00/data/ceres_data/8ju0_36658/12_2024/8ju0_36658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ju0_36658/12_2024/8ju0_36658.cif" } resolution = 2.98 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= -0.003 sd= 0.171 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 31 5.16 5 C 2117 2.51 5 N 519 2.21 5 O 532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3199 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3170 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 2 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SNL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.71, per 1000 atoms: 0.85 Number of scatterers: 3199 At special positions: 0 Unit cell: (58.455, 90.93, 68.1975, 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 31 16.00 O 532 8.00 N 519 7.00 C 2117 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 - 3.00 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: 0.90 Conformation dependent library (CDL) restraints added in 395.8 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 23 through 37 removed outlier: 3.573A pdb=" N LEU A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.683A pdb=" N SER A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 194 removed outlier: 4.073A pdb=" N LEU A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ARG A 172 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N LYS A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 227 removed outlier: 3.942A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 258 Processing helix chain 'A' and resid 260 through 275 Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 334 through 338 removed outlier: 3.835A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 338' Processing helix chain 'A' and resid 340 through 372 Processing helix chain 'A' and resid 374 through 400 Proline residue: A 388 - end of helix removed outlier: 4.174A pdb=" N PHE A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 423 removed outlier: 3.674A pdb=" N ILE A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 456 removed outlier: 3.623A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 488 Proline residue: A 481 - end of helix removed outlier: 4.396A pdb=" N ARG A 486 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' 235 hydrogen bonds defined for protein. 699 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: 0.87 Time building geometry restraints manager: 1.02 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: 478 1.31 - 1.43: 893 1.43 - 1.56: 1865 1.56 - 1.69: 2 1.69 - 1.81: 45 Bond restraints: 3283 Sorted by residual: bond pdb=" C15 SNL A 601 " pdb=" O58 SNL A 601 " ideal model delta sigma weight residual 1.332 1.545 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C22 SNL A 601 " pdb=" S61 SNL A 601 " ideal model delta sigma weight residual 1.829 1.651 0.178 2.00e-02 2.50e+03 7.89e+01 bond pdb=" C16 SNL A 601 " pdb=" S61 SNL A 601 " ideal model delta sigma weight residual 1.767 1.677 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C9 SNL A 601 " pdb=" O58 SNL A 601 " ideal model delta sigma weight residual 1.443 1.518 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C18 SNL A 601 " pdb=" C19 SNL A 601 " ideal model delta sigma weight residual 1.463 1.537 -0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 3278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 4455 3.48 - 6.96: 28 6.96 - 10.44: 8 10.44 - 13.91: 1 13.91 - 17.39: 2 Bond angle restraints: 4494 Sorted by residual: angle pdb=" C13 SNL A 601 " pdb=" C9 SNL A 601 " pdb=" C5 SNL A 601 " ideal model delta sigma weight residual 116.85 134.24 -17.39 3.00e+00 1.11e-01 3.36e+01 angle pdb=" C8 SNL A 601 " pdb=" C9 SNL A 601 " pdb=" O58 SNL A 601 " ideal model delta sigma weight residual 111.01 96.07 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" C16 SNL A 601 " pdb=" S61 SNL A 601 " pdb=" C22 SNL A 601 " ideal model delta sigma weight residual 101.80 115.41 -13.61 3.00e+00 1.11e-01 2.06e+01 angle pdb=" C1 SNL A 601 " pdb=" C2 SNL A 601 " pdb=" C24 SNL A 601 " ideal model delta sigma weight residual 108.42 117.77 -9.35 3.00e+00 1.11e-01 9.71e+00 angle pdb=" C5 SNL A 601 " pdb=" C9 SNL A 601 " pdb=" O58 SNL A 601 " ideal model delta sigma weight residual 111.22 102.15 9.07 3.00e+00 1.11e-01 9.15e+00 ... (remaining 4489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 1722 14.26 - 28.52: 156 28.52 - 42.77: 52 42.77 - 57.03: 15 57.03 - 71.29: 5 Dihedral angle restraints: 1950 sinusoidal: 721 harmonic: 1229 Sorted by residual: dihedral pdb=" SG CYS A 50 " pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " pdb=" CA CYS A 121 " ideal model delta sinusoidal sigma weight residual 79.00 9.30 69.70 1 2.00e+01 2.50e-03 1.57e+01 dihedral pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " ideal model delta sinusoidal sigma weight residual -73.00 -11.22 -61.78 1 2.00e+01 2.50e-03 1.27e+01 dihedral pdb=" CA ASN A 453 " pdb=" CB ASN A 453 " pdb=" CG ASN A 453 " pdb=" OD1 ASN A 453 " ideal model delta sinusoidal sigma weight residual 120.00 -172.00 -68.00 2 2.00e+01 2.50e-03 1.03e+01 ... (remaining 1947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 531 0.181 - 0.362: 3 0.362 - 0.542: 0 0.542 - 0.723: 1 0.723 - 0.904: 1 Chirality restraints: 536 Sorted by residual: chirality pdb=" C9 SNL A 601 " pdb=" C13 SNL A 601 " pdb=" C5 SNL A 601 " pdb=" C8 SNL A 601 " both_signs ideal model delta sigma weight residual False -2.67 -1.77 -0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb=" C2 SNL A 601 " pdb=" C1 SNL A 601 " pdb=" C20 SNL A 601 " pdb=" C24 SNL A 601 " both_signs ideal model delta sigma weight residual False -2.82 -2.20 -0.62 2.00e-01 2.50e+01 9.56e+00 chirality pdb=" C6 SNL A 601 " pdb=" C23 SNL A 601 " pdb=" C5 SNL A 601 " pdb=" C7 SNL A 601 " both_signs ideal model delta sigma weight residual False -2.43 -2.71 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 533 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 340 " -0.032 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO A 341 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO A 271 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 158 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C GLY A 158 " -0.027 2.00e-02 2.50e+03 pdb=" O GLY A 158 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 159 " 0.009 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 489 2.76 - 3.29: 3209 3.29 - 3.83: 5529 3.83 - 4.36: 6174 4.36 - 4.90: 10891 Nonbonded interactions: 26292 Sorted by model distance: nonbonded pdb=" O LYS A 147 " pdb=" OH TYR A 199 " model vdw 2.221 3.040 nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.240 3.040 nonbonded pdb=" O HIS A 367 " pdb=" OG1 THR A 371 " model vdw 2.246 3.040 nonbonded pdb=" O MET A 368 " pdb=" OG SER A 372 " model vdw 2.374 3.040 nonbonded pdb=" O ASN A 71 " pdb=" NH2 ARG A 113 " model vdw 2.375 3.120 ... (remaining 26287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.410 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 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 0.213 3283 Z= 0.459 Angle : 0.811 17.392 4494 Z= 0.350 Chirality : 0.063 0.904 536 Planarity : 0.004 0.050 551 Dihedral : 13.409 71.290 1153 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.42), residues: 425 helix: 1.50 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -0.12 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 44 TYR 0.016 0.001 TYR A 240 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.311 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.6169 time to fit residues: 28.1013 Evaluate side-chains 33 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3283 Z= 0.260 Angle : 0.561 5.427 4494 Z= 0.283 Chirality : 0.038 0.130 536 Planarity : 0.004 0.047 551 Dihedral : 5.238 25.094 529 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.24 % Allowed : 10.58 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.42), residues: 425 helix: 1.69 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -0.12 (0.64), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 260 PHE 0.010 0.001 PHE A 44 TYR 0.015 0.001 TYR A 240 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.305 Fit side-chains REVERT: A 447 GLN cc_start: 0.7496 (mm110) cc_final: 0.7183 (mm110) outliers start: 7 outliers final: 3 residues processed: 36 average time/residue: 0.7839 time to fit residues: 29.7591 Evaluate side-chains 34 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3283 Z= 0.218 Angle : 0.524 5.982 4494 Z= 0.265 Chirality : 0.038 0.196 536 Planarity : 0.004 0.045 551 Dihedral : 4.951 27.924 529 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.60 % Allowed : 12.18 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.43), residues: 425 helix: 1.62 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.10 (0.67), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 44 TYR 0.013 0.001 TYR A 240 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.329 Fit side-chains REVERT: A 144 ASP cc_start: 0.7853 (m-30) cc_final: 0.7478 (m-30) REVERT: A 200 MET cc_start: 0.7715 (mmm) cc_final: 0.7279 (tpp) REVERT: A 420 MET cc_start: 0.8255 (mtp) cc_final: 0.7558 (mtt) outliers start: 5 outliers final: 2 residues processed: 35 average time/residue: 0.7830 time to fit residues: 28.9090 Evaluate side-chains 33 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3283 Z= 0.220 Angle : 0.518 6.276 4494 Z= 0.263 Chirality : 0.038 0.160 536 Planarity : 0.004 0.044 551 Dihedral : 4.634 25.490 529 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.92 % Allowed : 14.10 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.42), residues: 425 helix: 1.64 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.10 (0.66), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.330 Fit side-chains REVERT: A 144 ASP cc_start: 0.7863 (m-30) cc_final: 0.7483 (m-30) REVERT: A 435 MET cc_start: 0.7618 (tpp) cc_final: 0.7358 (tpp) REVERT: A 448 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8244 (mpp) outliers start: 6 outliers final: 5 residues processed: 37 average time/residue: 0.7610 time to fit residues: 29.6645 Evaluate side-chains 37 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.0020 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3283 Z= 0.234 Angle : 0.526 5.738 4494 Z= 0.267 Chirality : 0.038 0.137 536 Planarity : 0.004 0.043 551 Dihedral : 4.566 24.807 529 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.56 % Allowed : 15.06 % Favored : 82.37 % 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: 1.86 (0.42), residues: 425 helix: 1.68 (0.30), residues: 319 sheet: None (None), residues: 0 loop : 0.01 (0.67), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.416 Fit side-chains REVERT: A 420 MET cc_start: 0.8292 (mtp) cc_final: 0.7606 (mtt) REVERT: A 435 MET cc_start: 0.7625 (tpp) cc_final: 0.7375 (tpp) outliers start: 8 outliers final: 5 residues processed: 39 average time/residue: 0.7281 time to fit residues: 29.9833 Evaluate side-chains 37 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.0070 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3283 Z= 0.223 Angle : 0.520 6.174 4494 Z= 0.264 Chirality : 0.038 0.131 536 Planarity : 0.004 0.042 551 Dihedral : 4.494 24.105 529 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.56 % Allowed : 15.38 % Favored : 82.05 % 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: 1.81 (0.42), residues: 425 helix: 1.66 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.12 (0.67), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.328 Fit side-chains REVERT: A 435 MET cc_start: 0.7623 (tpp) cc_final: 0.7360 (tpp) outliers start: 8 outliers final: 6 residues processed: 38 average time/residue: 0.6927 time to fit residues: 27.8736 Evaluate side-chains 38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3283 Z= 0.224 Angle : 0.524 6.723 4494 Z= 0.266 Chirality : 0.038 0.130 536 Planarity : 0.004 0.041 551 Dihedral : 4.478 24.222 529 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.21 % Allowed : 15.06 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.42), residues: 425 helix: 1.68 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.10 (0.67), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.330 Fit side-chains REVERT: A 420 MET cc_start: 0.8235 (mtp) cc_final: 0.7545 (mtt) REVERT: A 435 MET cc_start: 0.7624 (tpp) cc_final: 0.7371 (tpp) outliers start: 10 outliers final: 5 residues processed: 38 average time/residue: 0.6785 time to fit residues: 27.4269 Evaluate side-chains 35 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 VAL 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: 0.7980 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3283 Z= 0.221 Angle : 0.524 7.000 4494 Z= 0.266 Chirality : 0.038 0.132 536 Planarity : 0.004 0.041 551 Dihedral : 4.471 23.563 529 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.56 % Allowed : 15.38 % Favored : 82.05 % 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: 1.87 (0.43), residues: 425 helix: 1.71 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.11 (0.67), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.319 Fit side-chains REVERT: A 435 MET cc_start: 0.7617 (tpp) cc_final: 0.7353 (tpp) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.7432 time to fit residues: 28.2806 Evaluate side-chains 37 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 VAL 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: 0.5980 chunk 36 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3283 Z= 0.225 Angle : 0.528 7.176 4494 Z= 0.267 Chirality : 0.038 0.138 536 Planarity : 0.004 0.041 551 Dihedral : 4.470 22.518 529 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.53 % Allowed : 14.42 % Favored : 82.05 % 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: 1.86 (0.43), residues: 425 helix: 1.69 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.11 (0.67), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.341 Fit side-chains REVERT: A 420 MET cc_start: 0.8222 (mtp) cc_final: 0.7575 (mtt) REVERT: A 435 MET cc_start: 0.7618 (tpp) cc_final: 0.7364 (tpp) outliers start: 11 outliers final: 8 residues processed: 38 average time/residue: 0.6687 time to fit residues: 26.9520 Evaluate side-chains 37 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 20 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 0.0570 chunk 14 optimal weight: 0.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3283 Z= 0.170 Angle : 0.505 7.633 4494 Z= 0.255 Chirality : 0.037 0.138 536 Planarity : 0.004 0.041 551 Dihedral : 4.208 22.814 529 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.24 % Allowed : 15.71 % Favored : 82.05 % 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: 2.04 (0.43), residues: 425 helix: 1.84 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -0.08 (0.66), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 367 PHE 0.008 0.001 PHE A 44 TYR 0.010 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.297 Fit side-chains REVERT: A 420 MET cc_start: 0.8234 (mtp) cc_final: 0.7587 (mtt) REVERT: A 435 MET cc_start: 0.7484 (tpp) cc_final: 0.7189 (tpp) outliers start: 7 outliers final: 5 residues processed: 38 average time/residue: 0.6744 time to fit residues: 27.1846 Evaluate side-chains 36 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 16 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 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.200235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.152827 restraints weight = 2954.463| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.88 r_work: 0.3542 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3283 Z= 0.215 Angle : 0.537 7.335 4494 Z= 0.266 Chirality : 0.038 0.139 536 Planarity : 0.004 0.041 551 Dihedral : 4.297 22.876 529 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.92 % Allowed : 16.67 % Favored : 81.41 % 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: 1.94 (0.43), residues: 425 helix: 1.76 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.09 (0.66), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 367 PHE 0.009 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1267.65 seconds wall clock time: 23 minutes 54.18 seconds (1434.18 seconds total)