Starting phenix.real_space_refine on Fri Dec 27 08:14:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hiq_34826/12_2024/8hiq_34826_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hiq_34826/12_2024/8hiq_34826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hiq_34826/12_2024/8hiq_34826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hiq_34826/12_2024/8hiq_34826.map" model { file = "/net/cci-nas-00/data/ceres_data/8hiq_34826/12_2024/8hiq_34826_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hiq_34826/12_2024/8hiq_34826_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2083 2.51 5 N 553 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3226 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.75, per 1000 atoms: 0.84 Number of scatterers: 3274 At special positions: 0 Unit cell: (68.034, 71.978, 71.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 621 8.00 N 553 7.00 C 2083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.95 Conformation dependent library (CDL) restraints added in 392.5 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 56.0% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 79 through 97 removed outlier: 4.059A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.812A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.686A pdb=" N GLY A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.533A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 344 through 361 removed outlier: 4.490A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.553A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA A 143 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY A 70 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 7.479A pdb=" N ILE A 215 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 242 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A 217 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 531 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: 0.91 Time building geometry restraints manager: 1.08 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: 1062 1.34 - 1.46: 666 1.46 - 1.57: 1591 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3351 Sorted by residual: bond pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 1.736 1.614 0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.428 -0.053 2.00e-02 2.50e+03 7.04e+00 bond pdb=" C5D NAP A 501 " pdb=" O5D NAP A 501 " ideal model delta sigma weight residual 1.403 1.450 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" O5D NAP A 501 " pdb=" PN NAP A 501 " ideal model delta sigma weight residual 1.649 1.604 0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" O3 NAP A 501 " pdb=" PA NAP A 501 " ideal model delta sigma weight residual 1.647 1.604 0.043 2.00e-02 2.50e+03 4.53e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 4403 1.76 - 3.52: 125 3.52 - 5.27: 25 5.27 - 7.03: 5 7.03 - 8.79: 3 Bond angle restraints: 4561 Sorted by residual: angle pdb=" CA MET A 153 " pdb=" CB MET A 153 " pdb=" CG MET A 153 " ideal model delta sigma weight residual 114.10 107.08 7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" N GLY A 219 " pdb=" CA GLY A 219 " pdb=" C GLY A 219 " ideal model delta sigma weight residual 113.18 105.81 7.37 2.37e+00 1.78e-01 9.68e+00 angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 123.05 127.73 -4.68 1.57e+00 4.06e-01 8.89e+00 angle pdb=" N ARG A 166 " pdb=" CA ARG A 166 " pdb=" CB ARG A 166 " ideal model delta sigma weight residual 113.65 109.78 3.87 1.47e+00 4.63e-01 6.92e+00 angle pdb=" C2B NAP A 501 " pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 117.19 109.33 7.86 3.00e+00 1.11e-01 6.87e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 1791 17.85 - 35.71: 175 35.71 - 53.56: 40 53.56 - 71.41: 19 71.41 - 89.27: 7 Dihedral angle restraints: 2032 sinusoidal: 843 harmonic: 1189 Sorted by residual: dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CB GLU A 45 " pdb=" CG GLU A 45 " pdb=" CD GLU A 45 " pdb=" OE1 GLU A 45 " ideal model delta sinusoidal sigma weight residual 0.00 88.75 -88.75 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA LYS A 213 " pdb=" C LYS A 213 " pdb=" N LYS A 214 " pdb=" CA LYS A 214 " ideal model delta harmonic sigma weight residual 180.00 -163.96 -16.04 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 267 0.025 - 0.050: 126 0.050 - 0.075: 55 0.075 - 0.099: 30 0.099 - 0.124: 23 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA ILE A 108 " pdb=" N ILE A 108 " pdb=" C ILE A 108 " pdb=" CB ILE A 108 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE A 338 " pdb=" N ILE A 338 " pdb=" C ILE A 338 " pdb=" CB ILE A 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE A 174 " pdb=" N ILE A 174 " pdb=" C ILE A 174 " pdb=" CB ILE A 174 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP A 501 " -0.021 2.00e-02 2.50e+03 7.61e-02 1.16e+02 pdb=" C2N NAP A 501 " -0.071 2.00e-02 2.50e+03 pdb=" C3N NAP A 501 " -0.033 2.00e-02 2.50e+03 pdb=" C4N NAP A 501 " -0.125 2.00e-02 2.50e+03 pdb=" C5N NAP A 501 " 0.023 2.00e-02 2.50e+03 pdb=" C6N NAP A 501 " 0.108 2.00e-02 2.50e+03 pdb=" C7N NAP A 501 " 0.109 2.00e-02 2.50e+03 pdb=" N1N NAP A 501 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO A 142 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 323 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO A 324 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.022 5.00e-02 4.00e+02 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 889 2.81 - 3.33: 3394 3.33 - 3.85: 5887 3.85 - 4.38: 6769 4.38 - 4.90: 11289 Nonbonded interactions: 28228 Sorted by model distance: nonbonded pdb=" OG1 THR A 68 " pdb=" OD1 ASP A 140 " model vdw 2.284 3.040 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.300 3.120 nonbonded pdb=" O ASN A 308 " pdb=" NZ LYS A 310 " model vdw 2.319 3.120 nonbonded pdb=" OD1 ASN A 319 " pdb=" ND2 ASN A 344 " model vdw 2.320 3.120 nonbonded pdb=" NE2 GLN A 60 " pdb=" O VAL A 134 " model vdw 2.328 3.120 ... (remaining 28223 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 3351 Z= 0.275 Angle : 0.739 8.787 4561 Z= 0.405 Chirality : 0.043 0.124 501 Planarity : 0.006 0.076 579 Dihedral : 17.055 89.266 1274 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 1.52 (0.43), residues: 414 helix: 1.97 (0.36), residues: 209 sheet: -0.06 (0.62), residues: 70 loop : 0.19 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 89 HIS 0.002 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.007 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.671 Fit side-chains REVERT: A 166 ARG cc_start: 0.5204 (ttt-90) cc_final: 0.4757 (ttt-90) REVERT: A 388 HIS cc_start: 0.6928 (t70) cc_final: 0.6714 (t-170) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2417 time to fit residues: 17.4585 Evaluate side-chains 52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 3351 Z= 0.250 Angle : 0.553 7.376 4561 Z= 0.287 Chirality : 0.043 0.142 501 Planarity : 0.005 0.049 579 Dihedral : 10.494 59.450 517 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.61 % Allowed : 5.76 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.42), residues: 414 helix: 2.00 (0.35), residues: 213 sheet: 0.01 (0.69), residues: 60 loop : -0.22 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.008 0.001 TYR A 408 ARG 0.005 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.420 Fit side-chains REVERT: A 366 GLU cc_start: 0.8476 (tp30) cc_final: 0.8256 (tp30) outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 0.2277 time to fit residues: 14.8558 Evaluate side-chains 49 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7544 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 : 0.003 0.041 3351 Z= 0.166 Angle : 0.496 7.341 4561 Z= 0.258 Chirality : 0.042 0.128 501 Planarity : 0.005 0.047 579 Dihedral : 9.358 58.887 517 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.61 % Allowed : 10.30 % Favored : 89.09 % 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: 1.51 (0.42), residues: 414 helix: 2.15 (0.35), residues: 213 sheet: 0.09 (0.70), residues: 60 loop : -0.33 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.002 0.001 HIS A 394 PHE 0.007 0.001 PHE A 341 TYR 0.008 0.001 TYR A 408 ARG 0.004 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.375 Fit side-chains REVERT: A 395 MET cc_start: 0.8129 (mmm) cc_final: 0.7456 (tpt) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.2530 time to fit residues: 15.6534 Evaluate side-chains 50 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7526 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 0.044 3351 Z= 0.169 Angle : 0.501 6.928 4561 Z= 0.260 Chirality : 0.042 0.130 501 Planarity : 0.005 0.044 579 Dihedral : 8.666 57.372 517 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.82 % Allowed : 9.70 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.42), residues: 414 helix: 2.17 (0.35), residues: 213 sheet: 0.24 (0.70), residues: 60 loop : -0.51 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.010 0.001 TYR A 250 ARG 0.006 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.382 Fit side-chains REVERT: A 111 ASN cc_start: 0.8341 (t0) cc_final: 0.8052 (t0) REVERT: A 377 MET cc_start: 0.6702 (mmt) cc_final: 0.6341 (mmt) outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.2219 time to fit residues: 14.8726 Evaluate side-chains 53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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: 0.7558 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3351 Z= 0.204 Angle : 0.529 7.030 4561 Z= 0.270 Chirality : 0.043 0.129 501 Planarity : 0.005 0.045 579 Dihedral : 8.359 55.545 517 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.52 % Allowed : 11.21 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.42), residues: 414 helix: 2.19 (0.34), residues: 213 sheet: 0.20 (0.70), residues: 60 loop : -0.48 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 364 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.009 0.001 TYR A 20 ARG 0.007 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.393 Fit side-chains REVERT: A 111 ASN cc_start: 0.8338 (t0) cc_final: 0.8067 (t0) REVERT: A 377 MET cc_start: 0.6678 (mmt) cc_final: 0.6301 (mmt) outliers start: 5 outliers final: 5 residues processed: 53 average time/residue: 0.2361 time to fit residues: 14.6256 Evaluate side-chains 53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 0.0170 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- 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: 0.7521 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3351 Z= 0.171 Angle : 0.524 7.435 4561 Z= 0.267 Chirality : 0.042 0.133 501 Planarity : 0.005 0.045 579 Dihedral : 8.072 53.755 517 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.21 % Allowed : 11.82 % Favored : 86.97 % 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: 1.55 (0.43), residues: 414 helix: 2.22 (0.35), residues: 213 sheet: 0.39 (0.71), residues: 60 loop : -0.54 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.011 0.001 TYR A 20 ARG 0.006 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.384 Fit side-chains REVERT: A 111 ASN cc_start: 0.8292 (t0) cc_final: 0.8064 (t0) outliers start: 4 outliers final: 4 residues processed: 54 average time/residue: 0.2414 time to fit residues: 15.1879 Evaluate side-chains 52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.7597 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 3351 Z= 0.272 Angle : 0.578 7.690 4561 Z= 0.296 Chirality : 0.044 0.129 501 Planarity : 0.005 0.046 579 Dihedral : 8.150 55.094 517 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.82 % Allowed : 12.73 % Favored : 85.45 % 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: 1.45 (0.42), residues: 414 helix: 2.09 (0.34), residues: 214 sheet: 0.23 (0.67), residues: 65 loop : -0.47 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 364 HIS 0.005 0.001 HIS A 388 PHE 0.011 0.002 PHE A 341 TYR 0.015 0.001 TYR A 20 ARG 0.007 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.373 Fit side-chains REVERT: A 111 ASN cc_start: 0.8360 (t0) cc_final: 0.8110 (t0) REVERT: A 287 LEU cc_start: 0.6383 (tt) cc_final: 0.6180 (tt) outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 0.2297 time to fit residues: 15.4926 Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.0030 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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: 0.7531 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3351 Z= 0.179 Angle : 0.549 6.941 4561 Z= 0.282 Chirality : 0.043 0.128 501 Planarity : 0.005 0.046 579 Dihedral : 7.957 55.074 517 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.82 % Allowed : 13.94 % Favored : 84.24 % 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: 1.36 (0.42), residues: 414 helix: 2.07 (0.34), residues: 215 sheet: 0.27 (0.71), residues: 60 loop : -0.64 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.012 0.001 TYR A 147 ARG 0.006 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.359 Fit side-chains REVERT: A 400 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.6224 (t80) outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.2062 time to fit residues: 13.8665 Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 400 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7518 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3351 Z= 0.177 Angle : 0.560 6.555 4561 Z= 0.292 Chirality : 0.043 0.148 501 Planarity : 0.005 0.046 579 Dihedral : 7.846 55.314 517 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.82 % Allowed : 15.76 % Favored : 82.42 % 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: 1.42 (0.42), residues: 414 helix: 2.11 (0.35), residues: 215 sheet: 0.32 (0.72), residues: 58 loop : -0.60 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.022 0.001 TYR A 20 ARG 0.006 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.385 Fit side-chains REVERT: A 400 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.6490 (t80) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.2314 time to fit residues: 14.8640 Evaluate side-chains 51 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 400 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 8.9990 chunk 3 optimal weight: 0.0040 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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: 0.7513 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3351 Z= 0.181 Angle : 0.577 6.321 4561 Z= 0.300 Chirality : 0.043 0.147 501 Planarity : 0.005 0.059 579 Dihedral : 7.763 55.700 517 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.52 % Allowed : 16.67 % Favored : 81.82 % 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: 1.53 (0.42), residues: 414 helix: 2.19 (0.34), residues: 215 sheet: 0.42 (0.70), residues: 63 loop : -0.60 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.020 0.001 TYR A 20 ARG 0.008 0.001 ARG A 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.389 Fit side-chains REVERT: A 400 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.6165 (t80) outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 0.2356 time to fit residues: 14.3088 Evaluate side-chains 52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 400 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.158992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.134003 restraints weight = 7086.367| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.75 r_work: 0.3712 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3351 Z= 0.211 Angle : 0.582 6.850 4561 Z= 0.300 Chirality : 0.043 0.139 501 Planarity : 0.005 0.059 579 Dihedral : 7.779 57.573 517 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.21 % Allowed : 16.36 % Favored : 82.42 % 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: 1.49 (0.42), residues: 414 helix: 2.16 (0.34), residues: 215 sheet: 0.38 (0.69), residues: 65 loop : -0.62 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.009 0.001 TYR A 250 ARG 0.007 0.001 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1184.20 seconds wall clock time: 22 minutes 11.66 seconds (1331.66 seconds total)