Starting phenix.real_space_refine on Fri Dec 27 09:52:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtz_36657/12_2024/8jtz_36657.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtz_36657/12_2024/8jtz_36657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jtz_36657/12_2024/8jtz_36657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtz_36657/12_2024/8jtz_36657.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtz_36657/12_2024/8jtz_36657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtz_36657/12_2024/8jtz_36657.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.086 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 34 5.16 5 C 2620 2.51 5 N 650 2.21 5 O 695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 3999 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3970 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 27, 'TRANS': 502} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 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: 2.99, per 1000 atoms: 0.75 Number of scatterers: 3999 At special positions: 0 Unit cell: (111.498, 55.2075, 66.0325, 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 34 16.00 O 695 8.00 N 650 7.00 C 2620 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: 0.94 Conformation dependent library (CDL) restraints added in 465.5 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 974 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 74.3% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 15 through 31 removed outlier: 4.391A pdb=" N LEU A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.824A pdb=" N ALA A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 194 removed outlier: 4.351A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N LYS A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.518A pdb=" N MET A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.696A pdb=" N MET A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 269 through 278 removed outlier: 3.866A pdb=" N PHE A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 294 through 310 Processing helix chain 'A' and resid 314 through 318 removed outlier: 4.087A pdb=" N LYS A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 368 removed outlier: 4.022A pdb=" N MET A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 385 through 397 removed outlier: 4.437A pdb=" N GLY A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 427 through 456 removed outlier: 3.766A pdb=" N ASN A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 470 Processing helix chain 'A' and resid 470 through 491 removed outlier: 4.337A pdb=" N ASP A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) Proline residue: A 481 - end of helix 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' Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.872A pdb=" N ALA A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 529 " --> pdb=" O MET A 525 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.723A pdb=" N HIS A 49 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 126 " --> pdb=" O HIS A 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 260 hydrogen bonds defined for protein. 771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 1.11 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: 625 1.31 - 1.44: 1085 1.44 - 1.57: 2338 1.57 - 1.69: 2 1.69 - 1.82: 50 Bond restraints: 4100 Sorted by residual: bond pdb=" C15 SNL A 601 " pdb=" O58 SNL A 601 " ideal model delta sigma weight residual 1.332 1.553 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C22 SNL A 601 " pdb=" S61 SNL A 601 " ideal model delta sigma weight residual 1.829 1.676 0.153 2.00e-02 2.50e+03 5.86e+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 2.02e+01 bond pdb=" C9 SNL A 601 " pdb=" O58 SNL A 601 " ideal model delta sigma weight residual 1.443 1.527 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C18 SNL A 601 " pdb=" C19 SNL A 601 " ideal model delta sigma weight residual 1.463 1.536 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 4095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 5521 3.24 - 6.49: 68 6.49 - 9.73: 11 9.73 - 12.98: 1 12.98 - 16.22: 2 Bond angle restraints: 5603 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 116.85 133.07 -16.22 3.00e+00 1.11e-01 2.92e+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 97.51 13.50 3.00e+00 1.11e-01 2.03e+01 angle pdb=" N CYS A 26 " pdb=" CA CYS A 26 " pdb=" C CYS A 26 " ideal model delta sigma weight residual 113.01 108.27 4.74 1.20e+00 6.94e-01 1.56e+01 angle pdb=" N GLU A 529 " pdb=" CA GLU A 529 " pdb=" C GLU A 529 " ideal model delta sigma weight residual 112.54 107.82 4.72 1.22e+00 6.72e-01 1.50e+01 angle pdb=" CB MET A 448 " pdb=" CG MET A 448 " pdb=" SD MET A 448 " ideal model delta sigma weight residual 112.70 123.89 -11.19 3.00e+00 1.11e-01 1.39e+01 ... (remaining 5598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 2152 17.28 - 34.57: 229 34.57 - 51.85: 66 51.85 - 69.13: 13 69.13 - 86.42: 2 Dihedral angle restraints: 2462 sinusoidal: 944 harmonic: 1518 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -137.58 51.58 1 1.00e+01 1.00e-02 3.63e+01 dihedral pdb=" CA VAL A 461 " pdb=" C VAL A 461 " pdb=" N ARG A 462 " pdb=" CA ARG A 462 " ideal model delta harmonic sigma weight residual -180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 126.86 -33.86 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 2459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 650 0.140 - 0.280: 7 0.280 - 0.420: 0 0.420 - 0.560: 0 0.560 - 0.700: 2 Chirality restraints: 659 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 -1.97 -0.70 2.00e-01 2.50e+01 1.22e+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 -2.22 -0.59 2.00e-01 2.50e+01 8.84e+00 chirality pdb=" CG LEU A 192 " pdb=" CB LEU A 192 " pdb=" CD1 LEU A 192 " pdb=" CD2 LEU A 192 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 656 not shown) Planarity restraints: 699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 340 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A 341 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 279 " -0.008 2.00e-02 2.50e+03 1.37e-02 3.76e+00 pdb=" CG TYR A 279 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 279 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 279 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 279 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 279 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 279 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 279 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 393 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C ALA A 393 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA A 393 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 394 " 0.010 2.00e-02 2.50e+03 ... (remaining 696 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 777 2.77 - 3.30: 3806 3.30 - 3.84: 6889 3.84 - 4.37: 7472 4.37 - 4.90: 13237 Nonbonded interactions: 32181 Sorted by model distance: nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.239 3.040 nonbonded pdb=" NH1 ARG A 486 " pdb=" OE1 GLU A 489 " model vdw 2.356 3.120 nonbonded pdb=" O THR A 516 " pdb=" OG1 THR A 516 " model vdw 2.378 3.040 nonbonded pdb=" OD1 ASN A 186 " pdb=" OG SER A 213 " model vdw 2.384 3.040 nonbonded pdb=" NH2 ARG A 233 " pdb=" O VAL A 519 " model vdw 2.412 3.120 ... (remaining 32176 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: 0.420 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 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 0.221 4100 Z= 0.323 Angle : 0.904 16.225 5603 Z= 0.433 Chirality : 0.057 0.700 659 Planarity : 0.005 0.052 699 Dihedral : 15.420 86.417 1479 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.25 % Allowed : 22.17 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.34), residues: 528 helix: -0.20 (0.25), residues: 374 sheet: None (None), residues: 0 loop : -1.69 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 354 HIS 0.003 0.001 HIS A 48 PHE 0.009 0.001 PHE A 44 TYR 0.033 0.002 TYR A 279 ARG 0.004 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.386 Fit side-chains REVERT: A 173 PHE cc_start: 0.8210 (m-80) cc_final: 0.7963 (m-80) REVERT: A 368 MET cc_start: 0.7095 (tpp) cc_final: 0.6661 (tpp) outliers start: 1 outliers final: 1 residues processed: 68 average time/residue: 0.1676 time to fit residues: 14.2505 Evaluate side-chains 63 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.0570 chunk 30 optimal weight: 0.0970 chunk 48 optimal weight: 0.9980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4100 Z= 0.165 Angle : 0.525 5.683 5603 Z= 0.259 Chirality : 0.035 0.133 659 Planarity : 0.004 0.043 699 Dihedral : 4.745 57.629 638 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.97 % Allowed : 21.43 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.37), residues: 528 helix: 0.80 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.41 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 288 HIS 0.003 0.001 HIS A 48 PHE 0.009 0.001 PHE A 159 TYR 0.010 0.001 TYR A 168 ARG 0.002 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.417 Fit side-chains REVERT: A 368 MET cc_start: 0.7128 (tpp) cc_final: 0.6665 (tpp) REVERT: A 408 MET cc_start: 0.3685 (OUTLIER) cc_final: 0.3135 (ttt) outliers start: 8 outliers final: 4 residues processed: 71 average time/residue: 0.1417 time to fit residues: 12.9472 Evaluate side-chains 69 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 0.0970 chunk 47 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4100 Z= 0.157 Angle : 0.510 5.568 5603 Z= 0.252 Chirality : 0.036 0.141 659 Planarity : 0.004 0.045 699 Dihedral : 4.625 58.048 638 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.69 % Allowed : 21.18 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.38), residues: 528 helix: 1.16 (0.28), residues: 383 sheet: None (None), residues: 0 loop : -1.34 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 261 HIS 0.001 0.001 HIS A 48 PHE 0.006 0.001 PHE A 151 TYR 0.008 0.001 TYR A 168 ARG 0.003 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.457 Fit side-chains REVERT: A 35 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8557 (mp) REVERT: A 192 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7838 (mt) REVERT: A 239 MET cc_start: 0.7890 (ttp) cc_final: 0.7506 (ttp) REVERT: A 368 MET cc_start: 0.7089 (tpp) cc_final: 0.6632 (tpp) outliers start: 15 outliers final: 7 residues processed: 77 average time/residue: 0.1664 time to fit residues: 16.2329 Evaluate side-chains 78 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** 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: 0.7306 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4100 Z= 0.301 Angle : 0.585 6.266 5603 Z= 0.289 Chirality : 0.039 0.137 659 Planarity : 0.004 0.044 699 Dihedral : 4.698 54.500 638 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.68 % Allowed : 21.43 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.38), residues: 528 helix: 1.25 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -0.92 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS A 48 PHE 0.014 0.001 PHE A 227 TYR 0.012 0.002 TYR A 168 ARG 0.001 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.451 Fit side-chains REVERT: A 192 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8032 (mt) REVERT: A 227 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: A 368 MET cc_start: 0.7138 (tpp) cc_final: 0.6658 (tpp) outliers start: 19 outliers final: 9 residues processed: 86 average time/residue: 0.1504 time to fit residues: 16.6719 Evaluate side-chains 80 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 0.0010 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4100 Z= 0.191 Angle : 0.536 5.792 5603 Z= 0.264 Chirality : 0.036 0.130 659 Planarity : 0.004 0.046 699 Dihedral : 4.578 55.735 638 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.45 % Allowed : 22.91 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.39), residues: 528 helix: 1.47 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.93 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 288 HIS 0.001 0.001 HIS A 49 PHE 0.011 0.001 PHE A 227 TYR 0.010 0.001 TYR A 168 ARG 0.001 0.000 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.406 Fit side-chains REVERT: A 192 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7957 (mt) REVERT: A 227 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: A 368 MET cc_start: 0.7170 (tpp) cc_final: 0.6731 (tpp) outliers start: 14 outliers final: 8 residues processed: 81 average time/residue: 0.1732 time to fit residues: 17.4836 Evaluate side-chains 82 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4100 Z= 0.205 Angle : 0.545 8.231 5603 Z= 0.265 Chirality : 0.037 0.130 659 Planarity : 0.004 0.045 699 Dihedral : 4.569 54.765 638 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.68 % Allowed : 22.66 % Favored : 72.66 % 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: 1.17 (0.39), residues: 528 helix: 1.47 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -0.89 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 491 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 227 TYR 0.010 0.001 TYR A 168 ARG 0.001 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.448 Fit side-chains REVERT: A 192 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7986 (mt) REVERT: A 227 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7886 (m-80) REVERT: A 340 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8010 (t) REVERT: A 368 MET cc_start: 0.7236 (tpp) cc_final: 0.6872 (tpp) REVERT: A 529 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7721 (mm-30) outliers start: 19 outliers final: 13 residues processed: 81 average time/residue: 0.1570 time to fit residues: 16.1543 Evaluate side-chains 84 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS 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: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 51 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4100 Z= 0.204 Angle : 0.540 8.009 5603 Z= 0.265 Chirality : 0.037 0.131 659 Planarity : 0.004 0.045 699 Dihedral : 4.546 53.762 638 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.42 % Allowed : 21.43 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.39), residues: 528 helix: 1.48 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -0.80 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 491 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 227 TYR 0.009 0.001 TYR A 168 ARG 0.007 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.447 Fit side-chains REVERT: A 151 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7546 (t80) REVERT: A 175 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8065 (mpt180) REVERT: A 192 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7958 (mt) REVERT: A 227 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: A 239 MET cc_start: 0.7984 (ttp) cc_final: 0.7621 (ttp) REVERT: A 368 MET cc_start: 0.7250 (tpp) cc_final: 0.6888 (tpp) outliers start: 22 outliers final: 14 residues processed: 84 average time/residue: 0.1761 time to fit residues: 18.4258 Evaluate side-chains 85 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS 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: 53 random chunks: chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4100 Z= 0.227 Angle : 0.555 7.972 5603 Z= 0.271 Chirality : 0.037 0.133 659 Planarity : 0.004 0.045 699 Dihedral : 4.594 52.033 638 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.68 % Allowed : 22.17 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.39), residues: 528 helix: 1.56 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -0.83 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.011 0.001 PHE A 227 TYR 0.009 0.001 TYR A 168 ARG 0.001 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.363 Fit side-chains REVERT: A 151 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7626 (t80) REVERT: A 175 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7780 (mpt180) REVERT: A 192 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7959 (mt) REVERT: A 227 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: A 340 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8032 (t) REVERT: A 368 MET cc_start: 0.7155 (tpp) cc_final: 0.6874 (tpp) outliers start: 19 outliers final: 13 residues processed: 83 average time/residue: 0.1702 time to fit residues: 17.5781 Evaluate side-chains 86 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS 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: 53 random chunks: chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4100 Z= 0.214 Angle : 0.552 7.976 5603 Z= 0.270 Chirality : 0.037 0.132 659 Planarity : 0.004 0.045 699 Dihedral : 4.604 52.195 638 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.68 % Allowed : 22.41 % Favored : 72.91 % 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: 1.34 (0.39), residues: 528 helix: 1.59 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.80 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 227 TYR 0.009 0.001 TYR A 168 ARG 0.003 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.508 Fit side-chains REVERT: A 151 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7590 (t80) REVERT: A 175 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7782 (mpt180) REVERT: A 192 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7956 (mt) REVERT: A 218 MET cc_start: 0.7637 (tpp) cc_final: 0.7421 (tpp) REVERT: A 227 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: A 340 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8031 (t) REVERT: A 368 MET cc_start: 0.7112 (tpp) cc_final: 0.6855 (tpp) REVERT: A 529 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7919 (mm-30) outliers start: 19 outliers final: 13 residues processed: 82 average time/residue: 0.1705 time to fit residues: 17.3480 Evaluate side-chains 85 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS 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: 53 random chunks: chunk 52 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.0060 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 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 307 GLN ** 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: 0.7258 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4100 Z= 0.190 Angle : 0.554 8.474 5603 Z= 0.268 Chirality : 0.037 0.131 659 Planarity : 0.004 0.045 699 Dihedral : 4.562 52.539 638 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.19 % Allowed : 22.41 % Favored : 73.40 % 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 (0.39), residues: 528 helix: 1.62 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -0.77 (0.56), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 227 TYR 0.009 0.001 TYR A 168 ARG 0.001 0.000 ARG A 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.438 Fit side-chains REVERT: A 151 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7578 (t80) REVERT: A 192 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7982 (mm) REVERT: A 339 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7998 (ttm-80) REVERT: A 340 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.8017 (t) REVERT: A 368 MET cc_start: 0.7102 (tpp) cc_final: 0.6864 (tpp) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.1618 time to fit residues: 17.0220 Evaluate side-chains 83 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS 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: 53 random chunks: chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.124705 restraints weight = 4629.419| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.58 r_work: 0.3379 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4100 Z= 0.205 Angle : 0.548 8.338 5603 Z= 0.267 Chirality : 0.037 0.132 659 Planarity : 0.004 0.045 699 Dihedral : 3.942 30.629 636 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.43 % Allowed : 23.15 % Favored : 72.41 % 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: 1.40 (0.39), residues: 528 helix: 1.63 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -0.80 (0.55), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.008 0.001 PHE A 275 TYR 0.009 0.001 TYR A 168 ARG 0.001 0.000 ARG A 439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1220.42 seconds wall clock time: 22 minutes 55.20 seconds (1375.20 seconds total)