Starting phenix.real_space_refine on Fri Dec 27 05:42:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jt9_36637/12_2024/8jt9_36637.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jt9_36637/12_2024/8jt9_36637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jt9_36637/12_2024/8jt9_36637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jt9_36637/12_2024/8jt9_36637.map" model { file = "/net/cci-nas-00/data/ceres_data/8jt9_36637/12_2024/8jt9_36637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jt9_36637/12_2024/8jt9_36637.cif" } resolution = 2.97 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= 0.084 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 S 27 5.16 5 C 1915 2.51 5 N 444 2.21 5 O 485 1.98 5 F 1 1.80 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: 2872 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2843 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'UYX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.89, per 1000 atoms: 1.01 Number of scatterers: 2872 At special positions: 0 Unit cell: (54.94, 72.98, 80.36, 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 27 16.00 F 1 9.00 O 485 8.00 N 444 7.00 C 1915 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: 0.86 Conformation dependent library (CDL) restraints added in 370.1 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 692 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 92.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.645A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 54 removed outlier: 3.721A pdb=" N TYR A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 157 Proline residue: A 147 - end of helix removed outlier: 3.909A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 182 through 211 Processing helix chain 'A' and resid 213 through 246 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 270 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 323 removed outlier: 4.008A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 326 through 334 removed outlier: 4.085A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 4.337A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.439A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix removed outlier: 3.726A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 447 removed outlier: 3.681A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 4.473A pdb=" N GLY A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.746A pdb=" N ARG A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 744 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: 0.83 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 434 1.28 - 1.42: 750 1.42 - 1.55: 1711 1.55 - 1.68: 2 1.68 - 1.82: 46 Bond restraints: 2943 Sorted by residual: bond pdb=" C12 UYX A 501 " pdb=" N05 UYX A 501 " ideal model delta sigma weight residual 1.462 1.302 0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" C11 UYX A 501 " pdb=" N05 UYX A 501 " ideal model delta sigma weight residual 1.461 1.304 0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" C13 UYX A 501 " pdb=" N05 UYX A 501 " ideal model delta sigma weight residual 1.455 1.353 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C17 UYX A 501 " pdb=" C21 UYX A 501 " ideal model delta sigma weight residual 1.465 1.374 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C17 UYX A 501 " pdb=" N06 UYX A 501 " ideal model delta sigma weight residual 1.397 1.315 0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 2938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 3913 2.03 - 4.05: 61 4.05 - 6.08: 32 6.08 - 8.10: 1 8.10 - 10.13: 3 Bond angle restraints: 4010 Sorted by residual: angle pdb=" CA LEU A 133 " pdb=" CB LEU A 133 " pdb=" CG LEU A 133 " ideal model delta sigma weight residual 116.30 125.55 -9.25 3.50e+00 8.16e-02 6.98e+00 angle pdb=" CB GLU A 321 " pdb=" CG GLU A 321 " pdb=" CD GLU A 321 " ideal model delta sigma weight residual 112.60 116.97 -4.37 1.70e+00 3.46e-01 6.62e+00 angle pdb=" C PRO A 473 " pdb=" N PRO A 474 " pdb=" CD PRO A 474 " ideal model delta sigma weight residual 125.00 135.13 -10.13 4.10e+00 5.95e-02 6.10e+00 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 115.06 -5.25 2.21e+00 2.05e-01 5.65e+00 angle pdb=" CA GLU A 321 " pdb=" CB GLU A 321 " pdb=" CG GLU A 321 " ideal model delta sigma weight residual 114.10 118.74 -4.64 2.00e+00 2.50e-01 5.39e+00 ... (remaining 4005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1521 17.98 - 35.96: 157 35.96 - 53.94: 38 53.94 - 71.92: 8 71.92 - 89.90: 3 Dihedral angle restraints: 1727 sinusoidal: 641 harmonic: 1086 Sorted by residual: dihedral pdb=" CA ASN A 154 " pdb=" CB ASN A 154 " pdb=" CG ASN A 154 " pdb=" OD1 ASN A 154 " ideal model delta sinusoidal sigma weight residual 120.00 -168.13 -71.87 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CB GLU A 216 " pdb=" CG GLU A 216 " pdb=" CD GLU A 216 " pdb=" OE1 GLU A 216 " ideal model delta sinusoidal sigma weight residual 0.00 88.77 -88.77 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA TYR A 422 " pdb=" C TYR A 422 " pdb=" N ALA A 423 " pdb=" CA ALA A 423 " ideal model delta harmonic sigma weight residual 180.00 164.25 15.75 0 5.00e+00 4.00e-02 9.92e+00 ... (remaining 1724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 276 0.027 - 0.055: 103 0.055 - 0.082: 63 0.082 - 0.109: 27 0.109 - 0.137: 10 Chirality restraints: 479 Sorted by residual: chirality pdb=" C08 UYX A 501 " pdb=" C09 UYX A 501 " pdb=" C10 UYX A 501 " pdb=" C14 UYX A 501 " both_signs ideal model delta sigma weight residual False -2.61 -2.75 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA PHE A 348 " pdb=" N PHE A 348 " pdb=" C PHE A 348 " pdb=" CB PHE A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA GLU A 312 " pdb=" N GLU A 312 " pdb=" C GLU A 312 " pdb=" CB GLU A 312 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 476 not shown) Planarity restraints: 491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO A 161 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 328 " -0.012 2.00e-02 2.50e+03 1.02e-02 2.61e+00 pdb=" CG TRP A 328 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 328 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 328 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 328 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 328 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 328 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 328 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 328 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 328 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 44 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 45 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.022 5.00e-02 4.00e+02 ... (remaining 488 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 639 2.78 - 3.31: 2920 3.31 - 3.84: 4988 3.84 - 4.37: 5610 4.37 - 4.90: 9984 Nonbonded interactions: 24141 Sorted by model distance: nonbonded pdb=" OD2 ASP A 33 " pdb=" OG SER A 196 " model vdw 2.246 3.040 nonbonded pdb=" O MET A 175 " pdb=" OG SER A 179 " model vdw 2.330 3.040 nonbonded pdb=" O LEU A 30 " pdb=" ND2 ASN A 34 " model vdw 2.350 3.120 nonbonded pdb=" OH TYR A 47 " pdb=" OH TYR A 243 " model vdw 2.376 3.040 nonbonded pdb=" O VAL A 141 " pdb=" OG1 THR A 145 " model vdw 2.410 3.040 ... (remaining 24136 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.380 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: 0.000 Load rotamer database and sin/cos tables:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 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 : 0.007 0.160 2943 Z= 0.464 Angle : 0.763 10.130 4010 Z= 0.354 Chirality : 0.043 0.137 479 Planarity : 0.006 0.045 491 Dihedral : 15.908 89.895 1035 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.67 % Allowed : 26.09 % Favored : 73.24 % 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: 2.28 (0.44), residues: 380 helix: 1.86 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -0.32 (0.82), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 328 HIS 0.001 0.001 HIS A 353 PHE 0.018 0.002 PHE A 27 TYR 0.017 0.001 TYR A 422 ARG 0.009 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.293 Fit side-chains REVERT: A 206 MET cc_start: 0.8828 (ttt) cc_final: 0.8428 (ttt) REVERT: A 431 MET cc_start: 0.7735 (mmt) cc_final: 0.7361 (tpt) REVERT: A 453 MET cc_start: 0.8498 (mmt) cc_final: 0.8151 (mmt) outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 1.2178 time to fit residues: 67.5845 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 129 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 6.9990 chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 0.0870 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.0270 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2943 Z= 0.174 Angle : 0.659 9.981 4010 Z= 0.307 Chirality : 0.041 0.118 479 Planarity : 0.005 0.047 491 Dihedral : 5.001 28.780 427 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.01 % Allowed : 22.74 % Favored : 73.24 % 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: 2.63 (0.44), residues: 380 helix: 2.09 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -0.41 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.016 0.001 PHE A 27 TYR 0.013 0.001 TYR A 243 ARG 0.004 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.332 Fit side-chains REVERT: A 206 MET cc_start: 0.8817 (ttt) cc_final: 0.8451 (ttt) REVERT: A 243 TYR cc_start: 0.7797 (t80) cc_final: 0.7554 (t80) REVERT: A 310 MET cc_start: 0.8911 (mmm) cc_final: 0.8563 (mmm) REVERT: A 453 MET cc_start: 0.8614 (mmt) cc_final: 0.8373 (mmt) outliers start: 12 outliers final: 3 residues processed: 64 average time/residue: 1.0827 time to fit residues: 71.3568 Evaluate side-chains 60 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 420 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2943 Z= 0.229 Angle : 0.667 10.006 4010 Z= 0.309 Chirality : 0.041 0.125 479 Planarity : 0.005 0.051 491 Dihedral : 4.933 30.105 426 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.01 % Allowed : 23.75 % Favored : 72.24 % 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: 2.74 (0.44), residues: 380 helix: 2.18 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.48 (0.80), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 328 HIS 0.001 0.000 HIS A 353 PHE 0.018 0.001 PHE A 27 TYR 0.012 0.001 TYR A 243 ARG 0.003 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.318 Fit side-chains REVERT: A 243 TYR cc_start: 0.7832 (t80) cc_final: 0.7598 (t80) outliers start: 12 outliers final: 3 residues processed: 63 average time/residue: 1.1037 time to fit residues: 71.6766 Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 420 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2943 Z= 0.310 Angle : 0.688 9.939 4010 Z= 0.323 Chirality : 0.043 0.135 479 Planarity : 0.006 0.053 491 Dihedral : 5.070 30.026 426 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 5.02 % Allowed : 21.40 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.43), residues: 380 helix: 2.04 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.37 (0.84), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 328 HIS 0.001 0.001 HIS A 353 PHE 0.020 0.002 PHE A 27 TYR 0.018 0.002 TYR A 422 ARG 0.004 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.315 Fit side-chains REVERT: A 130 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6283 (mm-40) REVERT: A 243 TYR cc_start: 0.7870 (t80) cc_final: 0.7610 (t80) REVERT: A 245 PHE cc_start: 0.6486 (m-10) cc_final: 0.5782 (m-80) REVERT: A 248 LYS cc_start: 0.7583 (pttm) cc_final: 0.7017 (ptmm) REVERT: A 346 ASN cc_start: 0.8821 (m-40) cc_final: 0.8587 (m110) REVERT: A 379 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8040 (mttm) outliers start: 15 outliers final: 5 residues processed: 62 average time/residue: 1.2319 time to fit residues: 78.4980 Evaluate side-chains 59 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.8537 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2943 Z= 0.265 Angle : 0.679 9.716 4010 Z= 0.317 Chirality : 0.042 0.127 479 Planarity : 0.005 0.049 491 Dihedral : 5.069 30.837 426 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 5.69 % Allowed : 20.74 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.43), residues: 380 helix: 2.04 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.43 (0.83), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 328 HIS 0.001 0.000 HIS A 353 PHE 0.020 0.001 PHE A 27 TYR 0.013 0.001 TYR A 422 ARG 0.005 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.324 Fit side-chains REVERT: A 130 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6237 (mm-40) REVERT: A 185 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8509 (tp) REVERT: A 243 TYR cc_start: 0.7880 (t80) cc_final: 0.7610 (t80) REVERT: A 245 PHE cc_start: 0.6618 (m-10) cc_final: 0.5944 (m-80) REVERT: A 248 LYS cc_start: 0.7628 (pttm) cc_final: 0.7033 (ptmm) REVERT: A 268 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7059 (m-10) REVERT: A 346 ASN cc_start: 0.8803 (m-40) cc_final: 0.8542 (m110) outliers start: 17 outliers final: 5 residues processed: 66 average time/residue: 1.1613 time to fit residues: 78.8410 Evaluate side-chains 61 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 420 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2943 Z= 0.237 Angle : 0.679 9.789 4010 Z= 0.314 Chirality : 0.042 0.124 479 Planarity : 0.005 0.048 491 Dihedral : 5.034 31.373 426 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.35 % Allowed : 22.07 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.43), residues: 380 helix: 2.05 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.40 (0.85), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 328 HIS 0.001 0.000 HIS A 353 PHE 0.019 0.001 PHE A 27 TYR 0.013 0.001 TYR A 422 ARG 0.006 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.264 Fit side-chains REVERT: A 130 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.6124 (mm-40) REVERT: A 248 LYS cc_start: 0.7641 (pttm) cc_final: 0.7138 (ptmm) REVERT: A 346 ASN cc_start: 0.8806 (m-40) cc_final: 0.8542 (m110) REVERT: A 406 MET cc_start: 0.8968 (mmm) cc_final: 0.8069 (mmt) REVERT: A 453 MET cc_start: 0.8542 (mmt) cc_final: 0.8318 (mmt) outliers start: 13 outliers final: 6 residues processed: 68 average time/residue: 1.1945 time to fit residues: 83.3886 Evaluate side-chains 60 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 420 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8518 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2943 Z= 0.224 Angle : 0.691 9.885 4010 Z= 0.322 Chirality : 0.042 0.124 479 Planarity : 0.005 0.050 491 Dihedral : 4.957 30.821 426 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.68 % Allowed : 23.08 % Favored : 73.24 % 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: 2.28 (0.44), residues: 380 helix: 1.90 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.30 (0.85), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 328 HIS 0.001 0.000 HIS A 353 PHE 0.018 0.001 PHE A 27 TYR 0.014 0.001 TYR A 422 ARG 0.005 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.339 Fit side-chains REVERT: A 130 GLN cc_start: 0.6734 (OUTLIER) cc_final: 0.6181 (mm-40) REVERT: A 243 TYR cc_start: 0.7821 (t80) cc_final: 0.7550 (t80) REVERT: A 248 LYS cc_start: 0.7657 (pttm) cc_final: 0.6999 (ptmm) REVERT: A 255 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8305 (tt) REVERT: A 346 ASN cc_start: 0.8798 (m-40) cc_final: 0.8522 (m110) REVERT: A 445 LYS cc_start: 0.8720 (tppp) cc_final: 0.8106 (tptm) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 1.1120 time to fit residues: 76.7520 Evaluate side-chains 62 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 420 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 28 optimal weight: 0.0060 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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: 0.8509 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2943 Z= 0.212 Angle : 0.695 10.026 4010 Z= 0.323 Chirality : 0.042 0.129 479 Planarity : 0.005 0.050 491 Dihedral : 4.974 31.045 426 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.68 % Allowed : 23.41 % 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: 2.34 (0.44), residues: 380 helix: 1.95 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.35 (0.83), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 328 HIS 0.000 0.000 HIS A 353 PHE 0.017 0.001 PHE A 27 TYR 0.016 0.001 TYR A 422 ARG 0.006 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.329 Fit side-chains REVERT: A 130 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6179 (mm-40) REVERT: A 155 ARG cc_start: 0.7926 (mtm180) cc_final: 0.7424 (mtp180) REVERT: A 243 TYR cc_start: 0.7830 (t80) cc_final: 0.7577 (t80) REVERT: A 268 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7110 (m-10) REVERT: A 310 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8300 (mpt) REVERT: A 346 ASN cc_start: 0.8759 (m-40) cc_final: 0.8506 (m110) REVERT: A 445 LYS cc_start: 0.8714 (tppp) cc_final: 0.8136 (tptt) outliers start: 11 outliers final: 6 residues processed: 65 average time/residue: 1.1340 time to fit residues: 75.8316 Evaluate side-chains 61 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 420 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8486 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2943 Z= 0.192 Angle : 0.681 10.160 4010 Z= 0.316 Chirality : 0.041 0.131 479 Planarity : 0.005 0.050 491 Dihedral : 4.816 31.298 426 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.67 % Allowed : 25.75 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.44), residues: 380 helix: 2.02 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.45 (0.84), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 328 HIS 0.000 0.000 HIS A 414 PHE 0.016 0.001 PHE A 27 TYR 0.012 0.001 TYR A 243 ARG 0.008 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.339 Fit side-chains REVERT: A 130 GLN cc_start: 0.6720 (OUTLIER) cc_final: 0.6172 (mm-40) REVERT: A 155 ARG cc_start: 0.7900 (mtm180) cc_final: 0.7394 (mtp180) REVERT: A 243 TYR cc_start: 0.7817 (t80) cc_final: 0.7580 (t80) REVERT: A 346 ASN cc_start: 0.8698 (m-40) cc_final: 0.8468 (m110) REVERT: A 377 PHE cc_start: 0.8745 (m-80) cc_final: 0.8462 (m-10) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 1.1614 time to fit residues: 75.2047 Evaluate side-chains 60 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 375 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8492 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2943 Z= 0.209 Angle : 0.712 10.117 4010 Z= 0.327 Chirality : 0.042 0.139 479 Planarity : 0.005 0.050 491 Dihedral : 4.808 30.869 426 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.67 % Allowed : 26.09 % Favored : 72.24 % 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: 2.37 (0.44), residues: 380 helix: 1.99 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.41 (0.84), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 328 HIS 0.000 0.000 HIS A 353 PHE 0.016 0.001 PHE A 27 TYR 0.015 0.001 TYR A 422 ARG 0.008 0.001 ARG A 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.273 Fit side-chains REVERT: A 130 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6186 (mm-40) REVERT: A 133 LEU cc_start: 0.8821 (tm) cc_final: 0.8599 (tt) REVERT: A 155 ARG cc_start: 0.7898 (mtm180) cc_final: 0.7390 (mtp180) REVERT: A 243 TYR cc_start: 0.7837 (t80) cc_final: 0.7602 (t80) REVERT: A 346 ASN cc_start: 0.8691 (m-40) cc_final: 0.8480 (m110) REVERT: A 377 PHE cc_start: 0.8734 (m-80) cc_final: 0.8448 (m-10) REVERT: A 445 LYS cc_start: 0.8659 (tppp) cc_final: 0.8065 (tptm) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 1.1533 time to fit residues: 71.1767 Evaluate side-chains 59 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 375 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.102389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.087045 restraints weight = 4731.317| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.11 r_work: 0.2941 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2943 Z= 0.236 Angle : 0.722 10.172 4010 Z= 0.332 Chirality : 0.043 0.184 479 Planarity : 0.006 0.050 491 Dihedral : 4.962 30.863 426 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.34 % Allowed : 26.09 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.44), residues: 380 helix: 1.85 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.40 (0.84), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 328 HIS 0.001 0.000 HIS A 353 PHE 0.017 0.001 PHE A 27 TYR 0.018 0.001 TYR A 422 ARG 0.008 0.001 ARG A 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1714.54 seconds wall clock time: 31 minutes 30.87 seconds (1890.87 seconds total)