Starting phenix.real_space_refine on Wed Mar 5 16:46:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jt9_36637/03_2025/8jt9_36637.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jt9_36637/03_2025/8jt9_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_36637/03_2025/8jt9_36637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jt9_36637/03_2025/8jt9_36637.map" model { file = "/net/cci-nas-00/data/ceres_data/8jt9_36637/03_2025/8jt9_36637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jt9_36637/03_2025/8jt9_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-5624/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: 3.50, per 1000 atoms: 1.22 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: 0.79 Conformation dependent library (CDL) restraints added in 361.1 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: 0.23 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: 0.73 Time building geometry restraints manager: 0.90 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.970 Find NCS groups from input model: 0.020 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:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.420 ------------------------------------------------------------------------------- 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 : 0.306 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: 1.2422 time to fit residues: 68.8957 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 : 0.276 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.090018 restraints weight = 4697.144| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.16 r_work: 0.2989 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 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 : 0.299 Fit side-chains REVERT: A 206 MET cc_start: 0.8780 (ttt) cc_final: 0.8444 (ttt) REVERT: A 310 MET cc_start: 0.8929 (mmm) cc_final: 0.8578 (mmm) REVERT: A 453 MET cc_start: 0.8586 (mmt) cc_final: 0.8358 (mmt) outliers start: 12 outliers final: 3 residues processed: 64 average time/residue: 1.0457 time to fit residues: 68.9573 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 : 0.305 ------------------------------------------------------------------------------- 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 27 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.083345 restraints weight = 4760.340| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.11 r_work: 0.2891 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2943 Z= 0.359 Angle : 0.714 9.981 4010 Z= 0.337 Chirality : 0.044 0.140 479 Planarity : 0.006 0.052 491 Dihedral : 5.156 29.518 426 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.68 % Allowed : 24.41 % Favored : 71.91 % 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: 2.41 (0.43), residues: 380 helix: 1.95 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.48 (0.81), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 328 HIS 0.001 0.001 HIS A 353 PHE 0.020 0.002 PHE A 27 TYR 0.013 0.002 TYR A 422 ARG 0.004 0.001 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 64 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.330 Fit side-chains REVERT: A 185 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8367 (tp) outliers start: 11 outliers final: 3 residues processed: 61 average time/residue: 1.0979 time to fit residues: 68.9430 Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 185 LEU 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 10 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.099445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.083899 restraints weight = 4776.367| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.10 r_work: 0.2893 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2943 Z= 0.303 Angle : 0.683 9.765 4010 Z= 0.320 Chirality : 0.043 0.131 479 Planarity : 0.006 0.052 491 Dihedral : 5.171 29.567 426 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 6.02 % Allowed : 21.07 % 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: 2.46 (0.43), residues: 380 helix: 1.97 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.36 (0.82), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 328 HIS 0.001 0.001 HIS A 353 PHE 0.020 0.002 PHE A 27 TYR 0.014 0.001 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 74 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.282 Fit side-chains REVERT: A 130 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.6106 (mm-40) REVERT: A 245 PHE cc_start: 0.6626 (m-10) cc_final: 0.5988 (m-80) REVERT: A 248 LYS cc_start: 0.7674 (pttm) cc_final: 0.7170 (ptmm) REVERT: A 268 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7329 (m-10) REVERT: A 379 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8051 (mttm) outliers start: 18 outliers final: 4 residues processed: 66 average time/residue: 1.1825 time to fit residues: 80.1119 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 : 0.286 ------------------------------------------------------------------------------- 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 212 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 268 PHE 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 19 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 0.0170 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- 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 = 0.101814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.086589 restraints weight = 4726.563| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.03 r_work: 0.2917 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2943 Z= 0.193 Angle : 0.661 9.747 4010 Z= 0.306 Chirality : 0.041 0.125 479 Planarity : 0.005 0.048 491 Dihedral : 5.054 30.961 426 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.35 % Allowed : 22.41 % 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: 2.64 (0.44), residues: 380 helix: 2.12 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.51 (0.80), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 328 HIS 0.001 0.000 HIS A 353 PHE 0.018 0.001 PHE A 27 TYR 0.011 0.001 TYR A 243 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 69 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.313 Fit side-chains REVERT: A 130 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6032 (mm-40) REVERT: A 245 PHE cc_start: 0.6626 (m-10) cc_final: 0.5965 (m-80) REVERT: A 248 LYS cc_start: 0.7732 (pttm) cc_final: 0.7039 (ptmm) REVERT: A 310 MET cc_start: 0.8964 (mmm) cc_final: 0.8654 (mmm) REVERT: A 453 MET cc_start: 0.8590 (mmt) cc_final: 0.8368 (mmt) outliers start: 13 outliers final: 3 residues processed: 65 average time/residue: 1.1674 time to fit residues: 77.9120 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 : 0.303 ------------------------------------------------------------------------------- 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 420 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.0050 chunk 14 optimal weight: 0.3980 overall best weight: 0.2806 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.090117 restraints weight = 4702.073| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.02 r_work: 0.3001 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2943 Z= 0.163 Angle : 0.647 9.954 4010 Z= 0.298 Chirality : 0.040 0.123 479 Planarity : 0.005 0.047 491 Dihedral : 4.745 31.755 426 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.68 % Allowed : 22.07 % 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: 2.51 (0.44), residues: 380 helix: 2.06 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.37 (0.81), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 328 HIS 0.000 0.000 HIS A 414 PHE 0.015 0.001 PHE A 27 TYR 0.010 0.001 TYR A 422 ARG 0.007 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 75 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.309 Fit side-chains REVERT: A 35 MET cc_start: 0.8773 (ttt) cc_final: 0.8522 (ttm) REVERT: A 130 GLN cc_start: 0.6505 (OUTLIER) cc_final: 0.5802 (mm-40) REVERT: A 155 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7548 (mtp180) REVERT: A 310 MET cc_start: 0.8934 (mmm) cc_final: 0.8402 (mmm) REVERT: A 377 PHE cc_start: 0.8732 (m-80) cc_final: 0.8477 (m-10) outliers start: 14 outliers final: 5 residues processed: 73 average time/residue: 0.9869 time to fit residues: 74.3198 Evaluate side-chains 62 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 420 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.103345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.087486 restraints weight = 4852.019| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.15 r_work: 0.2953 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1713 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= 0.202 Angle : 0.693 10.058 4010 Z= 0.320 Chirality : 0.042 0.122 479 Planarity : 0.005 0.049 491 Dihedral : 4.784 30.936 426 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.68 % Allowed : 24.08 % 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: 2.31 (0.44), residues: 380 helix: 1.95 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.52 (0.79), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 328 HIS 0.000 0.000 HIS A 353 PHE 0.015 0.001 PHE A 27 TYR 0.015 0.001 TYR A 422 ARG 0.007 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 67 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.308 Fit side-chains REVERT: A 130 GLN cc_start: 0.6542 (OUTLIER) cc_final: 0.6003 (mm-40) REVERT: A 185 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8416 (tp) REVERT: A 245 PHE cc_start: 0.6624 (m-10) cc_final: 0.5999 (m-80) REVERT: A 377 PHE cc_start: 0.8779 (m-80) cc_final: 0.8524 (m-10) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 1.0549 time to fit residues: 72.7528 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 : 0.309 ------------------------------------------------------------------------------- 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 185 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 233 LEU 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 33 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.101735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.086147 restraints weight = 4769.665| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.06 r_work: 0.2935 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1795 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 : 0.703 10.060 4010 Z= 0.325 Chirality : 0.042 0.132 479 Planarity : 0.005 0.051 491 Dihedral : 4.873 30.777 426 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.34 % Allowed : 24.41 % 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: 2.55 (0.44), residues: 380 helix: 2.05 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.49 (0.83), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 328 HIS 0.001 0.000 HIS A 353 PHE 0.017 0.001 PHE A 27 TYR 0.013 0.001 TYR A 422 ARG 0.007 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 63 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.307 Fit side-chains REVERT: A 130 GLN cc_start: 0.6591 (OUTLIER) cc_final: 0.6034 (mm-40) REVERT: A 133 LEU cc_start: 0.8721 (tm) cc_final: 0.8505 (tt) REVERT: A 155 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7644 (mtp180) REVERT: A 245 PHE cc_start: 0.6770 (m-10) cc_final: 0.6175 (m-80) REVERT: A 327 LYS cc_start: 0.8467 (mppt) cc_final: 0.7773 (mptt) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 1.0458 time to fit residues: 66.7875 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 : 0.283 ------------------------------------------------------------------------------- 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 233 LEU 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 5 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.0370 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.3311 r_free = 0.3311 target = 0.104226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.089232 restraints weight = 4752.170| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.03 r_work: 0.2974 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2943 Z= 0.189 Angle : 0.693 10.099 4010 Z= 0.317 Chirality : 0.041 0.136 479 Planarity : 0.005 0.050 491 Dihedral : 4.804 30.500 426 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.01 % Allowed : 24.41 % 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: 2.34 (0.44), residues: 380 helix: 1.98 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.54 (0.79), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 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 422 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 71 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.303 Fit side-chains REVERT: A 130 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.5989 (mm-40) REVERT: A 133 LEU cc_start: 0.8709 (tm) cc_final: 0.8485 (tt) REVERT: A 155 ARG cc_start: 0.8069 (mtm180) cc_final: 0.7613 (mtp180) REVERT: A 245 PHE cc_start: 0.6787 (m-10) cc_final: 0.6192 (m-80) REVERT: A 377 PHE cc_start: 0.8818 (m-80) cc_final: 0.8576 (m-10) REVERT: A 445 LYS cc_start: 0.8557 (tttm) cc_final: 0.8330 (tppp) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 1.0904 time to fit residues: 79.6122 Evaluate side-chains 65 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 233 LEU Chi-restraints excluded: chain A residue 420 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.104565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.088634 restraints weight = 4789.040| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.15 r_work: 0.2971 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1983 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= 0.194 Angle : 0.717 10.097 4010 Z= 0.328 Chirality : 0.042 0.138 479 Planarity : 0.005 0.050 491 Dihedral : 4.774 30.463 426 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.34 % Allowed : 25.42 % 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: 2.28 (0.44), residues: 380 helix: 1.94 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.57 (0.80), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 328 HIS 0.000 0.000 HIS A 353 PHE 0.015 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 65 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.286 Fit side-chains REVERT: A 130 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.5963 (mm-40) REVERT: A 133 LEU cc_start: 0.8670 (tm) cc_final: 0.8433 (tt) REVERT: A 155 ARG cc_start: 0.8024 (mtm180) cc_final: 0.7555 (mtp180) REVERT: A 245 PHE cc_start: 0.6757 (m-10) cc_final: 0.6186 (m-80) REVERT: A 327 LYS cc_start: 0.8397 (mppt) cc_final: 0.8130 (tptt) REVERT: A 377 PHE cc_start: 0.8766 (m-80) cc_final: 0.8503 (m-10) REVERT: A 445 LYS cc_start: 0.8561 (tttm) cc_final: 0.8296 (tppp) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 1.0218 time to fit residues: 68.3940 Evaluate side-chains 64 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 233 LEU Chi-restraints excluded: chain A residue 420 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.103388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.087722 restraints weight = 4622.699| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.06 r_work: 0.2957 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1962 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= 0.226 Angle : 0.728 10.115 4010 Z= 0.334 Chirality : 0.042 0.135 479 Planarity : 0.005 0.050 491 Dihedral : 4.813 30.107 426 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.34 % Allowed : 24.75 % Favored : 71.91 % 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: 2.25 (0.44), residues: 380 helix: 1.92 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.57 (0.79), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 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 0.008 0.001 ARG A 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.94 seconds wall clock time: 43 minutes 13.78 seconds (2593.78 seconds total)