Starting phenix.real_space_refine on Mon Feb 10 21:48:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jt9_36637/02_2025/8jt9_36637.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jt9_36637/02_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_36637/02_2025/8jt9_36637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jt9_36637/02_2025/8jt9_36637.map" model { file = "/net/cci-nas-00/data/ceres_data/8jt9_36637/02_2025/8jt9_36637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jt9_36637/02_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-5592/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: 2.91, 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: 0.90 Conformation dependent library (CDL) restraints added in 382.3 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: 0.27 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: 0.84 Time building geometry restraints manager: 0.93 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.750 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.020 ------------------------------------------------------------------------------- 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 : 0.295 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: 1.2285 time to fit residues: 68.1205 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 : 0.504 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.105507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.089636 restraints weight = 4697.286| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.16 r_work: 0.2986 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 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 : 0.288 Fit side-chains REVERT: A 206 MET cc_start: 0.8778 (ttt) cc_final: 0.8442 (ttt) REVERT: A 310 MET cc_start: 0.8930 (mmm) cc_final: 0.8579 (mmm) REVERT: A 453 MET cc_start: 0.8584 (mmt) cc_final: 0.8356 (mmt) outliers start: 12 outliers final: 3 residues processed: 64 average time/residue: 1.0202 time to fit residues: 67.2769 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 : 0.285 ------------------------------------------------------------------------------- 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: 0.8980 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.100715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.084937 restraints weight = 4746.586| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.11 r_work: 0.2916 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2943 Z= 0.289 Angle : 0.689 10.008 4010 Z= 0.323 Chirality : 0.043 0.134 479 Planarity : 0.005 0.051 491 Dihedral : 5.067 29.875 426 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.01 % Allowed : 24.08 % 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: 2.59 (0.44), residues: 380 helix: 2.07 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.45 (0.81), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 328 HIS 0.001 0.001 HIS A 353 PHE 0.020 0.002 PHE A 27 TYR 0.012 0.001 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 66 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.326 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 62 average time/residue: 1.1610 time to fit residues: 74.1509 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 : 0.309 ------------------------------------------------------------------------------- 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 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 18 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.101793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.086005 restraints weight = 4755.858| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.13 r_work: 0.2928 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2943 Z= 0.221 Angle : 0.656 9.868 4010 Z= 0.304 Chirality : 0.042 0.123 479 Planarity : 0.005 0.052 491 Dihedral : 4.973 30.061 426 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 5.02 % Allowed : 21.74 % 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: 2.74 (0.44), residues: 380 helix: 2.17 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.38 (0.81), 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 0.013 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 72 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.287 Fit side-chains REVERT: A 130 GLN cc_start: 0.6578 (OUTLIER) cc_final: 0.6043 (mm-40) REVERT: A 453 MET cc_start: 0.8664 (mmt) cc_final: 0.8463 (mmt) outliers start: 15 outliers final: 3 residues processed: 65 average time/residue: 1.1321 time to fit residues: 75.6121 Evaluate side-chains 57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 435 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 0.0870 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- 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 = 0.3288 r_free = 0.3288 target = 0.102354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.086980 restraints weight = 4750.834| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.07 r_work: 0.2945 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2943 Z= 0.203 Angle : 0.659 9.835 4010 Z= 0.304 Chirality : 0.041 0.121 479 Planarity : 0.005 0.048 491 Dihedral : 4.965 31.029 426 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 5.35 % Allowed : 22.07 % 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: 2.76 (0.44), residues: 380 helix: 2.19 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.44 (0.81), 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 0.017 0.001 PHE A 27 TYR 0.012 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 72 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.326 Fit side-chains REVERT: A 130 GLN cc_start: 0.6629 (OUTLIER) cc_final: 0.5935 (mm-40) outliers start: 16 outliers final: 7 residues processed: 68 average time/residue: 1.0311 time to fit residues: 72.2594 Evaluate side-chains 63 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 0.0570 overall best weight: 1.3102 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.101396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.085891 restraints weight = 4741.193| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.10 r_work: 0.2932 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1438 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= 0.232 Angle : 0.677 9.886 4010 Z= 0.314 Chirality : 0.042 0.122 479 Planarity : 0.005 0.049 491 Dihedral : 4.949 30.321 426 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 5.02 % Allowed : 21.74 % 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: 2.61 (0.44), residues: 380 helix: 2.09 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.44 (0.83), 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 0.017 0.001 PHE A 27 TYR 0.014 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 70 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.378 Fit side-chains REVERT: A 130 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.5984 (mm-40) REVERT: A 245 PHE cc_start: 0.6585 (m-10) cc_final: 0.5963 (m-80) REVERT: A 255 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 327 LYS cc_start: 0.8389 (mptt) cc_final: 0.8138 (tptt) outliers start: 15 outliers final: 6 residues processed: 68 average time/residue: 1.1205 time to fit residues: 78.3697 Evaluate side-chains 60 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 255 LEU Chi-restraints excluded: chain A residue 375 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 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 = 0.3297 r_free = 0.3297 target = 0.102867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.087514 restraints weight = 4854.553| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.08 r_work: 0.2951 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1524 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= 0.194 Angle : 0.674 9.940 4010 Z= 0.312 Chirality : 0.041 0.126 479 Planarity : 0.005 0.050 491 Dihedral : 4.838 30.611 426 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.19 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: 2.71 (0.44), residues: 380 helix: 2.18 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -0.57 (0.81), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 328 HIS 0.000 0.000 HIS A 353 PHE 0.016 0.001 PHE A 27 TYR 0.013 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 66 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.317 Fit side-chains REVERT: A 130 GLN cc_start: 0.6567 (OUTLIER) cc_final: 0.6006 (mm-40) REVERT: A 185 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8435 (tp) REVERT: A 245 PHE cc_start: 0.6634 (m-10) cc_final: 0.5994 (m-80) REVERT: A 310 MET cc_start: 0.8922 (mmm) cc_final: 0.8595 (mpt) REVERT: A 327 LYS cc_start: 0.8410 (mptt) cc_final: 0.8107 (tptt) outliers start: 11 outliers final: 5 residues processed: 63 average time/residue: 1.0946 time to fit residues: 71.0455 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 : 0.393 ------------------------------------------------------------------------------- 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 311 LEU 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: 0.8980 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.102350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.086855 restraints weight = 4750.074| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.05 r_work: 0.2947 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1626 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= 0.213 Angle : 0.698 9.997 4010 Z= 0.321 Chirality : 0.042 0.128 479 Planarity : 0.005 0.050 491 Dihedral : 4.897 30.544 426 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.68 % Allowed : 23.75 % 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: 2.65 (0.44), residues: 380 helix: 2.12 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.53 (0.82), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 328 HIS 0.001 0.000 HIS A 353 PHE 0.017 0.001 PHE A 27 TYR 0.012 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 66 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.382 Fit side-chains REVERT: A 130 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.6024 (mm-40) REVERT: A 245 PHE cc_start: 0.6658 (m-10) cc_final: 0.6050 (m-80) REVERT: A 310 MET cc_start: 0.8937 (mmm) cc_final: 0.8690 (mpt) REVERT: A 445 LYS cc_start: 0.8564 (tttm) cc_final: 0.8358 (tppp) outliers start: 11 outliers final: 6 residues processed: 64 average time/residue: 1.1750 time to fit residues: 77.3812 Evaluate side-chains 61 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 311 LEU 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: 0.9990 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.103201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.087696 restraints weight = 4768.195| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.07 r_work: 0.2961 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1724 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= 0.200 Angle : 0.711 10.159 4010 Z= 0.325 Chirality : 0.042 0.133 479 Planarity : 0.005 0.050 491 Dihedral : 4.840 30.680 426 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.68 % Allowed : 23.75 % 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: 2.39 (0.44), residues: 380 helix: 2.02 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.58 (0.78), residues: 48 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 0.016 0.001 PHE A 27 TYR 0.016 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 67 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.323 Fit side-chains REVERT: A 130 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6017 (mm-40) REVERT: A 133 LEU cc_start: 0.8687 (tm) cc_final: 0.8460 (tt) REVERT: A 155 ARG cc_start: 0.8049 (mtm180) cc_final: 0.7632 (mtp180) REVERT: A 245 PHE cc_start: 0.6650 (m-10) cc_final: 0.6045 (m-80) REVERT: A 327 LYS cc_start: 0.8441 (mppt) cc_final: 0.8159 (tptt) REVERT: A 445 LYS cc_start: 0.8546 (tttm) cc_final: 0.8333 (tppp) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 1.1356 time to fit residues: 73.5736 Evaluate side-chains 65 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 175 MET 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 248 LYS Chi-restraints excluded: chain A residue 311 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 0.0000 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.105242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089810 restraints weight = 4815.897| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.07 r_work: 0.2987 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2943 Z= 0.187 Angle : 0.697 10.204 4010 Z= 0.320 Chirality : 0.042 0.144 479 Planarity : 0.005 0.050 491 Dihedral : 4.806 30.985 426 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.01 % Allowed : 25.08 % 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: 2.43 (0.44), residues: 380 helix: 2.04 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.57 (0.81), residues: 47 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 0.015 0.001 PHE A 27 TYR 0.016 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 69 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.333 Fit side-chains REVERT: A 130 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.5983 (mm-40) REVERT: A 133 LEU cc_start: 0.8670 (tm) cc_final: 0.8432 (tt) REVERT: A 155 ARG cc_start: 0.8043 (mtm180) cc_final: 0.7617 (mtp180) REVERT: A 245 PHE cc_start: 0.6646 (m-10) cc_final: 0.6040 (m-80) REVERT: A 321 GLU cc_start: 0.8574 (tp30) cc_final: 0.8272 (mt-10) REVERT: A 327 LYS cc_start: 0.8432 (mppt) cc_final: 0.8109 (tppt) REVERT: A 377 PHE cc_start: 0.8770 (m-80) cc_final: 0.8499 (m-10) REVERT: A 445 LYS cc_start: 0.8510 (tttm) cc_final: 0.8309 (tppp) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 1.1295 time to fit residues: 77.7867 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 : 0.328 ------------------------------------------------------------------------------- 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 248 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.102714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.087212 restraints weight = 4669.585| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.09 r_work: 0.2955 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2943 Z= 0.242 Angle : 0.718 10.120 4010 Z= 0.333 Chirality : 0.043 0.191 479 Planarity : 0.005 0.050 491 Dihedral : 4.874 30.698 426 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.01 % Allowed : 25.75 % Favored : 71.24 % 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: 2.29 (0.44), residues: 380 helix: 1.94 (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 0.001 0.000 HIS A 353 PHE 0.017 0.001 PHE A 27 TYR 0.019 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: 2431.70 seconds wall clock time: 43 minutes 31.39 seconds (2611.39 seconds total)