Starting phenix.real_space_refine on Thu Mar 6 01:54:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfl_34722/03_2025/8hfl_34722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfl_34722/03_2025/8hfl_34722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hfl_34722/03_2025/8hfl_34722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfl_34722/03_2025/8hfl_34722.map" model { file = "/net/cci-nas-00/data/ceres_data/8hfl_34722/03_2025/8hfl_34722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfl_34722/03_2025/8hfl_34722.cif" } resolution = 3.0 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= 0.002 sd= 0.140 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 20 5.16 5 Cl 2 4.86 5 C 2980 2.51 5 N 689 2.21 5 O 750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 4441 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4421 Classifications: {'peptide': 553} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 533} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 20 Unusual residues: {' CL': 1, '1XR': 1} Classifications: {'undetermined': 2, 'water': 3} Link IDs: {None: 4} Time building chain proxies: 3.25, per 1000 atoms: 0.73 Number of scatterers: 4441 At special positions: 0 Unit cell: (68.1975, 71.445, 98.5075, 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) Cl 2 17.00 S 20 16.00 O 750 8.00 N 689 7.00 C 2980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 525.6 milliseconds 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 1 sheets defined 80.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.515A pdb=" N VAL A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 4.367A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.629A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 148 Processing helix chain 'A' and resid 151 through 166 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 removed outlier: 3.590A pdb=" N LEU A 239 " --> pdb=" O TRP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 283 Proline residue: A 270 - end of helix removed outlier: 4.106A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.744A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 392 - end of helix removed outlier: 3.700A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.758A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.523A pdb=" N LYS A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.719A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.554A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.774A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 292 hydrogen bonds defined for protein. 849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1297 1.34 - 1.46: 974 1.46 - 1.58: 2277 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 4580 Sorted by residual: bond pdb=" N GLY A 60 " pdb=" CA GLY A 60 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.95e+00 bond pdb=" C2 1XR A 701 " pdb=" N1 1XR A 701 " ideal model delta sigma weight residual 1.441 1.477 -0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" C10 1XR A 701 " pdb=" N1 1XR A 701 " ideal model delta sigma weight residual 1.467 1.490 -0.023 2.00e-02 2.50e+03 1.30e+00 bond pdb=" CA LEU A 102 " pdb=" C LEU A 102 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.28e-02 6.10e+03 1.09e+00 bond pdb=" C1 1XR A 701 " pdb=" C2 1XR A 701 " ideal model delta sigma weight residual 1.542 1.522 0.020 2.00e-02 2.50e+03 9.88e-01 ... (remaining 4575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 6100 1.50 - 3.00: 111 3.00 - 4.50: 32 4.50 - 6.00: 4 6.00 - 7.50: 1 Bond angle restraints: 6248 Sorted by residual: angle pdb=" C GLY A 106 " pdb=" N MET A 107 " pdb=" CA MET A 107 " ideal model delta sigma weight residual 119.78 116.12 3.66 1.24e+00 6.50e-01 8.70e+00 angle pdb=" N VAL A 263 " pdb=" CA VAL A 263 " pdb=" C VAL A 263 " ideal model delta sigma weight residual 113.00 109.26 3.74 1.30e+00 5.92e-01 8.26e+00 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" C TYR A 205 " ideal model delta sigma weight residual 110.80 116.58 -5.78 2.13e+00 2.20e-01 7.36e+00 angle pdb=" C1 1XR A 701 " pdb=" C2 1XR A 701 " pdb=" N1 1XR A 701 " ideal model delta sigma weight residual 117.04 109.54 7.50 3.00e+00 1.11e-01 6.25e+00 angle pdb=" CA MET A 107 " pdb=" C MET A 107 " pdb=" N PRO A 108 " ideal model delta sigma weight residual 120.81 118.72 2.09 8.60e-01 1.35e+00 5.88e+00 ... (remaining 6243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 2237 16.52 - 33.04: 241 33.04 - 49.56: 62 49.56 - 66.08: 23 66.08 - 82.60: 2 Dihedral angle restraints: 2565 sinusoidal: 968 harmonic: 1597 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -157.01 -22.99 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -133.33 10.73 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 132.57 -9.77 0 2.50e+00 1.60e-01 1.53e+01 ... (remaining 2562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 666 0.088 - 0.176: 28 0.176 - 0.264: 0 0.264 - 0.351: 0 0.351 - 0.439: 2 Chirality restraints: 696 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CA HIS A 372 " pdb=" N HIS A 372 " pdb=" C HIS A 372 " pdb=" CB HIS A 372 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C2 1XR A 701 " pdb=" C1 1XR A 701 " pdb=" C3 1XR A 701 " pdb=" N1 1XR A 701 " both_signs ideal model delta sigma weight residual False -2.43 -2.59 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 693 not shown) Planarity restraints: 759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C ILE A 103 " -0.063 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 492 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C VAL A 492 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 492 " 0.015 2.00e-02 2.50e+03 pdb=" N SER A 493 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 102 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C LEU A 102 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU A 102 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE A 103 " 0.012 2.00e-02 2.50e+03 ... (remaining 756 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 26 2.56 - 3.15: 3663 3.15 - 3.73: 6973 3.73 - 4.32: 9679 4.32 - 4.90: 16767 Nonbonded interactions: 37108 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" OG SER A 419 " model vdw 1.981 3.040 nonbonded pdb=" OG1 THR A 479 " pdb=" OG SER A 536 " model vdw 2.179 3.040 nonbonded pdb=" NZ LYS A 189 " pdb=" OE2 GLU A 371 " model vdw 2.195 3.120 nonbonded pdb=" O ALA A 328 " pdb=" OG SER A 331 " model vdw 2.236 3.040 nonbonded pdb=" O THR A 283 " pdb=" OG1 THR A 283 " model vdw 2.303 3.040 ... (remaining 37103 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.003 0.039 4580 Z= 0.188 Angle : 0.548 7.502 6248 Z= 0.296 Chirality : 0.044 0.439 696 Planarity : 0.004 0.037 759 Dihedral : 15.471 82.598 1546 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.09 % Rotamer: Outliers : 1.72 % Allowed : 17.17 % Favored : 81.12 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.37), residues: 549 helix: 1.52 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.10 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.013 0.001 PHE A 403 TYR 0.014 0.001 TYR A 590 ARG 0.001 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.480 Fit side-chains REVERT: A 509 MET cc_start: 0.8973 (mtp) cc_final: 0.8715 (mtt) REVERT: A 606 ILE cc_start: 0.8230 (mm) cc_final: 0.8016 (mm) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.5617 time to fit residues: 31.3667 Evaluate side-chains 48 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 536 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.096369 restraints weight = 5135.871| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.80 r_work: 0.2879 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4580 Z= 0.212 Angle : 0.517 6.792 6248 Z= 0.268 Chirality : 0.040 0.173 696 Planarity : 0.004 0.034 759 Dihedral : 6.023 47.869 615 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.37 % Favored : 97.45 % Rotamer: Outliers : 2.79 % Allowed : 14.81 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.37), residues: 549 helix: 1.37 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.01 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.003 0.001 HIS A 370 PHE 0.015 0.001 PHE A 110 TYR 0.016 0.001 TYR A 590 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.436 Fit side-chains REVERT: A 271 TYR cc_start: 0.8411 (m-80) cc_final: 0.7977 (m-80) REVERT: A 377 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: A 421 MET cc_start: 0.7795 (mtp) cc_final: 0.7556 (mtm) REVERT: A 434 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8703 (m-30) REVERT: A 509 MET cc_start: 0.8941 (mtp) cc_final: 0.8660 (mtt) REVERT: A 606 ILE cc_start: 0.8039 (mm) cc_final: 0.7792 (mm) outliers start: 13 outliers final: 3 residues processed: 63 average time/residue: 0.5740 time to fit residues: 39.1743 Evaluate side-chains 52 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 434 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.0020 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.124175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.097345 restraints weight = 5129.401| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.74 r_work: 0.2877 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4580 Z= 0.190 Angle : 0.499 6.573 6248 Z= 0.257 Chirality : 0.039 0.141 696 Planarity : 0.004 0.032 759 Dihedral : 5.374 36.104 608 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.55 % Favored : 97.27 % Rotamer: Outliers : 2.15 % Allowed : 17.38 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.37), residues: 549 helix: 1.43 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.11 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 370 PHE 0.014 0.001 PHE A 110 TYR 0.016 0.001 TYR A 84 ARG 0.002 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.465 Fit side-chains REVERT: A 261 LYS cc_start: 0.3517 (OUTLIER) cc_final: 0.3258 (ptmm) REVERT: A 271 TYR cc_start: 0.8298 (m-80) cc_final: 0.7882 (m-80) REVERT: A 377 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: A 399 SER cc_start: 0.8068 (t) cc_final: 0.7848 (m) REVERT: A 421 MET cc_start: 0.7825 (mtp) cc_final: 0.7577 (mtm) REVERT: A 434 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8732 (m-30) REVERT: A 509 MET cc_start: 0.8840 (mtp) cc_final: 0.8568 (mtt) outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 0.5004 time to fit residues: 31.8498 Evaluate side-chains 56 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.0870 chunk 40 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.098940 restraints weight = 5162.180| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.74 r_work: 0.2914 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4580 Z= 0.199 Angle : 0.493 6.651 6248 Z= 0.255 Chirality : 0.039 0.133 696 Planarity : 0.004 0.031 759 Dihedral : 5.311 35.471 608 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.43 % Allowed : 17.38 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.37), residues: 549 helix: 1.49 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.22 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 370 PHE 0.012 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.479 Fit side-chains REVERT: A 261 LYS cc_start: 0.3353 (OUTLIER) cc_final: 0.3128 (pttp) REVERT: A 271 TYR cc_start: 0.8265 (m-80) cc_final: 0.7830 (m-80) REVERT: A 376 ILE cc_start: 0.7147 (mp) cc_final: 0.6777 (mp) REVERT: A 377 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: A 399 SER cc_start: 0.8267 (t) cc_final: 0.8033 (m) REVERT: A 421 MET cc_start: 0.7740 (mtp) cc_final: 0.7484 (mtm) REVERT: A 434 ASP cc_start: 0.8966 (OUTLIER) cc_final: 0.8672 (m-30) REVERT: A 606 ILE cc_start: 0.8070 (mm) cc_final: 0.7825 (mm) outliers start: 16 outliers final: 5 residues processed: 62 average time/residue: 0.4849 time to fit residues: 33.0199 Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.123071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.095667 restraints weight = 5227.024| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.78 r_work: 0.2895 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 4580 Z= 0.269 Angle : 0.522 6.834 6248 Z= 0.272 Chirality : 0.041 0.132 696 Planarity : 0.004 0.032 759 Dihedral : 5.391 34.560 608 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.86 % Allowed : 17.38 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.36), residues: 549 helix: 1.38 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.37 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.014 0.001 PHE A 94 TYR 0.021 0.001 TYR A 84 ARG 0.002 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.471 Fit side-chains REVERT: A 261 LYS cc_start: 0.3419 (OUTLIER) cc_final: 0.3182 (pttp) REVERT: A 317 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8332 (t80) REVERT: A 399 SER cc_start: 0.8318 (t) cc_final: 0.8047 (m) REVERT: A 434 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8672 (m-30) REVERT: A 508 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8432 (ttp) outliers start: 18 outliers final: 6 residues processed: 64 average time/residue: 0.5362 time to fit residues: 37.4382 Evaluate side-chains 59 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 53 optimal weight: 0.0060 chunk 50 optimal weight: 0.9990 overall best weight: 0.4754 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.125944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.099002 restraints weight = 5082.838| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.72 r_work: 0.2915 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 4580 Z= 0.166 Angle : 0.493 8.666 6248 Z= 0.250 Chirality : 0.039 0.130 696 Planarity : 0.004 0.030 759 Dihedral : 5.291 35.861 608 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.22 % Allowed : 18.03 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.37), residues: 549 helix: 1.54 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -0.40 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.001 0.000 HIS A 370 PHE 0.011 0.001 PHE A 110 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.472 Fit side-chains REVERT: A 261 LYS cc_start: 0.3289 (OUTLIER) cc_final: 0.3055 (pttp) REVERT: A 271 TYR cc_start: 0.8258 (m-80) cc_final: 0.7832 (m-80) REVERT: A 376 ILE cc_start: 0.7201 (mp) cc_final: 0.6940 (mp) REVERT: A 399 SER cc_start: 0.8237 (t) cc_final: 0.7978 (m) REVERT: A 420 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8154 (m) REVERT: A 434 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8626 (m-30) REVERT: A 587 ARG cc_start: 0.8450 (mtt90) cc_final: 0.7954 (mmt90) outliers start: 15 outliers final: 6 residues processed: 61 average time/residue: 0.5701 time to fit residues: 37.6589 Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 0.0370 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.097758 restraints weight = 5147.118| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.74 r_work: 0.2917 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4580 Z= 0.192 Angle : 0.503 8.840 6248 Z= 0.255 Chirality : 0.039 0.139 696 Planarity : 0.004 0.029 759 Dihedral : 5.251 35.498 608 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.22 % Allowed : 18.88 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.37), residues: 549 helix: 1.54 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -0.42 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.457 Fit side-chains REVERT: A 261 LYS cc_start: 0.3328 (OUTLIER) cc_final: 0.3084 (pttp) REVERT: A 271 TYR cc_start: 0.8367 (m-80) cc_final: 0.7918 (m-80) REVERT: A 376 ILE cc_start: 0.7356 (mp) cc_final: 0.7060 (mp) REVERT: A 399 SER cc_start: 0.8416 (t) cc_final: 0.8156 (m) REVERT: A 420 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8264 (m) REVERT: A 434 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8590 (m-30) REVERT: A 590 TYR cc_start: 0.8186 (m-80) cc_final: 0.7970 (m-80) outliers start: 15 outliers final: 6 residues processed: 61 average time/residue: 1.1965 time to fit residues: 77.0933 Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 0.0270 chunk 47 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.133200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107044 restraints weight = 5032.532| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.70 r_work: 0.2937 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4580 Z= 0.174 Angle : 0.490 8.543 6248 Z= 0.249 Chirality : 0.039 0.140 696 Planarity : 0.004 0.028 759 Dihedral : 5.184 35.450 608 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.00 % Allowed : 18.67 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.37), residues: 549 helix: 1.61 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -0.38 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.001 0.000 HIS A 370 PHE 0.010 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.550 Fit side-chains REVERT: A 261 LYS cc_start: 0.3375 (OUTLIER) cc_final: 0.3126 (pttp) REVERT: A 271 TYR cc_start: 0.8308 (m-80) cc_final: 0.7928 (m-80) REVERT: A 376 ILE cc_start: 0.7326 (mp) cc_final: 0.7061 (mp) REVERT: A 399 SER cc_start: 0.8399 (t) cc_final: 0.8144 (m) REVERT: A 420 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8306 (m) REVERT: A 434 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8526 (m-30) REVERT: A 459 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7142 (t80) outliers start: 14 outliers final: 6 residues processed: 58 average time/residue: 0.8770 time to fit residues: 55.2449 Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.125610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.098132 restraints weight = 5179.080| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.75 r_work: 0.2923 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4580 Z= 0.187 Angle : 0.498 8.586 6248 Z= 0.254 Chirality : 0.039 0.144 696 Planarity : 0.004 0.028 759 Dihedral : 5.194 34.905 608 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.36 % Allowed : 19.74 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.37), residues: 549 helix: 1.61 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.39 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.496 Fit side-chains REVERT: A 261 LYS cc_start: 0.3035 (OUTLIER) cc_final: 0.2459 (pttt) REVERT: A 271 TYR cc_start: 0.8296 (m-80) cc_final: 0.7960 (m-80) REVERT: A 376 ILE cc_start: 0.7242 (mp) cc_final: 0.6939 (mp) REVERT: A 399 SER cc_start: 0.8397 (t) cc_final: 0.8136 (m) REVERT: A 420 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8238 (m) REVERT: A 434 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8482 (m-30) REVERT: A 459 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.7111 (t80) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 0.5521 time to fit residues: 34.6374 Evaluate side-chains 55 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.0030 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.133511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.107186 restraints weight = 5081.603| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.73 r_work: 0.2938 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4580 Z= 0.174 Angle : 0.494 8.450 6248 Z= 0.252 Chirality : 0.039 0.142 696 Planarity : 0.004 0.028 759 Dihedral : 5.154 35.187 608 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.58 % Allowed : 19.96 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.37), residues: 549 helix: 1.65 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.38 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 370 PHE 0.010 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.789 Fit side-chains REVERT: A 271 TYR cc_start: 0.8298 (m-80) cc_final: 0.7908 (m-80) REVERT: A 304 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 365 LEU cc_start: 0.6770 (pp) cc_final: 0.6564 (mt) REVERT: A 376 ILE cc_start: 0.7459 (mp) cc_final: 0.7175 (mp) REVERT: A 399 SER cc_start: 0.8369 (t) cc_final: 0.8128 (m) REVERT: A 420 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8269 (m) REVERT: A 434 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8440 (m-30) REVERT: A 459 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.7129 (t80) REVERT: A 590 TYR cc_start: 0.8153 (m-80) cc_final: 0.7921 (m-80) outliers start: 12 outliers final: 5 residues processed: 61 average time/residue: 0.9388 time to fit residues: 62.9420 Evaluate side-chains 58 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.128536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.101854 restraints weight = 5118.334| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.74 r_work: 0.2919 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4580 Z= 0.192 Angle : 0.504 8.597 6248 Z= 0.257 Chirality : 0.040 0.140 696 Planarity : 0.004 0.028 759 Dihedral : 5.142 34.688 608 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.93 % Allowed : 20.39 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.37), residues: 549 helix: 1.62 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.41 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.018 0.001 TYR A 84 ARG 0.001 0.000 ARG A 341 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3113.24 seconds wall clock time: 56 minutes 42.65 seconds (3402.65 seconds total)