Starting phenix.real_space_refine on Wed Jun 4 23:07:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfl_34722/06_2025/8hfl_34722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfl_34722/06_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_34722/06_2025/8hfl_34722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfl_34722/06_2025/8hfl_34722.map" model { file = "/net/cci-nas-00/data/ceres_data/8hfl_34722/06_2025/8hfl_34722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfl_34722/06_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-5710/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: 3.08, per 1000 atoms: 0.69 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: 1.07 Conformation dependent library (CDL) restraints added in 490.0 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: 0.42 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: 1.13 Time building geometry restraints manager: 1.25 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: 0.480 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.110 Find NCS groups from input model: 0.040 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.370 ------------------------------------------------------------------------------- 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 4581 Z= 0.136 Angle : 0.548 7.502 6250 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 Details of bonding type rmsd hydrogen bonds : bond 0.13950 ( 292) hydrogen bonds : angle 5.43652 ( 849) SS BOND : bond 0.00009 ( 1) SS BOND : angle 1.44771 ( 2) covalent geometry : bond 0.00287 ( 4580) covalent geometry : angle 0.54792 ( 6248) *********************** 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 : 0.435 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: 0.5486 time to fit residues: 30.6133 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 : 0.488 ------------------------------------------------------------------------------- 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 4581 Z= 0.132 Angle : 0.518 6.792 6250 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 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 292) hydrogen bonds : angle 4.69227 ( 849) SS BOND : bond 0.00115 ( 1) SS BOND : angle 1.64055 ( 2) covalent geometry : bond 0.00314 ( 4580) covalent geometry : angle 0.51706 ( 6248) *********************** 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 : 0.472 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: 0.5796 time to fit residues: 39.5681 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 : 0.474 ------------------------------------------------------------------------------- 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 4581 Z= 0.121 Angle : 0.500 6.573 6250 Z= 0.258 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 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 292) hydrogen bonds : angle 4.57761 ( 849) SS BOND : bond 0.00134 ( 1) SS BOND : angle 1.47327 ( 2) covalent geometry : bond 0.00282 ( 4580) covalent geometry : angle 0.49938 ( 6248) *********************** 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 : 0.445 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: 0.9017 time to fit residues: 55.6874 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 : 0.365 ------------------------------------------------------------------------------- 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 4581 Z= 0.126 Angle : 0.494 6.651 6250 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 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 292) hydrogen bonds : angle 4.56106 ( 849) SS BOND : bond 0.00306 ( 1) SS BOND : angle 1.83028 ( 2) covalent geometry : bond 0.00298 ( 4580) covalent geometry : angle 0.49346 ( 6248) *********************** 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 : 0.505 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: 0.7557 time to fit residues: 50.6235 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 : 0.478 ------------------------------------------------------------------------------- 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: 0.0030 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 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: 0.6792 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.124902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.097632 restraints weight = 5226.317| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.76 r_work: 0.2917 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4581 Z= 0.123 Angle : 0.485 6.536 6250 Z= 0.251 Chirality : 0.039 0.133 696 Planarity : 0.004 0.029 759 Dihedral : 5.260 35.223 608 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.65 % Allowed : 17.60 % 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: 1.48 (0.37), residues: 549 helix: 1.52 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.28 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 PHE 0.012 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 442 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 292) hydrogen bonds : angle 4.51706 ( 849) SS BOND : bond 0.00201 ( 1) SS BOND : angle 1.59764 ( 2) covalent geometry : bond 0.00290 ( 4580) covalent geometry : angle 0.48388 ( 6248) *********************** 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: 17 poor density : 50 time to evaluate : 0.590 Fit side-chains REVERT: A 261 LYS cc_start: 0.3376 (OUTLIER) cc_final: 0.3157 (pttp) REVERT: A 271 TYR cc_start: 0.8255 (m-80) cc_final: 0.7819 (m-80) REVERT: A 376 ILE cc_start: 0.7136 (mp) cc_final: 0.6799 (mp) REVERT: A 377 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: A 399 SER cc_start: 0.8251 (t) cc_final: 0.8007 (m) REVERT: A 421 MET cc_start: 0.7751 (mtp) cc_final: 0.7497 (mtm) REVERT: A 434 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8628 (m-30) REVERT: A 459 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.7152 (t80) REVERT: A 587 ARG cc_start: 0.8432 (mtt90) cc_final: 0.7944 (mmt90) outliers start: 17 outliers final: 6 residues processed: 63 average time/residue: 0.8735 time to fit residues: 58.9286 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 : 0.433 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.124548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.097533 restraints weight = 5123.362| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.73 r_work: 0.2917 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4581 Z= 0.145 Angle : 0.519 6.550 6250 Z= 0.268 Chirality : 0.040 0.132 696 Planarity : 0.004 0.031 759 Dihedral : 5.331 34.956 608 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.65 % Allowed : 18.45 % 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: 1.42 (0.37), residues: 549 helix: 1.49 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.34 (0.49), 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 0.013 0.001 PHE A 110 TYR 0.020 0.001 TYR A 84 ARG 0.002 0.000 ARG A 341 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 292) hydrogen bonds : angle 4.59804 ( 849) SS BOND : bond 0.00160 ( 1) SS BOND : angle 2.13348 ( 2) covalent geometry : bond 0.00354 ( 4580) covalent geometry : angle 0.51793 ( 6248) *********************** 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 64 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.470 Fit side-chains REVERT: A 261 LYS cc_start: 0.3366 (OUTLIER) cc_final: 0.3125 (pttp) REVERT: A 271 TYR cc_start: 0.8369 (m-80) cc_final: 0.7978 (m-80) REVERT: A 399 SER cc_start: 0.8456 (t) cc_final: 0.8190 (m) REVERT: A 434 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8651 (m-30) REVERT: A 606 ILE cc_start: 0.8215 (mm) cc_final: 0.7960 (mp) outliers start: 17 outliers final: 6 residues processed: 59 average time/residue: 0.6464 time to fit residues: 41.0390 Evaluate side-chains 55 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.125131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.098225 restraints weight = 5144.261| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.73 r_work: 0.2881 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4581 Z= 0.134 Angle : 0.509 6.471 6250 Z= 0.262 Chirality : 0.040 0.137 696 Planarity : 0.004 0.030 759 Dihedral : 5.311 34.882 608 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.79 % Allowed : 19.10 % Favored : 78.11 % 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: 1.43 (0.37), residues: 549 helix: 1.50 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.36 (0.49), 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 0.012 0.001 PHE A 110 TYR 0.019 0.001 TYR A 84 ARG 0.002 0.000 ARG A 341 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 292) hydrogen bonds : angle 4.57732 ( 849) SS BOND : bond 0.00059 ( 1) SS BOND : angle 1.97720 ( 2) covalent geometry : bond 0.00325 ( 4580) covalent geometry : angle 0.50808 ( 6248) *********************** 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 62 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.531 Fit side-chains REVERT: A 261 LYS cc_start: 0.3326 (OUTLIER) cc_final: 0.3074 (pttp) REVERT: A 271 TYR cc_start: 0.8354 (m-80) cc_final: 0.7970 (m-80) REVERT: A 376 ILE cc_start: 0.7210 (mp) cc_final: 0.6892 (mp) REVERT: A 399 SER cc_start: 0.8426 (t) cc_final: 0.8156 (m) REVERT: A 420 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8229 (m) REVERT: A 434 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8599 (m-30) REVERT: A 606 ILE cc_start: 0.8198 (mm) cc_final: 0.7997 (mp) outliers start: 13 outliers final: 6 residues processed: 58 average time/residue: 1.1092 time to fit residues: 68.2261 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 : 0.457 ------------------------------------------------------------------------------- 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: 0.6980 chunk 26 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.133553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107256 restraints weight = 5019.928| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.71 r_work: 0.2944 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4581 Z= 0.110 Angle : 0.486 6.486 6250 Z= 0.249 Chirality : 0.039 0.139 696 Planarity : 0.004 0.029 759 Dihedral : 5.224 35.974 608 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.79 % Allowed : 19.53 % 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: 1.51 (0.37), residues: 549 helix: 1.59 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.42 (0.49), residues: 157 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 362 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 292) hydrogen bonds : angle 4.46873 ( 849) SS BOND : bond 0.00097 ( 1) SS BOND : angle 1.59455 ( 2) covalent geometry : bond 0.00251 ( 4580) covalent geometry : angle 0.48541 ( 6248) *********************** 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 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.488 Fit side-chains REVERT: A 261 LYS cc_start: 0.3345 (OUTLIER) cc_final: 0.3102 (pttp) REVERT: A 271 TYR cc_start: 0.8299 (m-80) cc_final: 0.7926 (m-80) REVERT: A 376 ILE cc_start: 0.7250 (mp) cc_final: 0.6992 (mp) REVERT: A 399 SER cc_start: 0.8376 (t) cc_final: 0.8122 (m) REVERT: A 420 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8288 (m) REVERT: A 434 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8485 (m-30) REVERT: A 590 TYR cc_start: 0.8152 (m-80) cc_final: 0.7909 (m-80) REVERT: A 606 ILE cc_start: 0.8193 (mm) cc_final: 0.7984 (mp) outliers start: 13 outliers final: 5 residues processed: 61 average time/residue: 0.5448 time to fit residues: 36.2629 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 : 0.437 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.099236 restraints weight = 5158.108| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.74 r_work: 0.2915 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4581 Z= 0.127 Angle : 0.512 6.596 6250 Z= 0.262 Chirality : 0.040 0.139 696 Planarity : 0.004 0.029 759 Dihedral : 5.237 34.817 608 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.15 % Allowed : 19.74 % Favored : 78.11 % 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: 1.56 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -0.44 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 264 HIS 0.002 0.001 HIS A 280 PHE 0.011 0.001 PHE A 94 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 442 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 292) hydrogen bonds : angle 4.53398 ( 849) SS BOND : bond 0.00056 ( 1) SS BOND : angle 1.79021 ( 2) covalent geometry : bond 0.00302 ( 4580) covalent geometry : angle 0.51094 ( 6248) *********************** 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 62 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.465 Fit side-chains REVERT: A 261 LYS cc_start: 0.3018 (OUTLIER) cc_final: 0.2444 (pttt) REVERT: A 271 TYR cc_start: 0.8351 (m-80) cc_final: 0.7942 (m-80) REVERT: A 304 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7053 (mm-30) REVERT: A 368 MET cc_start: 0.8185 (mtm) cc_final: 0.7920 (mtm) REVERT: A 399 SER cc_start: 0.8426 (t) cc_final: 0.8153 (m) REVERT: A 420 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8198 (m) REVERT: A 434 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8511 (m-30) outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 0.5411 time to fit residues: 34.7958 Evaluate side-chains 59 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.0070 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.133973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107620 restraints weight = 5076.149| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.73 r_work: 0.2903 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 4581 Z= 0.109 Angle : 0.482 6.424 6250 Z= 0.248 Chirality : 0.039 0.141 696 Planarity : 0.004 0.028 759 Dihedral : 5.146 35.525 608 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.72 % Allowed : 20.39 % 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: 1.59 (0.37), residues: 549 helix: 1.65 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.37 (0.50), residues: 157 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 362 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 292) hydrogen bonds : angle 4.45504 ( 849) SS BOND : bond 0.00064 ( 1) SS BOND : angle 1.56183 ( 2) covalent geometry : bond 0.00248 ( 4580) covalent geometry : angle 0.48169 ( 6248) ********************** 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 61 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.440 Fit side-chains REVERT: A 271 TYR cc_start: 0.8241 (m-80) cc_final: 0.7834 (m-80) REVERT: A 304 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7035 (mm-30) REVERT: A 376 ILE cc_start: 0.7191 (mp) cc_final: 0.6930 (mp) REVERT: A 399 SER cc_start: 0.8352 (t) cc_final: 0.8103 (m) REVERT: A 420 SER cc_start: 0.8672 (OUTLIER) cc_final: 0.8253 (m) REVERT: A 434 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8455 (m-30) outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 0.5633 time to fit residues: 36.1271 Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.101135 restraints weight = 5121.421| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.75 r_work: 0.2875 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4581 Z= 0.127 Angle : 0.502 6.594 6250 Z= 0.259 Chirality : 0.040 0.141 696 Planarity : 0.004 0.029 759 Dihedral : 5.160 34.730 608 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.15 % Allowed : 20.39 % 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: 1.58 (0.37), residues: 549 helix: 1.63 (0.27), residues: 390 sheet: None (None), residues: 0 loop : -0.33 (0.50), residues: 159 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 0.020 0.001 TYR A 590 ARG 0.001 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 292) hydrogen bonds : angle 4.51462 ( 849) SS BOND : bond 0.00051 ( 1) SS BOND : angle 1.72807 ( 2) covalent geometry : bond 0.00301 ( 4580) covalent geometry : angle 0.50134 ( 6248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3178.73 seconds wall clock time: 56 minutes 57.34 seconds (3417.34 seconds total)