Starting phenix.real_space_refine on Wed Mar 5 22:33:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j75_36027/03_2025/8j75_36027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j75_36027/03_2025/8j75_36027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j75_36027/03_2025/8j75_36027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j75_36027/03_2025/8j75_36027.map" model { file = "/net/cci-nas-00/data/ceres_data/8j75_36027/03_2025/8j75_36027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j75_36027/03_2025/8j75_36027.cif" } resolution = 3.6 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= 0.004 sd= 0.074 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: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2625 2.51 5 N 605 2.21 5 O 707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 3956 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3887 Classifications: {'peptide': 515} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 22, 'TRANS': 492} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'HC6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.13, per 1000 atoms: 0.79 Number of scatterers: 3956 At special positions: 0 Unit cell: (87.74, 73.8, 86.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 707 8.00 N 605 7.00 C 2625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 301 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 498.7 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 1 sheets defined 76.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 4 through 30 removed outlier: 3.934A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.559A pdb=" N GLY A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 81 through 84 Processing helix chain 'A' and resid 85 through 102 removed outlier: 4.702A pdb=" N ILE A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.712A pdb=" N LYS A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 110 " --> pdb=" O MET A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 123 through 157 removed outlier: 3.555A pdb=" N LEU A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 160 through 179 removed outlier: 4.023A pdb=" N SER A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 208 removed outlier: 3.675A pdb=" N VAL A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 266 through 297 removed outlier: 4.023A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.620A pdb=" N ILE A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 368 removed outlier: 3.973A pdb=" N PHE A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 398 removed outlier: 3.538A pdb=" N VAL A 378 " --> pdb=" O ASP A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 427 removed outlier: 4.641A pdb=" N PHE A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 450 removed outlier: 3.596A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 467 273 hydrogen bonds defined for protein. 804 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: 1.03 Time building geometry restraints manager: 1.34 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: 1132 1.34 - 1.46: 833 1.46 - 1.58: 2066 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 4065 Sorted by residual: bond pdb=" C TYR A 462 " pdb=" N PRO A 463 " ideal model delta sigma weight residual 1.332 1.366 -0.035 1.30e-02 5.92e+03 7.06e+00 bond pdb=" N VAL A 237 " pdb=" CA VAL A 237 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.12e+00 bond pdb=" CA TYR A 462 " pdb=" CB TYR A 462 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.57e-02 4.06e+03 6.11e+00 bond pdb=" N TYR A 67 " pdb=" CA TYR A 67 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.31e+00 bond pdb=" N GLU A 236 " pdb=" CA GLU A 236 " ideal model delta sigma weight residual 1.462 1.487 -0.024 1.20e-02 6.94e+03 4.13e+00 ... (remaining 4060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 5368 1.70 - 3.40: 147 3.40 - 5.10: 32 5.10 - 6.81: 11 6.81 - 8.51: 4 Bond angle restraints: 5562 Sorted by residual: angle pdb=" N PRO A 508 " pdb=" CA PRO A 508 " pdb=" C PRO A 508 " ideal model delta sigma weight residual 110.70 114.66 -3.96 1.22e+00 6.72e-01 1.05e+01 angle pdb=" CB MET A 139 " pdb=" CG MET A 139 " pdb=" SD MET A 139 " ideal model delta sigma weight residual 112.70 121.21 -8.51 3.00e+00 1.11e-01 8.04e+00 angle pdb=" N GLY A 79 " pdb=" CA GLY A 79 " pdb=" C GLY A 79 " ideal model delta sigma weight residual 114.67 110.71 3.96 1.41e+00 5.03e-01 7.90e+00 angle pdb=" N TYR A 462 " pdb=" CA TYR A 462 " pdb=" C TYR A 462 " ideal model delta sigma weight residual 109.48 113.24 -3.76 1.44e+00 4.82e-01 6.81e+00 angle pdb=" N VAL A 220 " pdb=" CA VAL A 220 " pdb=" C VAL A 220 " ideal model delta sigma weight residual 109.34 114.63 -5.29 2.08e+00 2.31e-01 6.48e+00 ... (remaining 5557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.99: 2188 25.99 - 51.98: 136 51.98 - 77.97: 17 77.97 - 103.96: 21 103.96 - 129.95: 4 Dihedral angle restraints: 2366 sinusoidal: 887 harmonic: 1479 Sorted by residual: dihedral pdb=" CAS HC6 A 601 " pdb=" CAU HC6 A 601 " pdb=" OAT HC6 A 601 " pdb=" CAV HC6 A 601 " ideal model delta sinusoidal sigma weight residual -59.78 70.17 -129.95 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" CAB HC6 A 601 " pdb=" CAF HC6 A 601 " pdb=" OAE HC6 A 601 " pdb=" CAD HC6 A 601 " ideal model delta sinusoidal sigma weight residual 59.04 -70.03 129.07 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.99 108.72 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 2363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 523 0.055 - 0.109: 119 0.109 - 0.164: 7 0.164 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 652 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA VAL A 237 " pdb=" N VAL A 237 " pdb=" C VAL A 237 " pdb=" CB VAL A 237 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TYR A 238 " pdb=" N TYR A 238 " pdb=" C TYR A 238 " pdb=" CB TYR A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 649 not shown) Planarity restraints: 675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAD HC6 A 601 " -0.030 2.00e-02 2.50e+03 1.76e-02 6.18e+00 pdb=" CAG HC6 A 601 " 0.009 2.00e-02 2.50e+03 pdb=" CAH HC6 A 601 " 0.010 2.00e-02 2.50e+03 pdb=" CAI HC6 A 601 " 0.010 2.00e-02 2.50e+03 pdb=" CAJ HC6 A 601 " 0.009 2.00e-02 2.50e+03 pdb=" CAK HC6 A 601 " 0.010 2.00e-02 2.50e+03 pdb=" CAL HC6 A 601 " 0.011 2.00e-02 2.50e+03 pdb=" CAM HC6 A 601 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 451 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 452 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 461 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C PHE A 461 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE A 461 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 462 " -0.010 2.00e-02 2.50e+03 ... (remaining 672 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1037 2.79 - 3.32: 3999 3.32 - 3.84: 6572 3.84 - 4.37: 7148 4.37 - 4.90: 12449 Nonbonded interactions: 31205 Sorted by model distance: nonbonded pdb=" O3 NAG B 2 " pdb=" O2 BMA B 3 " model vdw 2.261 3.040 nonbonded pdb=" O ALA A 390 " pdb=" OG1 THR A 393 " model vdw 2.263 3.040 nonbonded pdb=" O ALA A 213 " pdb=" OG SER A 297 " model vdw 2.312 3.040 nonbonded pdb=" NH2 ARG A 47 " pdb=" O TYR A 111 " model vdw 2.313 3.120 nonbonded pdb=" N SER A 34 " pdb=" OE1 GLU A 37 " model vdw 2.354 3.120 ... (remaining 31200 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.130 Find NCS groups from input model: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 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 : 0.004 0.039 4065 Z= 0.248 Angle : 0.721 8.507 5562 Z= 0.371 Chirality : 0.045 0.274 652 Planarity : 0.005 0.046 674 Dihedral : 20.252 129.948 1430 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.99 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 26.97 % Favored : 73.03 % 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: 0.40 (0.40), residues: 513 helix: 1.45 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -2.53 (0.50), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 228 HIS 0.001 0.000 HIS A 4 PHE 0.014 0.001 PHE A 244 TYR 0.017 0.001 TYR A 175 ARG 0.007 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.512 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1518 time to fit residues: 16.9268 Evaluate side-chains 84 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** 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 = 0.4240 r_free = 0.4240 target = 0.197816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.183966 restraints weight = 6232.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.187310 restraints weight = 3563.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.189587 restraints weight = 2298.218| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4065 Z= 0.204 Angle : 0.680 7.951 5562 Z= 0.332 Chirality : 0.044 0.293 652 Planarity : 0.004 0.033 674 Dihedral : 14.843 89.963 650 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.99 % Favored : 91.81 % Rotamer: Outliers : 5.60 % Allowed : 24.43 % Favored : 69.97 % 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: 0.66 (0.40), residues: 513 helix: 1.63 (0.29), residues: 354 sheet: None (None), residues: 0 loop : -2.46 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 24 HIS 0.001 0.000 HIS A 209 PHE 0.013 0.001 PHE A 368 TYR 0.013 0.001 TYR A 175 ARG 0.005 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.389 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 100 average time/residue: 0.1444 time to fit residues: 18.4170 Evaluate side-chains 94 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 490 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 0.0060 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** 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 = 0.4261 r_free = 0.4261 target = 0.200318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.186397 restraints weight = 6238.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.189899 restraints weight = 3535.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.192133 restraints weight = 2256.594| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4065 Z= 0.168 Angle : 0.602 7.730 5562 Z= 0.303 Chirality : 0.041 0.162 652 Planarity : 0.004 0.034 674 Dihedral : 11.406 72.092 650 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 4.83 % Allowed : 27.99 % Favored : 67.18 % 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: 0.82 (0.40), residues: 513 helix: 1.72 (0.29), residues: 354 sheet: None (None), residues: 0 loop : -2.29 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 24 HIS 0.001 0.000 HIS A 209 PHE 0.010 0.001 PHE A 244 TYR 0.013 0.001 TYR A 111 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.314 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 94 average time/residue: 0.1409 time to fit residues: 16.7999 Evaluate side-chains 89 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 428 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 37 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** 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 = 0.4255 r_free = 0.4255 target = 0.199095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.185243 restraints weight = 6217.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.188683 restraints weight = 3523.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.190879 restraints weight = 2242.539| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4065 Z= 0.171 Angle : 0.597 7.748 5562 Z= 0.301 Chirality : 0.041 0.146 652 Planarity : 0.004 0.034 674 Dihedral : 9.519 59.732 650 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.60 % Favored : 92.20 % Rotamer: Outliers : 6.11 % Allowed : 27.74 % Favored : 66.16 % 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: 0.87 (0.41), residues: 513 helix: 1.74 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.27 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 24 HIS 0.001 0.000 HIS A 209 PHE 0.009 0.001 PHE A 244 TYR 0.009 0.001 TYR A 111 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.407 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 97 average time/residue: 0.1457 time to fit residues: 18.2414 Evaluate side-chains 98 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 490 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 22 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** 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 = 0.4259 r_free = 0.4259 target = 0.200318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.185864 restraints weight = 6438.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.189462 restraints weight = 3624.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.191845 restraints weight = 2305.606| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4065 Z= 0.195 Angle : 0.604 7.774 5562 Z= 0.301 Chirality : 0.040 0.151 652 Planarity : 0.004 0.035 674 Dihedral : 7.845 42.683 650 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 6.36 % Allowed : 28.50 % Favored : 65.14 % 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: 0.86 (0.40), residues: 513 helix: 1.73 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.24 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 24 HIS 0.001 0.000 HIS A 209 PHE 0.011 0.001 PHE A 140 TYR 0.012 0.001 TYR A 111 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.386 Fit side-chains REVERT: A 4 HIS cc_start: 0.5487 (OUTLIER) cc_final: 0.4231 (m-70) outliers start: 25 outliers final: 20 residues processed: 101 average time/residue: 0.1494 time to fit residues: 19.3517 Evaluate side-chains 106 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 490 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 0.0770 chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** 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 = 0.4244 r_free = 0.4244 target = 0.198271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.184139 restraints weight = 6231.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.187600 restraints weight = 3543.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.189845 restraints weight = 2284.399| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4065 Z= 0.195 Angle : 0.626 8.426 5562 Z= 0.310 Chirality : 0.040 0.139 652 Planarity : 0.004 0.035 674 Dihedral : 6.677 38.394 650 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.80 % Favored : 92.01 % Rotamer: Outliers : 6.36 % Allowed : 29.01 % Favored : 64.63 % 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: 0.86 (0.40), residues: 513 helix: 1.73 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.26 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 240 HIS 0.001 0.000 HIS A 209 PHE 0.009 0.001 PHE A 140 TYR 0.012 0.001 TYR A 175 ARG 0.005 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.413 Fit side-chains REVERT: A 4 HIS cc_start: 0.5418 (OUTLIER) cc_final: 0.4231 (m-70) outliers start: 25 outliers final: 20 residues processed: 99 average time/residue: 0.1462 time to fit residues: 18.3866 Evaluate side-chains 103 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 490 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** 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 = 0.4254 r_free = 0.4254 target = 0.199736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.185333 restraints weight = 6295.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.188791 restraints weight = 3607.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.191111 restraints weight = 2321.900| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4065 Z= 0.197 Angle : 0.631 8.069 5562 Z= 0.312 Chirality : 0.041 0.158 652 Planarity : 0.004 0.038 674 Dihedral : 6.258 38.764 650 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 6.11 % Allowed : 29.77 % Favored : 64.12 % 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: 0.83 (0.40), residues: 513 helix: 1.70 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.27 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 240 HIS 0.001 0.000 HIS A 209 PHE 0.010 0.001 PHE A 140 TYR 0.015 0.001 TYR A 111 ARG 0.006 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.375 Fit side-chains REVERT: A 4 HIS cc_start: 0.5477 (OUTLIER) cc_final: 0.4289 (m-70) outliers start: 24 outliers final: 22 residues processed: 101 average time/residue: 0.1438 time to fit residues: 18.3958 Evaluate side-chains 104 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 490 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 0.0670 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** 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 = 0.4253 r_free = 0.4253 target = 0.199652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.185525 restraints weight = 6235.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.188986 restraints weight = 3550.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.191265 restraints weight = 2278.684| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4065 Z= 0.199 Angle : 0.641 7.736 5562 Z= 0.318 Chirality : 0.041 0.182 652 Planarity : 0.004 0.041 674 Dihedral : 5.959 38.846 650 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.41 % Favored : 92.40 % Rotamer: Outliers : 6.36 % Allowed : 29.26 % Favored : 64.38 % 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: 0.82 (0.40), residues: 513 helix: 1.69 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.25 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 228 HIS 0.001 0.000 HIS A 209 PHE 0.010 0.001 PHE A 140 TYR 0.012 0.001 TYR A 175 ARG 0.006 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.411 Fit side-chains REVERT: A 4 HIS cc_start: 0.5537 (OUTLIER) cc_final: 0.4333 (m-70) REVERT: A 139 MET cc_start: 0.7177 (mmm) cc_final: 0.6938 (mmm) outliers start: 25 outliers final: 22 residues processed: 97 average time/residue: 0.1524 time to fit residues: 18.6266 Evaluate side-chains 102 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 490 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.0770 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** 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 = 0.4276 r_free = 0.4276 target = 0.202352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.187867 restraints weight = 6293.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.191369 restraints weight = 3547.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.193728 restraints weight = 2267.882| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4065 Z= 0.181 Angle : 0.631 7.820 5562 Z= 0.314 Chirality : 0.040 0.156 652 Planarity : 0.004 0.036 674 Dihedral : 5.613 37.575 650 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.98 % Rotamer: Outliers : 5.85 % Allowed : 30.28 % Favored : 63.87 % 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: 0.88 (0.40), residues: 513 helix: 1.73 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.23 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.001 0.000 HIS A 209 PHE 0.010 0.001 PHE A 140 TYR 0.018 0.001 TYR A 111 ARG 0.007 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.414 Fit side-chains REVERT: A 4 HIS cc_start: 0.5540 (OUTLIER) cc_final: 0.4349 (m-70) REVERT: A 320 LEU cc_start: 0.8882 (tp) cc_final: 0.8650 (mt) outliers start: 23 outliers final: 19 residues processed: 97 average time/residue: 0.1524 time to fit residues: 18.6369 Evaluate side-chains 101 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.0000 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** 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 = 0.4262 r_free = 0.4262 target = 0.200555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.186432 restraints weight = 6319.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.189954 restraints weight = 3563.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.192148 restraints weight = 2268.660| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4065 Z= 0.192 Angle : 0.652 8.211 5562 Z= 0.326 Chirality : 0.041 0.171 652 Planarity : 0.004 0.041 674 Dihedral : 5.525 37.473 650 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.80 % Favored : 92.01 % Rotamer: Outliers : 5.34 % Allowed : 30.03 % Favored : 64.63 % 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: 0.92 (0.41), residues: 513 helix: 1.68 (0.29), residues: 361 sheet: None (None), residues: 0 loop : -2.12 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 240 HIS 0.001 0.000 HIS A 209 PHE 0.009 0.001 PHE A 258 TYR 0.013 0.001 TYR A 175 ARG 0.007 0.001 ARG A 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.404 Fit side-chains REVERT: A 4 HIS cc_start: 0.5572 (OUTLIER) cc_final: 0.4375 (m-70) REVERT: A 139 MET cc_start: 0.7247 (mmm) cc_final: 0.6893 (mmm) REVERT: A 320 LEU cc_start: 0.8894 (tp) cc_final: 0.8665 (mt) outliers start: 21 outliers final: 17 residues processed: 96 average time/residue: 0.1508 time to fit residues: 18.2254 Evaluate side-chains 103 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** 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 = 0.4248 r_free = 0.4248 target = 0.198996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.185063 restraints weight = 6174.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.188440 restraints weight = 3498.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.190711 restraints weight = 2250.925| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4065 Z= 0.198 Angle : 0.657 7.712 5562 Z= 0.325 Chirality : 0.041 0.189 652 Planarity : 0.005 0.046 674 Dihedral : 5.613 38.824 650 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 4.83 % Allowed : 30.79 % Favored : 64.38 % 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: 0.91 (0.40), residues: 513 helix: 1.73 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.15 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 240 HIS 0.001 0.000 HIS A 209 PHE 0.011 0.001 PHE A 140 TYR 0.017 0.001 TYR A 175 ARG 0.007 0.001 ARG A 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1559.74 seconds wall clock time: 27 minutes 53.80 seconds (1673.80 seconds total)