Starting phenix.real_space_refine on Fri Aug 22 15:57:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tr9_41574/08_2025/8tr9_41574.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tr9_41574/08_2025/8tr9_41574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tr9_41574/08_2025/8tr9_41574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tr9_41574/08_2025/8tr9_41574.map" model { file = "/net/cci-nas-00/data/ceres_data/8tr9_41574/08_2025/8tr9_41574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tr9_41574/08_2025/8tr9_41574.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.004 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 P 2 5.49 5 S 30 5.16 5 C 3431 2.51 5 N 937 2.21 5 O 1042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5442 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5414 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 32, 'TRANS': 651} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.78, per 1000 atoms: 0.33 Number of scatterers: 5442 At special positions: 0 Unit cell: (55.836, 78.067, 123.563, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 2 15.00 O 1042 8.00 N 937 7.00 C 3431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 239.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1268 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 19.0% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 244 through 248 removed outlier: 4.346A pdb=" N ASP A 247 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.767A pdb=" N ILE A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 292 Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 389 through 399 removed outlier: 3.753A pdb=" N VAL A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 Processing helix chain 'A' and resid 547 through 552 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 11 removed outlier: 4.300A pdb=" N ARG A 9 " --> pdb=" O HIS A 44 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP A 94 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN A 103 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 92 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR A 105 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA A 90 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 34 removed outlier: 4.462A pdb=" N LEU A 31 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 120 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 34 removed outlier: 4.462A pdb=" N LEU A 31 " --> pdb=" O HIS A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 239 Processing sheet with id=AA6, first strand: chain 'A' and resid 374 through 375 removed outlier: 3.514A pdb=" N VAL A 374 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN A 333 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL A 297 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS A 429 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 317 removed outlier: 7.942A pdb=" N VAL A 401 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN A 417 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP A 403 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR A 575 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 577 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU A 560 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 566 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR A 503 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 532 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N CYS A 505 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A 530 " --> pdb=" O CYS A 505 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 507 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR A 528 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 509 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR A 526 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA A 511 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A 513 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 474 through 478 Processing sheet with id=AA9, first strand: chain 'A' and resid 590 through 594 removed outlier: 3.652A pdb=" N VAL A 604 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 634 through 637 Processing sheet with id=AB2, first strand: chain 'A' and resid 660 through 663 removed outlier: 4.139A pdb=" N GLY A 660 " --> pdb=" O ILE A 684 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.72 Time building geometry restraints manager: 0.67 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: 1823 1.34 - 1.46: 1140 1.46 - 1.58: 2556 1.58 - 1.69: 3 1.69 - 1.81: 40 Bond restraints: 5562 Sorted by residual: bond pdb=" C5 GDP A 701 " pdb=" C4 GDP A 701 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" CA GLY A 170 " pdb=" C GLY A 170 " ideal model delta sigma weight residual 1.523 1.513 0.010 1.19e-02 7.06e+03 7.68e-01 bond pdb=" C PHE A 77 " pdb=" N PRO A 78 " ideal model delta sigma weight residual 1.326 1.338 -0.012 1.44e-02 4.82e+03 7.16e-01 bond pdb=" CA GLN A 234 " pdb=" CB GLN A 234 " ideal model delta sigma weight residual 1.526 1.539 -0.013 1.68e-02 3.54e+03 6.30e-01 bond pdb=" CG1 ILE A 495 " pdb=" CD1 ILE A 495 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.18e-01 ... (remaining 5557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 7422 1.73 - 3.46: 114 3.46 - 5.18: 13 5.18 - 6.91: 6 6.91 - 8.64: 1 Bond angle restraints: 7556 Sorted by residual: angle pdb=" C ASN A 49 " pdb=" CA ASN A 49 " pdb=" CB ASN A 49 " ideal model delta sigma weight residual 110.42 116.86 -6.44 1.99e+00 2.53e-01 1.05e+01 angle pdb=" N ARG A 48 " pdb=" CA ARG A 48 " pdb=" C ARG A 48 " ideal model delta sigma weight residual 113.28 109.65 3.63 1.22e+00 6.72e-01 8.83e+00 angle pdb=" CB MET A 483 " pdb=" CG MET A 483 " pdb=" SD MET A 483 " ideal model delta sigma weight residual 112.70 121.34 -8.64 3.00e+00 1.11e-01 8.29e+00 angle pdb=" CB LYS A 674 " pdb=" CG LYS A 674 " pdb=" CD LYS A 674 " ideal model delta sigma weight residual 111.30 116.50 -5.20 2.30e+00 1.89e-01 5.11e+00 angle pdb=" CA GLN A 234 " pdb=" CB GLN A 234 " pdb=" CG GLN A 234 " ideal model delta sigma weight residual 114.10 117.98 -3.88 2.00e+00 2.50e-01 3.77e+00 ... (remaining 7551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 2926 15.50 - 31.00: 314 31.00 - 46.50: 74 46.50 - 62.00: 11 62.00 - 77.50: 4 Dihedral angle restraints: 3329 sinusoidal: 1355 harmonic: 1974 Sorted by residual: dihedral pdb=" CA LEU A 507 " pdb=" C LEU A 507 " pdb=" N LEU A 508 " pdb=" CA LEU A 508 " ideal model delta harmonic sigma weight residual -180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LYS A 273 " pdb=" C LYS A 273 " pdb=" N TYR A 274 " pdb=" CA TYR A 274 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ALA A 474 " pdb=" C ALA A 474 " pdb=" N MET A 475 " pdb=" CA MET A 475 " ideal model delta harmonic sigma weight residual -180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 3326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 580 0.036 - 0.072: 167 0.072 - 0.108: 59 0.108 - 0.144: 24 0.144 - 0.180: 1 Chirality restraints: 831 Sorted by residual: chirality pdb=" CA ILE A 495 " pdb=" N ILE A 495 " pdb=" C ILE A 495 " pdb=" CB ILE A 495 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA ILE A 167 " pdb=" N ILE A 167 " pdb=" C ILE A 167 " pdb=" CB ILE A 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 589 " pdb=" N ILE A 589 " pdb=" C ILE A 589 " pdb=" CB ILE A 589 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 828 not shown) Planarity restraints: 984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 344 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO A 345 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 110 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 111 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 37 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 38 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.016 5.00e-02 4.00e+02 ... (remaining 981 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 766 2.76 - 3.29: 5088 3.29 - 3.83: 9027 3.83 - 4.36: 10792 4.36 - 4.90: 18801 Nonbonded interactions: 44474 Sorted by model distance: nonbonded pdb=" OE2 GLU A 606 " pdb=" NZ LYS A 649 " model vdw 2.224 3.120 nonbonded pdb=" OG SER A 250 " pdb=" OE1 GLU A 557 " model vdw 2.234 3.040 nonbonded pdb=" OG SER A 365 " pdb=" OE2 GLU A 366 " model vdw 2.265 3.040 nonbonded pdb=" O PRO A 111 " pdb=" OH TYR A 115 " model vdw 2.278 3.040 nonbonded pdb=" NZ LYS A 364 " pdb=" O CYS A 370 " model vdw 2.315 3.120 ... (remaining 44469 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: 10.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.220 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 0.002 0.031 5562 Z= 0.113 Angle : 0.542 8.638 7556 Z= 0.279 Chirality : 0.043 0.180 831 Planarity : 0.003 0.060 984 Dihedral : 13.533 77.501 2061 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.34), residues: 682 helix: 1.57 (0.51), residues: 111 sheet: -0.65 (0.34), residues: 252 loop : -0.51 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.011 0.001 TYR A 168 PHE 0.010 0.001 PHE A 39 TRP 0.011 0.001 TRP A 241 HIS 0.003 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 5562) covalent geometry : angle 0.54222 ( 7556) hydrogen bonds : bond 0.14157 ( 202) hydrogen bonds : angle 7.36426 ( 576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.189 Fit side-chains REVERT: A 94 ASP cc_start: 0.8283 (t0) cc_final: 0.8044 (t0) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0747 time to fit residues: 3.6896 Evaluate side-chains 26 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 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 = 0.3470 r_free = 0.3470 target = 0.089252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.070974 restraints weight = 11350.363| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.35 r_work: 0.2971 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 5562 Z= 0.239 Angle : 0.597 9.801 7556 Z= 0.301 Chirality : 0.046 0.165 831 Planarity : 0.003 0.039 984 Dihedral : 4.797 28.027 756 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.17 % Allowed : 4.87 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.34), residues: 682 helix: 1.32 (0.49), residues: 119 sheet: -0.82 (0.33), residues: 253 loop : -0.41 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 156 TYR 0.019 0.001 TYR A 551 PHE 0.014 0.001 PHE A 392 TRP 0.006 0.001 TRP A 241 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 5562) covalent geometry : angle 0.59680 ( 7556) hydrogen bonds : bond 0.03357 ( 202) hydrogen bonds : angle 6.28011 ( 576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.197 Fit side-chains REVERT: A 94 ASP cc_start: 0.8541 (t0) cc_final: 0.8146 (t0) REVERT: A 400 ASP cc_start: 0.8807 (t0) cc_final: 0.8587 (t0) outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.0794 time to fit residues: 3.5141 Evaluate side-chains 30 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.4980 chunk 5 optimal weight: 0.0050 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.092095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.074049 restraints weight = 11296.845| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.37 r_work: 0.3032 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5562 Z= 0.109 Angle : 0.512 8.185 7556 Z= 0.257 Chirality : 0.043 0.139 831 Planarity : 0.003 0.035 984 Dihedral : 4.511 27.050 756 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.34 % Allowed : 7.90 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.34), residues: 682 helix: 1.39 (0.49), residues: 120 sheet: -0.73 (0.34), residues: 249 loop : -0.36 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.017 0.001 TYR A 551 PHE 0.010 0.001 PHE A 39 TRP 0.008 0.001 TRP A 241 HIS 0.005 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5562) covalent geometry : angle 0.51220 ( 7556) hydrogen bonds : bond 0.02776 ( 202) hydrogen bonds : angle 5.90267 ( 576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.8550 (t0) cc_final: 0.8115 (t0) REVERT: A 227 MET cc_start: 0.9415 (mmm) cc_final: 0.8973 (tpt) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.0826 time to fit residues: 4.0258 Evaluate side-chains 30 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 0.0270 chunk 25 optimal weight: 0.5980 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 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 = 0.3490 r_free = 0.3490 target = 0.090163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.072628 restraints weight = 11394.532| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.27 r_work: 0.2980 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5562 Z= 0.186 Angle : 0.534 6.419 7556 Z= 0.270 Chirality : 0.044 0.167 831 Planarity : 0.003 0.032 984 Dihedral : 4.702 27.666 756 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.84 % Allowed : 9.58 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.33), residues: 682 helix: 1.39 (0.49), residues: 119 sheet: -0.82 (0.33), residues: 255 loop : -0.41 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.016 0.001 TYR A 551 PHE 0.012 0.001 PHE A 59 TRP 0.009 0.001 TRP A 278 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 5562) covalent geometry : angle 0.53402 ( 7556) hydrogen bonds : bond 0.02914 ( 202) hydrogen bonds : angle 5.86652 ( 576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.8570 (t0) cc_final: 0.8113 (t0) REVERT: A 227 MET cc_start: 0.9413 (mmm) cc_final: 0.8926 (tpt) REVERT: A 400 ASP cc_start: 0.8762 (t0) cc_final: 0.8560 (t0) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.0744 time to fit residues: 3.8893 Evaluate side-chains 33 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 3 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 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 = 0.3518 r_free = 0.3518 target = 0.092188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.074132 restraints weight = 11501.370| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.40 r_work: 0.3046 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5562 Z= 0.106 Angle : 0.502 8.363 7556 Z= 0.250 Chirality : 0.043 0.184 831 Planarity : 0.003 0.032 984 Dihedral : 4.474 28.937 756 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.01 % Allowed : 9.92 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.34), residues: 682 helix: 1.46 (0.49), residues: 120 sheet: -0.71 (0.33), residues: 255 loop : -0.31 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.016 0.001 TYR A 551 PHE 0.010 0.001 PHE A 59 TRP 0.008 0.001 TRP A 337 HIS 0.003 0.000 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 5562) covalent geometry : angle 0.50189 ( 7556) hydrogen bonds : bond 0.02581 ( 202) hydrogen bonds : angle 5.55238 ( 576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.8553 (t0) cc_final: 0.8082 (t0) REVERT: A 227 MET cc_start: 0.9419 (mmm) cc_final: 0.8918 (tpt) outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 0.0650 time to fit residues: 3.6168 Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.088544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.070313 restraints weight = 11499.749| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.32 r_work: 0.2972 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5562 Z= 0.212 Angle : 0.552 8.204 7556 Z= 0.277 Chirality : 0.044 0.195 831 Planarity : 0.003 0.032 984 Dihedral : 4.822 28.985 756 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.84 % Allowed : 11.26 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.34), residues: 682 helix: 1.39 (0.49), residues: 119 sheet: -0.79 (0.33), residues: 255 loop : -0.37 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.016 0.001 TYR A 388 PHE 0.012 0.001 PHE A 59 TRP 0.007 0.001 TRP A 278 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 5562) covalent geometry : angle 0.55243 ( 7556) hydrogen bonds : bond 0.02938 ( 202) hydrogen bonds : angle 5.73893 ( 576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.285 Fit side-chains REVERT: A 94 ASP cc_start: 0.8599 (t0) cc_final: 0.8128 (t0) REVERT: A 227 MET cc_start: 0.9417 (mmm) cc_final: 0.8893 (tpt) outliers start: 5 outliers final: 4 residues processed: 35 average time/residue: 0.0788 time to fit residues: 3.8440 Evaluate side-chains 32 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 59 optimal weight: 0.0020 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 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 = 0.3491 r_free = 0.3491 target = 0.090490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.072252 restraints weight = 11469.500| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.38 r_work: 0.3004 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5562 Z= 0.132 Angle : 0.524 8.058 7556 Z= 0.261 Chirality : 0.043 0.185 831 Planarity : 0.003 0.037 984 Dihedral : 4.675 29.095 756 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.67 % Allowed : 11.26 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.34), residues: 682 helix: 1.46 (0.49), residues: 119 sheet: -0.75 (0.32), residues: 255 loop : -0.32 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.016 0.001 TYR A 551 PHE 0.012 0.001 PHE A 59 TRP 0.007 0.001 TRP A 337 HIS 0.003 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5562) covalent geometry : angle 0.52352 ( 7556) hydrogen bonds : bond 0.02666 ( 202) hydrogen bonds : angle 5.57636 ( 576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.216 Fit side-chains REVERT: A 94 ASP cc_start: 0.8587 (t0) cc_final: 0.8106 (t0) REVERT: A 227 MET cc_start: 0.9423 (mmm) cc_final: 0.8892 (tpt) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.0774 time to fit residues: 3.7966 Evaluate side-chains 35 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 53 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.090486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072496 restraints weight = 11391.584| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.34 r_work: 0.3012 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5562 Z= 0.133 Angle : 0.512 7.958 7556 Z= 0.256 Chirality : 0.043 0.179 831 Planarity : 0.003 0.036 984 Dihedral : 4.578 30.076 756 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.01 % Allowed : 11.93 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.34), residues: 682 helix: 1.50 (0.49), residues: 119 sheet: -0.72 (0.32), residues: 255 loop : -0.32 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.015 0.001 TYR A 551 PHE 0.011 0.001 PHE A 59 TRP 0.006 0.001 TRP A 337 HIS 0.003 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5562) covalent geometry : angle 0.51211 ( 7556) hydrogen bonds : bond 0.02602 ( 202) hydrogen bonds : angle 5.47179 ( 576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.238 Fit side-chains REVERT: A 94 ASP cc_start: 0.8589 (t0) cc_final: 0.8187 (t0) REVERT: A 227 MET cc_start: 0.9423 (mmm) cc_final: 0.8886 (tpt) REVERT: A 485 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.7882 (tmm) outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 0.0788 time to fit residues: 4.5111 Evaluate side-chains 37 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 3 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.090323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.072194 restraints weight = 11394.432| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.35 r_work: 0.3005 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5562 Z= 0.149 Angle : 0.527 8.257 7556 Z= 0.263 Chirality : 0.043 0.176 831 Planarity : 0.003 0.036 984 Dihedral : 4.626 29.833 756 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.84 % Allowed : 12.27 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.33), residues: 682 helix: 1.49 (0.49), residues: 119 sheet: -0.72 (0.32), residues: 255 loop : -0.34 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.015 0.001 TYR A 551 PHE 0.012 0.001 PHE A 59 TRP 0.006 0.001 TRP A 337 HIS 0.002 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5562) covalent geometry : angle 0.52740 ( 7556) hydrogen bonds : bond 0.02646 ( 202) hydrogen bonds : angle 5.48401 ( 576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.231 Fit side-chains REVERT: A 94 ASP cc_start: 0.8596 (t0) cc_final: 0.8194 (t0) REVERT: A 227 MET cc_start: 0.9406 (mmm) cc_final: 0.8894 (tpt) REVERT: A 485 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.7883 (tmm) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 0.0816 time to fit residues: 4.0805 Evaluate side-chains 37 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 0.0470 chunk 32 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 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 = 0.3491 r_free = 0.3491 target = 0.090507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072524 restraints weight = 11440.904| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.34 r_work: 0.3016 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5562 Z= 0.135 Angle : 0.520 8.731 7556 Z= 0.259 Chirality : 0.043 0.175 831 Planarity : 0.003 0.036 984 Dihedral : 4.613 30.640 756 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.67 % Allowed : 12.27 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.33), residues: 682 helix: 1.50 (0.49), residues: 119 sheet: -0.70 (0.32), residues: 255 loop : -0.33 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.015 0.001 TYR A 551 PHE 0.012 0.001 PHE A 59 TRP 0.007 0.001 TRP A 337 HIS 0.002 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 5562) covalent geometry : angle 0.51982 ( 7556) hydrogen bonds : bond 0.02609 ( 202) hydrogen bonds : angle 5.44576 ( 576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.244 Fit side-chains REVERT: A 94 ASP cc_start: 0.8588 (t0) cc_final: 0.8182 (t0) REVERT: A 227 MET cc_start: 0.9418 (mmm) cc_final: 0.8904 (tpt) REVERT: A 485 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.7881 (tmm) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.0841 time to fit residues: 4.0762 Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 0.0370 chunk 32 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 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 = 0.3515 r_free = 0.3515 target = 0.091910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.074105 restraints weight = 11349.380| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.28 r_work: 0.3050 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5562 Z= 0.108 Angle : 0.509 8.577 7556 Z= 0.253 Chirality : 0.042 0.172 831 Planarity : 0.003 0.036 984 Dihedral : 4.467 31.671 756 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.01 % Allowed : 12.27 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.34), residues: 682 helix: 1.53 (0.49), residues: 120 sheet: -0.58 (0.33), residues: 250 loop : -0.34 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.015 0.001 TYR A 551 PHE 0.011 0.001 PHE A 59 TRP 0.007 0.001 TRP A 337 HIS 0.002 0.000 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 5562) covalent geometry : angle 0.50857 ( 7556) hydrogen bonds : bond 0.02480 ( 202) hydrogen bonds : angle 5.33223 ( 576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1619.38 seconds wall clock time: 28 minutes 33.10 seconds (1713.10 seconds total)