Starting phenix.real_space_refine on Thu Jul 2 15:24:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n3p_24143/07_2026/7n3p_24143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n3p_24143/07_2026/7n3p_24143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n3p_24143/07_2026/7n3p_24143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n3p_24143/07_2026/7n3p_24143.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7n3p_24143/07_2026/7n3p_24143.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n3p_24143/07_2026/7n3p_24143.cif" model { file = "/net/cci-nas-00/data/ceres_data/7n3p_24143/07_2026/7n3p_24143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n3p_24143/07_2026/7n3p_24143.cif" } resolution = 3.65 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= 0.004 sd= 0.108 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 259 5.49 5 S 12 5.16 5 C 4737 2.51 5 N 1634 2.21 5 O 2413 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9055 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3561 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 16, 'TRANS': 437} Chain breaks: 3 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 4883 Classifications: {'RNA': 229} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 14, 'rna3p_pur': 103, 'rna3p_pyr': 95} Link IDs: {'rna2p': 31, 'rna3p': 197} Chain breaks: 4 Chain: "C" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 399 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Time building chain proxies: 2.07, per 1000 atoms: 0.23 Number of scatterers: 9055 At special positions: 0 Unit cell: (100.8, 105, 124.95, 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 12 16.00 P 259 15.00 O 2413 8.00 N 1634 7.00 C 4737 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: 0.95 Conformation dependent library (CDL) restraints added in 157.4 milliseconds 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 858 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 58.6% alpha, 11.9% beta 80 base pairs and 151 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.651A pdb=" N ARG A 17 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 41 Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 57 through 68 Proline residue: A 65 - end of helix removed outlier: 3.896A pdb=" N THR A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 102 Processing helix chain 'A' and resid 321 through 338 removed outlier: 3.752A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.785A pdb=" N LEU A 346 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 406 removed outlier: 3.700A pdb=" N GLU A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 429 removed outlier: 3.656A pdb=" N THR A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 485 through 505 removed outlier: 3.696A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 538 Processing helix chain 'A' and resid 550 through 567 Processing helix chain 'A' and resid 570 through 585 removed outlier: 3.519A pdb=" N GLN A 574 " --> pdb=" O TYR A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 605 removed outlier: 3.969A pdb=" N LEU A 593 " --> pdb=" O SER A 589 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 637 Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 285 removed outlier: 6.389A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 295 Processing sheet with id=AA3, first strand: chain 'A' and resid 471 through 475 removed outlier: 3.665A pdb=" N ALA A 473 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER A 445 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER A 542 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 447 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL A 544 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 449 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 607 " --> pdb=" O GLY A 541 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 203 hydrogen bonds 380 hydrogen bond angles 0 basepair planarities 80 basepair parallelities 151 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1456 1.33 - 1.45: 3855 1.45 - 1.57: 3931 1.57 - 1.69: 511 1.69 - 1.81: 18 Bond restraints: 9771 Sorted by residual: bond pdb=" C3' DC C 50 " pdb=" C2' DC C 50 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.01e+00 bond pdb=" C3' DC C 49 " pdb=" C2' DC C 49 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.85e+00 bond pdb=" C3' DC C 41 " pdb=" C2' DC C 41 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.27e+00 bond pdb=" O5' G B 57 " pdb=" C5' G B 57 " ideal model delta sigma weight residual 1.420 1.454 -0.034 1.50e-02 4.44e+03 5.25e+00 bond pdb=" C3' DG D 11 " pdb=" C2' DG D 11 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.73e+00 ... (remaining 9766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 14063 1.64 - 3.28: 322 3.28 - 4.91: 58 4.91 - 6.55: 10 6.55 - 8.19: 6 Bond angle restraints: 14459 Sorted by residual: angle pdb=" O3' G B 56 " pdb=" C3' G B 56 " pdb=" C2' G B 56 " ideal model delta sigma weight residual 109.50 116.76 -7.26 1.50e+00 4.44e-01 2.34e+01 angle pdb=" O3' G B 189 " pdb=" C3' G B 189 " pdb=" C2' G B 189 " ideal model delta sigma weight residual 109.50 116.52 -7.02 1.50e+00 4.44e-01 2.19e+01 angle pdb=" N3 DT C 51 " pdb=" C4 DT C 51 " pdb=" O4 DT C 51 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" O4' DG D 12 " pdb=" C4' DG D 12 " pdb=" C3' DG D 12 " ideal model delta sigma weight residual 106.00 103.46 2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" C4' G B 56 " pdb=" C3' G B 56 " pdb=" O3' G B 56 " ideal model delta sigma weight residual 109.40 115.70 -6.30 1.50e+00 4.44e-01 1.76e+01 ... (remaining 14454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 4901 35.08 - 70.15: 310 70.15 - 105.23: 18 105.23 - 140.30: 2 140.30 - 175.38: 11 Dihedral angle restraints: 5242 sinusoidal: 3919 harmonic: 1323 Sorted by residual: dihedral pdb=" C4' G B 189 " pdb=" C3' G B 189 " pdb=" C2' G B 189 " pdb=" C1' G B 189 " ideal model delta sinusoidal sigma weight residual -35.00 32.64 -67.64 1 8.00e+00 1.56e-02 9.29e+01 dihedral pdb=" C5' G B 189 " pdb=" C4' G B 189 " pdb=" C3' G B 189 " pdb=" O3' G B 189 " ideal model delta sinusoidal sigma weight residual 147.00 79.79 67.21 1 8.00e+00 1.56e-02 9.19e+01 dihedral pdb=" O4' C B 196 " pdb=" C1' C B 196 " pdb=" N1 C B 196 " pdb=" C2 C B 196 " ideal model delta sinusoidal sigma weight residual 200.00 26.02 173.98 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 5239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1745 0.083 - 0.165: 62 0.165 - 0.248: 7 0.248 - 0.330: 3 0.330 - 0.413: 2 Chirality restraints: 1819 Sorted by residual: chirality pdb=" C3' G B 189 " pdb=" C4' G B 189 " pdb=" O3' G B 189 " pdb=" C2' G B 189 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C3' G B 56 " pdb=" C4' G B 56 " pdb=" O3' G B 56 " pdb=" C2' G B 56 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" P G B 57 " pdb=" OP1 G B 57 " pdb=" OP2 G B 57 " pdb=" O5' G B 57 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1816 not shown) Planarity restraints: 887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 96 " 0.025 2.00e-02 2.50e+03 1.54e-02 5.33e+00 pdb=" N1 C B 96 " -0.032 2.00e-02 2.50e+03 pdb=" C2 C B 96 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C B 96 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C B 96 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C B 96 " 0.020 2.00e-02 2.50e+03 pdb=" N4 C B 96 " -0.004 2.00e-02 2.50e+03 pdb=" C5 C B 96 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C B 96 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 97 " 0.030 2.00e-02 2.50e+03 1.51e-02 5.16e+00 pdb=" N1 C B 97 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C B 97 " -0.006 2.00e-02 2.50e+03 pdb=" O2 C B 97 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C B 97 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C B 97 " 0.007 2.00e-02 2.50e+03 pdb=" N4 C B 97 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C B 97 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C B 97 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 45 " 0.029 2.00e-02 2.50e+03 1.46e-02 4.81e+00 pdb=" N1 U B 45 " -0.030 2.00e-02 2.50e+03 pdb=" C2 U B 45 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U B 45 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U B 45 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U B 45 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 45 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U B 45 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U B 45 " -0.009 2.00e-02 2.50e+03 ... (remaining 884 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1338 2.76 - 3.29: 8146 3.29 - 3.83: 18195 3.83 - 4.36: 20224 4.36 - 4.90: 28501 Nonbonded interactions: 76404 Sorted by model distance: nonbonded pdb=" O6 G B 165 " pdb=" O4 U B 173 " model vdw 2.224 2.432 nonbonded pdb=" O2' G B 189 " pdb=" O5' A B 190 " model vdw 2.266 3.040 nonbonded pdb=" O2' A B 190 " pdb=" O4' A B 191 " model vdw 2.284 3.040 nonbonded pdb=" O2 U B 30 " pdb=" N1 G B 31 " model vdw 2.288 3.120 nonbonded pdb=" ND2 ASN A 379 " pdb=" OE1 GLN A 603 " model vdw 2.294 3.120 ... (remaining 76399 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: 0.700 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.050 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9771 Z= 0.226 Angle : 0.606 8.191 14459 Z= 0.378 Chirality : 0.039 0.413 1819 Planarity : 0.003 0.047 887 Dihedral : 19.069 175.377 4384 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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 are not related in a simple way. whole: 1.68 (0.40), residues: 446 helix: 2.21 (0.33), residues: 244 sheet: -0.00 (0.61), residues: 67 loop : -0.27 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 327 TYR 0.013 0.001 TYR A 570 PHE 0.012 0.002 PHE A 325 TRP 0.009 0.001 TRP A 94 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.23 ( 9771) covalent geometry : angle 0.60628 / 0.38 (14459) hydrogen bonds : bond 0.10406 / 7.15 ( 418) hydrogen bonds : angle 4.34532 / 2.98 ( 1010) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.202 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0798 time to fit residues: 7.3145 Evaluate side-chains 47 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 40.0000 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN A 489 ASN A 496 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.136048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.097166 restraints weight = 21887.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.099124 restraints weight = 9283.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.099241 restraints weight = 6178.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.099858 restraints weight = 5801.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.099822 restraints weight = 5321.652| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 9771 Z= 0.400 Angle : 0.815 8.367 14459 Z= 0.420 Chirality : 0.044 0.365 1819 Planarity : 0.005 0.040 887 Dihedral : 19.472 176.728 3548 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.97 % Allowed : 11.62 % Favored : 85.41 % 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 are not related in a simple way. whole: 0.99 (0.40), residues: 446 helix: 1.72 (0.33), residues: 246 sheet: -0.12 (0.65), residues: 69 loop : -0.91 (0.51), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 17 TYR 0.014 0.003 TYR A 80 PHE 0.016 0.003 PHE A 313 TRP 0.010 0.002 TRP A 48 HIS 0.007 0.002 HIS A 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.40 ( 9771) covalent geometry : angle 0.81519 / 0.42 (14459) hydrogen bonds : bond 0.07700 / 5.38 ( 418) hydrogen bonds : angle 3.76032 / 2.78 ( 1010) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.200 Fit side-chains REVERT: A 89 TYR cc_start: 0.7917 (m-10) cc_final: 0.7583 (m-10) REVERT: A 310 ASP cc_start: 0.8642 (p0) cc_final: 0.8387 (p0) outliers start: 11 outliers final: 5 residues processed: 50 average time/residue: 0.0559 time to fit residues: 4.6945 Evaluate side-chains 41 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 50.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN A 496 GLN A 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.135275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.096008 restraints weight = 21135.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.098860 restraints weight = 8948.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.100635 restraints weight = 5913.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.101483 restraints weight = 4900.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101549 restraints weight = 4519.958| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9771 Z= 0.152 Angle : 0.563 7.436 14459 Z= 0.304 Chirality : 0.034 0.299 1819 Planarity : 0.004 0.045 887 Dihedral : 19.296 177.392 3548 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.43 % Allowed : 12.97 % Favored : 84.59 % 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 are not related in a simple way. whole: 1.54 (0.41), residues: 446 helix: 2.31 (0.33), residues: 242 sheet: -0.08 (0.64), residues: 69 loop : -0.76 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 17 TYR 0.014 0.001 TYR A 441 PHE 0.014 0.002 PHE A 325 TRP 0.006 0.001 TRP A 588 HIS 0.004 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 ( 9771) covalent geometry : angle 0.56300 / 0.30 (14459) hydrogen bonds : bond 0.05573 / 3.93 ( 418) hydrogen bonds : angle 3.35589 / 2.51 ( 1010) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.122 Fit side-chains REVERT: A 89 TYR cc_start: 0.7869 (m-10) cc_final: 0.7502 (m-10) REVERT: A 310 ASP cc_start: 0.8587 (p0) cc_final: 0.8264 (p0) REVERT: A 486 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7978 (pt0) outliers start: 9 outliers final: 4 residues processed: 50 average time/residue: 0.0603 time to fit residues: 4.7222 Evaluate side-chains 47 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 60 optimal weight: 50.0000 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.135711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.097837 restraints weight = 21275.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.100015 restraints weight = 9827.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.100279 restraints weight = 6301.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.100878 restraints weight = 5968.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.100800 restraints weight = 5730.723| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9771 Z= 0.156 Angle : 0.567 10.361 14459 Z= 0.301 Chirality : 0.035 0.307 1819 Planarity : 0.004 0.039 887 Dihedral : 19.211 177.176 3548 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.97 % Allowed : 14.32 % Favored : 82.70 % 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 are not related in a simple way. whole: 1.64 (0.41), residues: 446 helix: 2.40 (0.34), residues: 242 sheet: -0.02 (0.65), residues: 69 loop : -0.74 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 17 TYR 0.016 0.002 TYR A 80 PHE 0.012 0.002 PHE A 325 TRP 0.005 0.001 TRP A 382 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 ( 9771) covalent geometry : angle 0.56738 / 0.30 (14459) hydrogen bonds : bond 0.05541 / 3.92 ( 418) hydrogen bonds : angle 3.23157 / 2.42 ( 1010) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.207 Fit side-chains REVERT: A 89 TYR cc_start: 0.7898 (m-10) cc_final: 0.7551 (m-10) REVERT: A 486 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7911 (pt0) outliers start: 11 outliers final: 5 residues processed: 55 average time/residue: 0.0624 time to fit residues: 5.3467 Evaluate side-chains 49 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 62 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 59 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN A 479 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.133447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.093694 restraints weight = 21210.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.096444 restraints weight = 9014.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.098208 restraints weight = 5990.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.098890 restraints weight = 4990.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.099435 restraints weight = 4644.385| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9771 Z= 0.201 Angle : 0.597 7.941 14459 Z= 0.315 Chirality : 0.036 0.259 1819 Planarity : 0.004 0.040 887 Dihedral : 19.238 179.243 3548 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.78 % Allowed : 15.14 % Favored : 81.08 % 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 are not related in a simple way. whole: 1.48 (0.40), residues: 446 helix: 2.21 (0.33), residues: 242 sheet: 0.17 (0.68), residues: 64 loop : -0.82 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 17 TYR 0.012 0.002 TYR A 570 PHE 0.010 0.002 PHE A 325 TRP 0.007 0.001 TRP A 94 HIS 0.004 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 ( 9771) covalent geometry : angle 0.59663 / 0.31 (14459) hydrogen bonds : bond 0.05583 / 3.89 ( 418) hydrogen bonds : angle 3.32136 / 2.48 ( 1010) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.202 Fit side-chains REVERT: A 89 TYR cc_start: 0.7970 (m-10) cc_final: 0.7630 (m-10) outliers start: 14 outliers final: 8 residues processed: 52 average time/residue: 0.0655 time to fit residues: 5.3430 Evaluate side-chains 47 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 21 optimal weight: 0.2980 chunk 69 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN A 446 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.135335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.096218 restraints weight = 21018.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.099023 restraints weight = 8790.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.100731 restraints weight = 5805.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.101644 restraints weight = 4822.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.101938 restraints weight = 4431.159| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9771 Z= 0.126 Angle : 0.549 7.989 14459 Z= 0.290 Chirality : 0.034 0.232 1819 Planarity : 0.004 0.042 887 Dihedral : 19.150 179.226 3548 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.97 % Allowed : 16.76 % Favored : 80.27 % 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 are not related in a simple way. whole: 1.67 (0.40), residues: 446 helix: 2.35 (0.33), residues: 242 sheet: 0.22 (0.68), residues: 64 loop : -0.70 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 327 TYR 0.011 0.001 TYR A 441 PHE 0.012 0.002 PHE A 325 TRP 0.005 0.001 TRP A 588 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 ( 9771) covalent geometry : angle 0.54913 / 0.29 (14459) hydrogen bonds : bond 0.05240 / 3.69 ( 418) hydrogen bonds : angle 3.14610 / 2.35 ( 1010) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.235 Fit side-chains REVERT: A 89 TYR cc_start: 0.7948 (m-10) cc_final: 0.7564 (m-10) REVERT: A 486 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7995 (pt0) outliers start: 11 outliers final: 8 residues processed: 55 average time/residue: 0.0455 time to fit residues: 4.0797 Evaluate side-chains 54 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 33 optimal weight: 0.0970 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 0.0010 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 ASN ** A 574 GLN ** 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 = 0.3950 r_free = 0.3950 target = 0.133602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094010 restraints weight = 21196.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096753 restraints weight = 8961.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.098450 restraints weight = 5957.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.099284 restraints weight = 4963.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.099395 restraints weight = 4584.465| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9771 Z= 0.203 Angle : 0.582 8.725 14459 Z= 0.307 Chirality : 0.036 0.223 1819 Planarity : 0.004 0.040 887 Dihedral : 19.157 179.402 3548 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.97 % Allowed : 17.30 % Favored : 79.73 % 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 are not related in a simple way. whole: 1.60 (0.40), residues: 446 helix: 2.32 (0.33), residues: 242 sheet: 0.21 (0.68), residues: 64 loop : -0.79 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 17 TYR 0.011 0.002 TYR A 570 PHE 0.011 0.002 PHE A 305 TRP 0.005 0.001 TRP A 588 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 ( 9771) covalent geometry : angle 0.58158 / 0.31 (14459) hydrogen bonds : bond 0.05458 / 3.81 ( 418) hydrogen bonds : angle 3.23049 / 2.40 ( 1010) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.149 Fit side-chains REVERT: A 89 TYR cc_start: 0.8014 (m-10) cc_final: 0.7651 (m-10) REVERT: A 290 ASP cc_start: 0.7918 (t0) cc_final: 0.7569 (t0) REVERT: A 486 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8052 (pt0) outliers start: 11 outliers final: 7 residues processed: 53 average time/residue: 0.0620 time to fit residues: 5.3410 Evaluate side-chains 53 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 62 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 61 optimal weight: 40.0000 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.134971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.095636 restraints weight = 21139.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.098408 restraints weight = 8933.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.100173 restraints weight = 5922.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.101013 restraints weight = 4922.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.101176 restraints weight = 4544.197| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9771 Z= 0.131 Angle : 0.550 9.349 14459 Z= 0.289 Chirality : 0.034 0.222 1819 Planarity : 0.004 0.041 887 Dihedral : 19.127 179.538 3548 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.43 % Allowed : 18.65 % Favored : 78.92 % 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 are not related in a simple way. whole: 1.69 (0.41), residues: 446 helix: 2.42 (0.33), residues: 242 sheet: 0.21 (0.68), residues: 64 loop : -0.78 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 17 TYR 0.010 0.001 TYR A 570 PHE 0.021 0.002 PHE A 347 TRP 0.005 0.001 TRP A 588 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 9771) covalent geometry : angle 0.54974 / 0.29 (14459) hydrogen bonds : bond 0.05187 / 3.64 ( 418) hydrogen bonds : angle 3.15091 / 2.34 ( 1010) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.212 Fit side-chains REVERT: A 89 TYR cc_start: 0.7966 (m-10) cc_final: 0.7555 (m-10) REVERT: A 486 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7985 (pt0) outliers start: 9 outliers final: 7 residues processed: 53 average time/residue: 0.0701 time to fit residues: 5.8088 Evaluate side-chains 54 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 8.9990 chunk 59 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 60 optimal weight: 50.0000 chunk 47 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.131202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091768 restraints weight = 21573.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.094533 restraints weight = 8774.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.096235 restraints weight = 5753.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.097156 restraints weight = 4790.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.097422 restraints weight = 4399.379| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 9771 Z= 0.341 Angle : 0.720 9.272 14459 Z= 0.372 Chirality : 0.041 0.236 1819 Planarity : 0.005 0.040 887 Dihedral : 19.327 177.869 3548 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.24 % Allowed : 18.11 % Favored : 78.65 % 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 are not related in a simple way. whole: 1.13 (0.40), residues: 446 helix: 1.95 (0.33), residues: 242 sheet: 0.14 (0.69), residues: 64 loop : -1.09 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 78 TYR 0.016 0.003 TYR A 80 PHE 0.017 0.003 PHE A 305 TRP 0.012 0.002 TRP A 382 HIS 0.005 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.34 ( 9771) covalent geometry : angle 0.71989 / 0.37 (14459) hydrogen bonds : bond 0.06440 / 4.39 ( 418) hydrogen bonds : angle 3.59105 / 2.66 ( 1010) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.208 Fit side-chains REVERT: A 89 TYR cc_start: 0.8010 (m-10) cc_final: 0.7669 (m-10) REVERT: A 290 ASP cc_start: 0.7958 (t0) cc_final: 0.7523 (t0) outliers start: 12 outliers final: 8 residues processed: 49 average time/residue: 0.0595 time to fit residues: 4.8262 Evaluate side-chains 46 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.131176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.091162 restraints weight = 21141.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.093911 restraints weight = 9029.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.095576 restraints weight = 6001.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.096401 restraints weight = 4988.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096822 restraints weight = 4605.584| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9771 Z= 0.180 Angle : 0.600 9.313 14459 Z= 0.316 Chirality : 0.036 0.253 1819 Planarity : 0.004 0.045 887 Dihedral : 19.253 179.252 3548 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.16 % Allowed : 20.54 % Favored : 77.30 % 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 are not related in a simple way. whole: 1.32 (0.40), residues: 446 helix: 2.13 (0.33), residues: 242 sheet: 0.05 (0.67), residues: 64 loop : -0.96 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 17 TYR 0.011 0.002 TYR A 570 PHE 0.025 0.002 PHE A 305 TRP 0.007 0.001 TRP A 94 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 ( 9771) covalent geometry : angle 0.59985 / 0.32 (14459) hydrogen bonds : bond 0.05531 / 3.85 ( 418) hydrogen bonds : angle 3.37697 / 2.51 ( 1010) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.156 Fit side-chains REVERT: A 89 TYR cc_start: 0.7993 (m-10) cc_final: 0.7650 (m-10) REVERT: A 290 ASP cc_start: 0.7974 (t0) cc_final: 0.7768 (t0) outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 0.0554 time to fit residues: 4.5074 Evaluate side-chains 51 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 42 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.133136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.094986 restraints weight = 20907.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097384 restraints weight = 10762.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.097512 restraints weight = 6367.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.097848 restraints weight = 6130.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.097863 restraints weight = 5861.167| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9771 Z= 0.177 Angle : 0.580 9.533 14459 Z= 0.307 Chirality : 0.036 0.252 1819 Planarity : 0.004 0.043 887 Dihedral : 19.190 179.616 3548 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.43 % Allowed : 20.00 % Favored : 77.57 % 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 are not related in a simple way. whole: 1.45 (0.40), residues: 446 helix: 2.24 (0.33), residues: 242 sheet: 0.05 (0.67), residues: 64 loop : -0.89 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 17 TYR 0.011 0.001 TYR A 91 PHE 0.015 0.002 PHE A 305 TRP 0.005 0.001 TRP A 588 HIS 0.002 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 ( 9771) covalent geometry : angle 0.58045 / 0.31 (14459) hydrogen bonds : bond 0.05401 / 3.76 ( 418) hydrogen bonds : angle 3.29630 / 2.44 ( 1010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1359.80 seconds wall clock time: 24 minutes 10.70 seconds (1450.70 seconds total)