Starting phenix.real_space_refine on Fri Sep 11 11:14:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n3p_24143/09_2026/7n3p_24143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n3p_24143/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7n3p_24143/09_2026/7n3p_24143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n3p_24143/09_2026/7n3p_24143.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7n3p_24143/09_2026/7n3p_24143.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n3p_24143/09_2026/7n3p_24143.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n3p_24143/09_2026/7n3p_24143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n3p_24143/09_2026/7n3p_24143.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: {'RNAv2': 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: 1.53, per 1000 atoms: 0.17 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: 0.89 Conformation dependent library (CDL) restraints added in 146.2 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: 1.03 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: 1.54 Time building geometry restraints manager: 1.17 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=" O3' U B 98 " pdb=" P G B 99 " ideal model delta sigma weight residual 1.607 1.636 -0.029 1.20e-02 6.94e+03 5.69e+00 bond pdb=" O3' U B 192 " pdb=" P C B 193 " ideal model delta sigma weight residual 1.607 1.635 -0.028 1.20e-02 6.94e+03 5.62e+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 ... (remaining 9766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 13457 1.64 - 3.28: 822 3.28 - 4.91: 158 4.91 - 6.55: 18 6.55 - 8.19: 4 Bond angle restraints: 14459 Sorted by residual: 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=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT C 38 " pdb=" C4 DT C 38 " pdb=" O4 DT C 38 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT C 43 " pdb=" C4 DT C 43 " pdb=" O4 DT C 43 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 ... (remaining 14454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 4640 35.08 - 70.15: 559 70.15 - 105.23: 36 105.23 - 140.30: 0 140.30 - 175.38: 7 Dihedral angle restraints: 5242 sinusoidal: 3919 harmonic: 1323 Sorted by residual: dihedral pdb=" C4' G B 236 " pdb=" C3' G B 236 " pdb=" C2' G B 236 " pdb=" C1' G B 236 " ideal model delta sinusoidal sigma weight residual 36.34 -38.14 74.48 1 3.10e+00 1.04e-01 7.32e+02 dihedral pdb=" C4' U B 98 " pdb=" C3' U B 98 " pdb=" C2' U B 98 " pdb=" C1' U B 98 " ideal model delta sinusoidal sigma weight residual 36.34 -37.91 74.26 1 3.10e+00 1.04e-01 7.28e+02 dihedral pdb=" C4' G B 47 " pdb=" C3' G B 47 " pdb=" C2' G B 47 " pdb=" C1' G B 47 " ideal model delta sinusoidal sigma weight residual 36.34 -37.34 73.68 1 3.10e+00 1.04e-01 7.18e+02 ... (remaining 5239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1509 0.110 - 0.220: 25 0.220 - 0.330: 282 0.330 - 0.440: 0 0.440 - 0.549: 3 Chirality restraints: 1819 Sorted by residual: 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 2.17 -2.72 -0.55 2.00e-01 2.50e+01 7.55e+00 chirality pdb=" P G B 56 " pdb=" OP1 G B 56 " pdb=" OP2 G B 56 " pdb=" O5' G B 56 " both_signs ideal model delta sigma weight residual True 2.17 -2.71 -0.53 2.00e-01 2.50e+01 7.12e+00 chirality pdb=" P G B 224 " pdb=" OP1 G B 224 " pdb=" OP2 G B 224 " pdb=" O5' G B 224 " both_signs ideal model delta sigma weight residual True 2.17 -2.71 -0.53 2.00e-01 2.50e+01 7.11e+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: 0.540 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.530 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.380 ------------------------------------------------------------------------------- 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= 0.238 Angle : 0.882 8.191 14459 Z= 0.430 Chirality : 0.105 0.549 1819 Planarity : 0.003 0.047 887 Dihedral : 22.541 175.377 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 0.00348 / 0.24 ( 9771) covalent geometry : angle 0.88211 / 0.43 (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 : 0.210 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0722 time to fit residues: 6.7977 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 : 0.195 ------------------------------------------------------------------------------- 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: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.135717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.095748 restraints weight = 21309.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.098532 restraints weight = 9243.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.100266 restraints weight = 6180.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.101164 restraints weight = 5147.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.101320 restraints weight = 4735.607| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 9771 Z= 0.410 Angle : 1.611 19.625 14459 Z= 0.636 Chirality : 0.140 2.150 1819 Planarity : 0.005 0.037 887 Dihedral : 21.524 174.938 3548 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.70 % Allowed : 10.54 % Favored : 86.76 % 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 are not related in a simple way. whole: 1.25 (0.40), residues: 446 helix: 1.95 (0.33), residues: 246 sheet: -0.12 (0.64), residues: 69 loop : -0.76 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 17 TYR 0.013 0.003 TYR A 91 PHE 0.013 0.002 PHE A 313 TRP 0.009 0.002 TRP A 382 HIS 0.007 0.002 HIS A 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.41 ( 9771) covalent geometry : angle 1.61066 / 0.64 (14459) hydrogen bonds : bond 0.07503 / 5.28 ( 418) hydrogen bonds : angle 3.69602 / 2.76 ( 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 55 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.218 Fit side-chains REVERT: A 62 LEU cc_start: 0.8423 (tp) cc_final: 0.8171 (tt) REVERT: A 89 TYR cc_start: 0.7853 (m-10) cc_final: 0.7519 (m-10) REVERT: A 310 ASP cc_start: 0.8641 (p0) cc_final: 0.8360 (p0) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 0.0693 time to fit residues: 5.7727 Evaluate side-chains 43 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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: 5.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 30.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.138375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.098893 restraints weight = 21093.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.101844 restraints weight = 8677.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.103677 restraints weight = 5634.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.104547 restraints weight = 4638.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.105040 restraints weight = 4258.961| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9771 Z= 0.184 Angle : 1.114 17.303 14459 Z= 0.448 Chirality : 0.094 1.296 1819 Planarity : 0.004 0.045 887 Dihedral : 21.414 179.142 3548 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.16 % Allowed : 12.43 % 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: 1.62 (0.41), residues: 446 helix: 2.40 (0.33), residues: 242 sheet: -0.12 (0.63), residues: 69 loop : -0.73 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 17 TYR 0.016 0.001 TYR A 441 PHE 0.017 0.002 PHE A 325 TRP 0.006 0.001 TRP A 293 HIS 0.004 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 ( 9771) covalent geometry : angle 1.11384 / 0.45 (14459) hydrogen bonds : bond 0.05949 / 4.17 ( 418) hydrogen bonds : angle 3.36435 / 2.52 ( 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 57 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.133 Fit side-chains REVERT: A 62 LEU cc_start: 0.8272 (tp) cc_final: 0.8033 (tt) REVERT: A 89 TYR cc_start: 0.7821 (m-10) cc_final: 0.7438 (m-10) REVERT: A 310 ASP cc_start: 0.8625 (p0) cc_final: 0.8299 (p0) REVERT: A 486 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7947 (pt0) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.0702 time to fit residues: 5.6424 Evaluate side-chains 48 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 550 ASP 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: 0.7980 chunk 48 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN ** 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 = 0.3916 r_free = 0.3916 target = 0.131002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.090937 restraints weight = 21437.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.093590 restraints weight = 9486.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.095205 restraints weight = 6376.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.096087 restraints weight = 5324.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.096115 restraints weight = 4908.516| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 9771 Z= 0.359 Angle : 1.238 16.090 14459 Z= 0.503 Chirality : 0.089 0.780 1819 Planarity : 0.005 0.042 887 Dihedral : 21.594 179.247 3548 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.32 % Allowed : 12.97 % 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: 1.10 (0.40), residues: 446 helix: 2.00 (0.33), residues: 242 sheet: -0.37 (0.63), residues: 69 loop : -1.02 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 17 TYR 0.016 0.002 TYR A 441 PHE 0.014 0.002 PHE A 325 TRP 0.007 0.002 TRP A 588 HIS 0.006 0.002 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00735 / 0.36 ( 9771) covalent geometry : angle 1.23811 / 0.50 (14459) hydrogen bonds : bond 0.07120 / 4.96 ( 418) hydrogen bonds : angle 3.70480 / 2.78 ( 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 53 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.189 Fit side-chains REVERT: A 89 TYR cc_start: 0.7998 (m-10) cc_final: 0.7667 (m-10) REVERT: A 273 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7820 (pp) REVERT: A 518 GLU cc_start: 0.8107 (tt0) cc_final: 0.7891 (tt0) outliers start: 16 outliers final: 10 residues processed: 51 average time/residue: 0.0607 time to fit residues: 5.2247 Evaluate side-chains 47 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 273 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 62 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 59 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN 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 = 0.3966 r_free = 0.3966 target = 0.134723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.095441 restraints weight = 21307.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.098242 restraints weight = 9005.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.099967 restraints weight = 5932.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.100817 restraints weight = 4916.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.101072 restraints weight = 4534.261| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9771 Z= 0.171 Angle : 1.037 15.706 14459 Z= 0.419 Chirality : 0.080 0.726 1819 Planarity : 0.004 0.047 887 Dihedral : 21.409 178.801 3548 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.70 % Allowed : 15.14 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.39 (0.41), residues: 446 helix: 2.24 (0.33), residues: 242 sheet: -0.20 (0.66), residues: 64 loop : -0.89 (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 0.014 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 0.00343 / 0.17 ( 9771) covalent geometry : angle 1.03733 / 0.42 (14459) hydrogen bonds : bond 0.05915 / 4.12 ( 418) hydrogen bonds : angle 3.40986 / 2.54 ( 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 54 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.200 Fit side-chains REVERT: A 89 TYR cc_start: 0.7983 (m-10) cc_final: 0.7676 (m-10) outliers start: 10 outliers final: 5 residues processed: 51 average time/residue: 0.0738 time to fit residues: 5.9366 Evaluate side-chains 45 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 486 GLU Chi-restraints excluded: chain A residue 526 LEU 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: 0.9990 chunk 7 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 40 optimal weight: 0.4980 chunk 54 optimal weight: 20.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.134149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.094899 restraints weight = 21247.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.097670 restraints weight = 8994.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.099372 restraints weight = 5942.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100204 restraints weight = 4927.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.100297 restraints weight = 4545.549| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3026 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= 0.192 Angle : 1.017 12.949 14459 Z= 0.411 Chirality : 0.076 0.729 1819 Planarity : 0.004 0.044 887 Dihedral : 21.381 178.970 3548 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: 1.43 (0.40), residues: 446 helix: 2.23 (0.33), residues: 242 sheet: -0.19 (0.65), residues: 64 loop : -0.79 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 327 TYR 0.011 0.001 TYR A 570 PHE 0.014 0.002 PHE A 325 TRP 0.006 0.001 TRP A 588 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 ( 9771) covalent geometry : angle 1.01655 / 0.41 (14459) hydrogen bonds : bond 0.05876 / 4.10 ( 418) hydrogen bonds : angle 3.34135 / 2.50 ( 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 56 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.205 Fit side-chains REVERT: A 89 TYR cc_start: 0.7996 (m-10) cc_final: 0.7659 (m-10) REVERT: A 486 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8042 (pt0) outliers start: 11 outliers final: 7 residues processed: 52 average time/residue: 0.0621 time to fit residues: 5.3186 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 : 0.203 ------------------------------------------------------------------------------- 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 526 LEU 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: 0.9990 chunk 64 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 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 = 0.3979 r_free = 0.3979 target = 0.135517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096406 restraints weight = 21296.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.099209 restraints weight = 9024.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.100898 restraints weight = 5962.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101812 restraints weight = 4943.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.101935 restraints weight = 4550.001| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9771 Z= 0.176 Angle : 0.981 11.314 14459 Z= 0.398 Chirality : 0.074 0.725 1819 Planarity : 0.004 0.042 887 Dihedral : 21.318 179.577 3548 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.70 % Allowed : 17.03 % 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: 1.50 (0.40), residues: 446 helix: 2.28 (0.33), residues: 242 sheet: -0.06 (0.66), residues: 64 loop : -0.80 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 17 TYR 0.011 0.001 TYR A 570 PHE 0.017 0.002 PHE A 347 TRP 0.005 0.001 TRP A 293 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 0.98052 / 0.40 (14459) hydrogen bonds : bond 0.05692 / 3.99 ( 418) hydrogen bonds : angle 3.30894 / 2.47 ( 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: 10 poor density : 47 time to evaluate : 0.179 Fit side-chains REVERT: A 89 TYR cc_start: 0.7986 (m-10) cc_final: 0.7618 (m-10) REVERT: A 290 ASP cc_start: 0.7911 (t0) cc_final: 0.7563 (t0) REVERT: A 486 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8010 (pt0) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.0703 time to fit residues: 5.9297 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 : 0.200 ------------------------------------------------------------------------------- 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 526 LEU 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: 6.9990 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.0270 chunk 42 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.3044 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.137352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.098559 restraints weight = 21157.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101407 restraints weight = 8824.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.103154 restraints weight = 5768.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104052 restraints weight = 4761.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104249 restraints weight = 4386.795| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9771 Z= 0.153 Angle : 0.945 11.513 14459 Z= 0.383 Chirality : 0.071 0.729 1819 Planarity : 0.004 0.047 887 Dihedral : 21.255 177.991 3548 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.43 % Allowed : 19.46 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.48 (0.33), residues: 242 sheet: -0.11 (0.67), residues: 64 loop : -0.73 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 327 TYR 0.010 0.001 TYR A 80 PHE 0.013 0.002 PHE A 305 TRP 0.006 0.001 TRP A 356 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 9771) covalent geometry : angle 0.94464 / 0.38 (14459) hydrogen bonds : bond 0.05529 / 3.90 ( 418) hydrogen bonds : angle 3.16391 / 2.36 ( 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 58 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.200 Fit side-chains REVERT: A 89 TYR cc_start: 0.7862 (m-10) cc_final: 0.7474 (m-10) REVERT: A 290 ASP cc_start: 0.7972 (t0) cc_final: 0.7640 (t0) REVERT: A 486 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7935 (pt0) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.0714 time to fit residues: 6.2070 Evaluate side-chains 57 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 526 LEU 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: 7.9990 chunk 59 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.132608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.094985 restraints weight = 21367.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.097308 restraints weight = 11056.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.097298 restraints weight = 6939.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097716 restraints weight = 6659.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.097808 restraints weight = 6238.351| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9771 Z= 0.302 Angle : 1.068 10.320 14459 Z= 0.435 Chirality : 0.076 0.710 1819 Planarity : 0.005 0.043 887 Dihedral : 21.397 179.414 3548 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.70 % Allowed : 20.00 % 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: 1.33 (0.40), residues: 446 helix: 2.20 (0.33), residues: 242 sheet: -0.14 (0.68), residues: 64 loop : -0.98 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 17 TYR 0.015 0.002 TYR A 91 PHE 0.013 0.002 PHE A 305 TRP 0.009 0.001 TRP A 382 HIS 0.005 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.30 ( 9771) covalent geometry : angle 1.06773 / 0.44 (14459) hydrogen bonds : bond 0.06245 / 4.38 ( 418) hydrogen bonds : angle 3.47076 / 2.58 ( 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 55 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.157 Fit side-chains REVERT: A 89 TYR cc_start: 0.7941 (m-10) cc_final: 0.7591 (m-10) REVERT: A 290 ASP cc_start: 0.7987 (t0) cc_final: 0.7400 (t0) outliers start: 10 outliers final: 8 residues processed: 51 average time/residue: 0.0643 time to fit residues: 5.4256 Evaluate side-chains 49 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.131090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.091236 restraints weight = 21328.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.093865 restraints weight = 9382.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095499 restraints weight = 6311.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096372 restraints weight = 5252.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096377 restraints weight = 4843.211| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9771 Z= 0.296 Angle : 1.082 10.736 14459 Z= 0.443 Chirality : 0.078 0.719 1819 Planarity : 0.005 0.046 887 Dihedral : 21.446 179.903 3548 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.43 % Allowed : 20.54 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.05 (0.33), residues: 242 sheet: -0.27 (0.68), residues: 64 loop : -1.08 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 78 TYR 0.012 0.002 TYR A 441 PHE 0.021 0.002 PHE A 305 TRP 0.009 0.002 TRP A 382 HIS 0.004 0.001 HIS A 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.30 ( 9771) covalent geometry : angle 1.08215 / 0.44 (14459) hydrogen bonds : bond 0.06200 / 4.35 ( 418) hydrogen bonds : angle 3.54762 / 2.64 ( 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 51 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.201 Fit side-chains REVERT: A 89 TYR cc_start: 0.7969 (m-10) cc_final: 0.7622 (m-10) REVERT: A 290 ASP cc_start: 0.7885 (t0) cc_final: 0.7657 (t0) REVERT: A 310 ASP cc_start: 0.8503 (p0) cc_final: 0.8217 (p0) REVERT: A 461 VAL cc_start: 0.9442 (t) cc_final: 0.9230 (p) outliers start: 9 outliers final: 9 residues processed: 48 average time/residue: 0.0626 time to fit residues: 4.9721 Evaluate side-chains 51 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 GLN ** 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 = 0.4003 r_free = 0.4003 target = 0.138101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.100684 restraints weight = 20799.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.102822 restraints weight = 10326.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.103065 restraints weight = 6105.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.104020 restraints weight = 5779.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.103949 restraints weight = 5382.919| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9771 Z= 0.152 Angle : 0.966 10.331 14459 Z= 0.393 Chirality : 0.072 0.751 1819 Planarity : 0.004 0.054 887 Dihedral : 21.313 179.363 3548 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.16 % Allowed : 20.81 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.51 (0.41), residues: 446 helix: 2.38 (0.33), residues: 242 sheet: -0.35 (0.65), residues: 64 loop : -0.82 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 327 TYR 0.017 0.002 TYR A 91 PHE 0.011 0.002 PHE A 305 TRP 0.006 0.001 TRP A 293 HIS 0.003 0.001 HIS A 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 ( 9771) covalent geometry : angle 0.96576 / 0.39 (14459) hydrogen bonds : bond 0.05553 / 3.91 ( 418) hydrogen bonds : angle 3.30299 / 2.46 ( 1010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1613.89 seconds wall clock time: 28 minutes 43.82 seconds (1723.82 seconds total)