Starting phenix.real_space_refine on Tue Aug 4 13:32:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z5u_73824/08_2026/9z5u_73824.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z5u_73824/08_2026/9z5u_73824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z5u_73824/08_2026/9z5u_73824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z5u_73824/08_2026/9z5u_73824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z5u_73824/08_2026/9z5u_73824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z5u_73824/08_2026/9z5u_73824.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2112 2.51 5 N 567 2.21 5 O 643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3348 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1571 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 22, 'TRANS': 180} Chain breaks: 1 Chain: "H" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 876 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.04, per 1000 atoms: 0.31 Number of scatterers: 3348 At special positions: 0 Unit cell: (66.774, 64.62, 82.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 643 8.00 N 567 7.00 C 2112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 452 " - pdb=" SG CYS A 620 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 508 " - pdb=" SG CYS A 552 " distance=2.03 Simple disulfide: pdb=" SG CYS A 569 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 607 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 801 " - " ASN A 532 " " NAG A 802 " - " ASN A 623 " " NAG B 1 " - " ASN A 556 " " NAG C 1 " - " ASN A 645 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 134.5 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 10 sheets defined 9.2% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 452 through 458 removed outlier: 3.957A pdb=" N SER A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 619 through 622 Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.061A pdb=" N ALA L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.250A pdb=" N SER A 473 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU A 579 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 498 removed outlier: 3.997A pdb=" N VAL A 497 " --> pdb=" O PHE A 537 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 513 through 515 removed outlier: 3.624A pdb=" N GLY A 551 " --> pdb=" O PHE A 509 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 607 through 610 removed outlier: 4.556A pdb=" N ASP A 641 " --> pdb=" O ASP A 610 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 636 through 638 removed outlier: 3.604A pdb=" N ALA H 60 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N MET H 48 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N TYR H 32 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU H 10 " --> pdb=" O ILE H 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 636 through 638 removed outlier: 3.604A pdb=" N ALA H 60 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N MET H 48 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N TYR H 32 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.082A pdb=" N THR L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AB1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.182A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) 90 hydrogen bonds defined for protein. 219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.35 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1016 1.34 - 1.46: 794 1.46 - 1.58: 1606 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 3448 Sorted by residual: bond pdb=" CA PHE A 509 " pdb=" C PHE A 509 " ideal model delta sigma weight residual 1.526 1.468 0.058 1.22e-02 6.72e+03 2.23e+01 bond pdb=" CA TYR A 507 " pdb=" C TYR A 507 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.27e-02 6.20e+03 1.22e+01 bond pdb=" N VAL A 514 " pdb=" CA VAL A 514 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.29e-02 6.01e+03 1.01e+01 bond pdb=" CA PRO A 513 " pdb=" C PRO A 513 " ideal model delta sigma weight residual 1.520 1.479 0.041 1.31e-02 5.83e+03 9.59e+00 bond pdb=" CA SER A 512 " pdb=" CB SER A 512 " ideal model delta sigma weight residual 1.532 1.486 0.045 1.50e-02 4.44e+03 9.17e+00 ... (remaining 3443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 4554 2.46 - 4.93: 130 4.93 - 7.39: 14 7.39 - 9.85: 2 9.85 - 12.31: 1 Bond angle restraints: 4701 Sorted by residual: angle pdb=" CA PHE A 509 " pdb=" CB PHE A 509 " pdb=" CG PHE A 509 " ideal model delta sigma weight residual 113.80 105.25 8.55 1.00e+00 1.00e+00 7.31e+01 angle pdb=" N THR A 510 " pdb=" CA THR A 510 " pdb=" C THR A 510 " ideal model delta sigma weight residual 109.81 97.50 12.31 2.21e+00 2.05e-01 3.10e+01 angle pdb=" CA PRO A 513 " pdb=" C PRO A 513 " pdb=" O PRO A 513 " ideal model delta sigma weight residual 121.67 115.81 5.86 1.22e+00 6.72e-01 2.30e+01 angle pdb=" N THR A 542 " pdb=" CA THR A 542 " pdb=" C THR A 542 " ideal model delta sigma weight residual 109.65 102.82 6.83 1.56e+00 4.11e-01 1.92e+01 angle pdb=" CA TYR A 507 " pdb=" C TYR A 507 " pdb=" O TYR A 507 " ideal model delta sigma weight residual 120.46 115.80 4.66 1.07e+00 8.73e-01 1.90e+01 ... (remaining 4696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.83: 1895 12.83 - 25.66: 156 25.66 - 38.48: 52 38.48 - 51.31: 10 51.31 - 64.14: 7 Dihedral angle restraints: 2120 sinusoidal: 920 harmonic: 1200 Sorted by residual: dihedral pdb=" CA LEU A 640 " pdb=" C LEU A 640 " pdb=" N ASP A 641 " pdb=" CA ASP A 641 " ideal model delta harmonic sigma weight residual 180.00 154.24 25.76 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ASN A 541 " pdb=" C ASN A 541 " pdb=" N THR A 542 " pdb=" CA THR A 542 " ideal model delta harmonic sigma weight residual 180.00 155.00 25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA TYR H 91 " pdb=" C TYR H 91 " pdb=" N CYS H 92 " pdb=" CA CYS H 92 " ideal model delta harmonic sigma weight residual 180.00 157.50 22.50 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 2117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 368 0.048 - 0.095: 102 0.095 - 0.143: 45 0.143 - 0.190: 2 0.190 - 0.238: 1 Chirality restraints: 518 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.51e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 645 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE H 52 " pdb=" N ILE H 52 " pdb=" C ILE H 52 " pdb=" CB ILE H 52 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.56e-01 ... (remaining 515 not shown) Planarity restraints: 599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 509 " -0.033 2.00e-02 2.50e+03 2.30e-02 9.25e+00 pdb=" CG PHE A 509 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 509 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 509 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 509 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 509 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 509 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 645 " -0.006 2.00e-02 2.50e+03 2.39e-02 7.13e+00 pdb=" CG ASN A 645 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 645 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A 645 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 604 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 605 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " -0.024 5.00e-02 4.00e+02 ... (remaining 596 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 71 2.65 - 3.22: 3139 3.22 - 3.78: 5290 3.78 - 4.34: 7477 4.34 - 4.90: 12358 Nonbonded interactions: 28335 Sorted by model distance: nonbonded pdb=" OG SER L 63 " pdb=" O THR L 74 " model vdw 2.093 3.040 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.169 3.040 nonbonded pdb=" OG1 THR A 518 " pdb=" OG1 THR A 526 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 624 " pdb=" O7 NAG C 1 " model vdw 2.251 3.040 nonbonded pdb=" O GLU A 533 " pdb=" OG1 THR A 534 " model vdw 2.289 3.040 ... (remaining 28330 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.340 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 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 : 0.005 0.058 3465 Z= 0.284 Angle : 1.001 15.412 4742 Z= 0.525 Chirality : 0.052 0.238 518 Planarity : 0.007 0.044 595 Dihedral : 11.066 64.135 1330 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.32 (0.41), residues: 415 helix: 0.17 (1.69), residues: 12 sheet: -1.64 (0.53), residues: 95 loop : -1.68 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 614 TYR 0.019 0.002 TYR A 624 PHE 0.046 0.003 PHE A 509 TRP 0.017 0.002 TRP A 549 HIS 0.013 0.002 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.28 ( 3448) covalent geometry : angle 0.93417 / 0.51 ( 4701) SS BOND : bond 0.00440 / 0.33 ( 10) SS BOND : angle 1.74770 / 0.85 ( 20) hydrogen bonds : bond 0.19585 / 12.93 ( 81) hydrogen bonds : angle 11.15127 / 7.72 ( 219) link_BETA1-4 : bond 0.01635 / 0.81 ( 3) link_BETA1-4 : angle 3.94376 / 2.79 ( 9) link_NAG-ASN : bond 0.00250 / 0.13 ( 4) link_NAG-ASN : angle 6.08140 / 3.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 516 VAL cc_start: 0.8904 (m) cc_final: 0.8658 (t) REVERT: A 625 THR cc_start: 0.6936 (p) cc_final: 0.5194 (p) REVERT: A 627 PHE cc_start: 0.6985 (m-10) cc_final: 0.6486 (m-10) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0421 time to fit residues: 3.0254 Evaluate side-chains 46 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 16 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 ASN ** H 6 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 = 0.4855 r_free = 0.4855 target = 0.259204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.224365 restraints weight = 3813.239| |-----------------------------------------------------------------------------| r_work (start): 0.4611 rms_B_bonded: 2.54 r_work: 0.4415 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 3465 Z= 0.166 Angle : 0.761 10.433 4742 Z= 0.364 Chirality : 0.048 0.180 518 Planarity : 0.006 0.036 595 Dihedral : 7.061 50.963 604 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.56 % Allowed : 8.76 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.00 (0.42), residues: 415 helix: 0.60 (1.88), residues: 12 sheet: -1.65 (0.50), residues: 107 loop : -1.33 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 639 TYR 0.021 0.002 TYR L 50 PHE 0.026 0.002 PHE A 509 TRP 0.013 0.001 TRP A 616 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 3448) covalent geometry : angle 0.70499 / 0.35 ( 4701) SS BOND : bond 0.00299 / 0.18 ( 10) SS BOND : angle 1.13306 / 0.83 ( 20) hydrogen bonds : bond 0.03757 / 2.43 ( 81) hydrogen bonds : angle 8.77411 / 6.51 ( 219) link_BETA1-4 : bond 0.01262 / 0.63 ( 3) link_BETA1-4 : angle 3.10588 / 2.07 ( 9) link_NAG-ASN : bond 0.00505 / 0.26 ( 4) link_NAG-ASN : angle 4.95254 / 2.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 SER cc_start: 0.6869 (m) cc_final: 0.6467 (p) REVERT: A 625 THR cc_start: 0.6947 (p) cc_final: 0.5550 (p) REVERT: A 627 PHE cc_start: 0.7162 (m-10) cc_final: 0.6684 (m-10) REVERT: H 5 VAL cc_start: 0.7799 (t) cc_final: 0.7449 (m) outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 0.0627 time to fit residues: 4.0841 Evaluate side-chains 50 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.253135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.217565 restraints weight = 3766.210| |-----------------------------------------------------------------------------| r_work (start): 0.4570 rms_B_bonded: 2.55 r_work: 0.4401 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 3465 Z= 0.178 Angle : 0.723 9.158 4742 Z= 0.348 Chirality : 0.047 0.142 518 Planarity : 0.006 0.037 595 Dihedral : 6.870 52.371 604 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.13 % Allowed : 10.17 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.15 (0.41), residues: 415 helix: -0.42 (1.36), residues: 18 sheet: -1.82 (0.49), residues: 108 loop : -1.37 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 606 TYR 0.018 0.002 TYR A 611 PHE 0.018 0.002 PHE A 509 TRP 0.013 0.001 TRP A 616 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 3448) covalent geometry : angle 0.68179 / 0.34 ( 4701) SS BOND : bond 0.00304 / 0.17 ( 10) SS BOND : angle 0.97519 / 0.80 ( 20) hydrogen bonds : bond 0.04016 / 2.63 ( 81) hydrogen bonds : angle 8.33115 / 6.26 ( 219) link_BETA1-4 : bond 0.01160 / 0.57 ( 3) link_BETA1-4 : angle 2.72290 / 1.80 ( 9) link_NAG-ASN : bond 0.00407 / 0.21 ( 4) link_NAG-ASN : angle 4.15262 / 2.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 625 THR cc_start: 0.7258 (p) cc_final: 0.5973 (p) REVERT: A 627 PHE cc_start: 0.7241 (m-10) cc_final: 0.6767 (m-10) REVERT: L 48 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8493 (mp) outliers start: 4 outliers final: 1 residues processed: 46 average time/residue: 0.0669 time to fit residues: 3.8955 Evaluate side-chains 43 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 0.0060 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 ASN H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.253008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.217171 restraints weight = 3710.636| |-----------------------------------------------------------------------------| r_work (start): 0.4544 rms_B_bonded: 2.53 r_work: 0.4349 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3465 Z= 0.166 Angle : 0.701 8.218 4742 Z= 0.334 Chirality : 0.045 0.124 518 Planarity : 0.005 0.041 595 Dihedral : 6.898 52.745 604 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.11 % Allowed : 9.60 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -2.03 (0.41), residues: 415 helix: -0.24 (1.40), residues: 18 sheet: -1.70 (0.50), residues: 108 loop : -1.32 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 606 TYR 0.016 0.002 TYR L 50 PHE 0.015 0.001 PHE A 509 TRP 0.011 0.001 TRP A 616 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 3448) covalent geometry : angle 0.66427 / 0.33 ( 4701) SS BOND : bond 0.00289 / 0.15 ( 10) SS BOND : angle 0.95013 / 0.76 ( 20) hydrogen bonds : bond 0.03577 / 2.39 ( 81) hydrogen bonds : angle 8.06221 / 6.09 ( 219) link_BETA1-4 : bond 0.01089 / 0.54 ( 3) link_BETA1-4 : angle 2.59068 / 1.73 ( 9) link_NAG-ASN : bond 0.00348 / 0.18 ( 4) link_NAG-ASN : angle 3.84277 / 2.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 550 PHE cc_start: 0.7660 (m-80) cc_final: 0.7318 (m-10) REVERT: A 594 TYR cc_start: 0.6495 (t80) cc_final: 0.5678 (t80) REVERT: A 625 THR cc_start: 0.7321 (p) cc_final: 0.6551 (p) REVERT: A 627 PHE cc_start: 0.7243 (m-10) cc_final: 0.6875 (m-10) REVERT: H 5 VAL cc_start: 0.7825 (t) cc_final: 0.7586 (m) REVERT: L 48 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8478 (mp) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.0643 time to fit residues: 4.0954 Evaluate side-chains 51 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.252487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.216609 restraints weight = 3720.708| |-----------------------------------------------------------------------------| r_work (start): 0.4542 rms_B_bonded: 2.52 r_work: 0.4345 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3465 Z= 0.161 Angle : 0.689 8.305 4742 Z= 0.329 Chirality : 0.045 0.128 518 Planarity : 0.005 0.043 595 Dihedral : 6.861 53.122 604 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.11 % Allowed : 9.89 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -2.02 (0.41), residues: 415 helix: -0.07 (1.43), residues: 18 sheet: -1.74 (0.49), residues: 108 loop : -1.30 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 606 TYR 0.018 0.002 TYR L 50 PHE 0.015 0.001 PHE A 509 TRP 0.011 0.001 TRP A 487 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 3448) covalent geometry : angle 0.65541 / 0.32 ( 4701) SS BOND : bond 0.00269 / 0.13 ( 10) SS BOND : angle 0.95759 / 0.81 ( 20) hydrogen bonds : bond 0.03636 / 2.41 ( 81) hydrogen bonds : angle 7.95424 / 6.02 ( 219) link_BETA1-4 : bond 0.01047 / 0.52 ( 3) link_BETA1-4 : angle 2.50462 / 1.68 ( 9) link_NAG-ASN : bond 0.00307 / 0.16 ( 4) link_NAG-ASN : angle 3.63559 / 2.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 625 THR cc_start: 0.7329 (p) cc_final: 0.6656 (p) REVERT: A 627 PHE cc_start: 0.7246 (m-10) cc_final: 0.6964 (m-10) REVERT: H 5 VAL cc_start: 0.7810 (t) cc_final: 0.7605 (m) REVERT: L 48 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8489 (mp) outliers start: 11 outliers final: 9 residues processed: 50 average time/residue: 0.0643 time to fit residues: 4.0880 Evaluate side-chains 53 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 30 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.4814 r_free = 0.4814 target = 0.254017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.216777 restraints weight = 3722.520| |-----------------------------------------------------------------------------| r_work (start): 0.4541 rms_B_bonded: 2.64 r_work: 0.4341 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3465 Z= 0.148 Angle : 0.679 8.257 4742 Z= 0.324 Chirality : 0.044 0.127 518 Planarity : 0.006 0.050 595 Dihedral : 6.818 53.355 604 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.82 % Allowed : 11.58 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -1.98 (0.41), residues: 415 helix: 0.01 (1.45), residues: 18 sheet: -1.73 (0.50), residues: 108 loop : -1.27 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 606 TYR 0.017 0.002 TYR L 50 PHE 0.027 0.002 PHE A 550 TRP 0.012 0.001 TRP A 487 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 3448) covalent geometry : angle 0.64836 / 0.32 ( 4701) SS BOND : bond 0.00242 / 0.11 ( 10) SS BOND : angle 0.87383 / 0.75 ( 20) hydrogen bonds : bond 0.03532 / 2.35 ( 81) hydrogen bonds : angle 7.84980 / 5.94 ( 219) link_BETA1-4 : bond 0.01016 / 0.50 ( 3) link_BETA1-4 : angle 2.42375 / 1.64 ( 9) link_NAG-ASN : bond 0.00278 / 0.14 ( 4) link_NAG-ASN : angle 3.47577 / 1.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 625 THR cc_start: 0.7305 (p) cc_final: 0.6634 (p) REVERT: A 627 PHE cc_start: 0.7228 (m-10) cc_final: 0.6950 (m-10) REVERT: L 48 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8454 (mp) outliers start: 10 outliers final: 8 residues processed: 45 average time/residue: 0.0738 time to fit residues: 4.1529 Evaluate side-chains 49 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.251681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.214592 restraints weight = 3827.558| |-----------------------------------------------------------------------------| r_work (start): 0.4519 rms_B_bonded: 2.60 r_work: 0.4318 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3465 Z= 0.162 Angle : 0.681 7.794 4742 Z= 0.329 Chirality : 0.045 0.127 518 Planarity : 0.006 0.046 595 Dihedral : 6.808 53.893 604 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.39 % Allowed : 11.02 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -1.94 (0.41), residues: 415 helix: 0.02 (1.45), residues: 18 sheet: -1.81 (0.49), residues: 108 loop : -1.19 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 606 TYR 0.018 0.002 TYR L 50 PHE 0.018 0.002 PHE A 550 TRP 0.015 0.001 TRP A 487 HIS 0.003 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 3448) covalent geometry : angle 0.65235 / 0.32 ( 4701) SS BOND : bond 0.00254 / 0.13 ( 10) SS BOND : angle 0.86465 / 0.75 ( 20) hydrogen bonds : bond 0.03624 / 2.44 ( 81) hydrogen bonds : angle 7.72371 / 5.88 ( 219) link_BETA1-4 : bond 0.01010 / 0.50 ( 3) link_BETA1-4 : angle 2.33414 / 1.58 ( 9) link_NAG-ASN : bond 0.00291 / 0.15 ( 4) link_NAG-ASN : angle 3.37527 / 1.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 625 THR cc_start: 0.7438 (p) cc_final: 0.6811 (p) REVERT: A 627 PHE cc_start: 0.7301 (m-10) cc_final: 0.7019 (m-10) REVERT: L 48 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8482 (mp) outliers start: 12 outliers final: 10 residues processed: 47 average time/residue: 0.0589 time to fit residues: 3.6348 Evaluate side-chains 51 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 0.0050 chunk 4 optimal weight: 0.3980 chunk 5 optimal weight: 0.0670 chunk 8 optimal weight: 0.0030 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 0.2142 ------------------------------------------------------------------------------- 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 = 0.4819 r_free = 0.4819 target = 0.255216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.218789 restraints weight = 3820.056| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 2.60 r_work: 0.4358 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3465 Z= 0.125 Angle : 0.660 7.423 4742 Z= 0.316 Chirality : 0.044 0.127 518 Planarity : 0.005 0.047 595 Dihedral : 6.712 53.666 604 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.11 % Allowed : 10.73 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -1.90 (0.41), residues: 415 helix: -0.05 (1.43), residues: 18 sheet: -1.74 (0.49), residues: 108 loop : -1.17 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 606 TYR 0.019 0.002 TYR L 50 PHE 0.013 0.001 PHE A 550 TRP 0.016 0.001 TRP A 487 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 ( 3448) covalent geometry : angle 0.63339 / 0.31 ( 4701) SS BOND : bond 0.00199 / 0.09 ( 10) SS BOND : angle 0.78596 / 0.68 ( 20) hydrogen bonds : bond 0.03294 / 2.20 ( 81) hydrogen bonds : angle 7.54738 / 5.75 ( 219) link_BETA1-4 : bond 0.00973 / 0.48 ( 3) link_BETA1-4 : angle 2.19856 / 1.51 ( 9) link_NAG-ASN : bond 0.00230 / 0.12 ( 4) link_NAG-ASN : angle 3.23900 / 1.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: A 625 THR cc_start: 0.7328 (p) cc_final: 0.6726 (p) REVERT: A 627 PHE cc_start: 0.7229 (m-10) cc_final: 0.7007 (m-10) REVERT: H 43 GLN cc_start: 0.5782 (pm20) cc_final: 0.5521 (pm20) outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 0.0390 time to fit residues: 2.4966 Evaluate side-chains 48 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 13 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 38 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 589 HIS ** 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 = 0.4792 r_free = 0.4792 target = 0.251651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.214952 restraints weight = 3781.669| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 2.56 r_work: 0.4328 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3465 Z= 0.168 Angle : 0.692 8.115 4742 Z= 0.334 Chirality : 0.044 0.131 518 Planarity : 0.006 0.044 595 Dihedral : 6.752 54.289 604 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.82 % Allowed : 12.43 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -1.89 (0.41), residues: 415 helix: 0.06 (1.45), residues: 18 sheet: -1.74 (0.50), residues: 108 loop : -1.17 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 606 TYR 0.017 0.002 TYR L 50 PHE 0.016 0.002 PHE A 550 TRP 0.017 0.001 TRP A 487 HIS 0.004 0.001 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 3448) covalent geometry : angle 0.66609 / 0.33 ( 4701) SS BOND : bond 0.00264 / 0.13 ( 10) SS BOND : angle 0.88605 / 0.75 ( 20) hydrogen bonds : bond 0.03634 / 2.44 ( 81) hydrogen bonds : angle 7.56934 / 5.78 ( 219) link_BETA1-4 : bond 0.00945 / 0.47 ( 3) link_BETA1-4 : angle 2.19270 / 1.49 ( 9) link_NAG-ASN : bond 0.00271 / 0.14 ( 4) link_NAG-ASN : angle 3.20528 / 1.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: A 625 THR cc_start: 0.7452 (p) cc_final: 0.6861 (p) REVERT: A 627 PHE cc_start: 0.7286 (m-10) cc_final: 0.7033 (m-10) REVERT: L 48 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8487 (mp) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.0363 time to fit residues: 2.2408 Evaluate side-chains 50 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 589 HIS ** 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 = 0.4789 r_free = 0.4789 target = 0.251077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.214221 restraints weight = 3774.579| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 2.57 r_work: 0.4322 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3465 Z= 0.169 Angle : 0.692 8.043 4742 Z= 0.333 Chirality : 0.045 0.135 518 Planarity : 0.006 0.045 595 Dihedral : 6.765 54.291 604 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.54 % Allowed : 12.99 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -1.89 (0.41), residues: 415 helix: 0.16 (1.48), residues: 18 sheet: -1.78 (0.50), residues: 108 loop : -1.16 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 606 TYR 0.018 0.002 TYR L 50 PHE 0.014 0.002 PHE A 550 TRP 0.017 0.001 TRP A 487 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 3448) covalent geometry : angle 0.66705 / 0.33 ( 4701) SS BOND : bond 0.00269 / 0.13 ( 10) SS BOND : angle 0.88793 / 0.76 ( 20) hydrogen bonds : bond 0.03644 / 2.43 ( 81) hydrogen bonds : angle 7.58341 / 5.79 ( 219) link_BETA1-4 : bond 0.00939 / 0.46 ( 3) link_BETA1-4 : angle 2.15560 / 1.47 ( 9) link_NAG-ASN : bond 0.00252 / 0.13 ( 4) link_NAG-ASN : angle 3.17014 / 1.81 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 625 THR cc_start: 0.7484 (p) cc_final: 0.6903 (p) REVERT: A 627 PHE cc_start: 0.7330 (m-10) cc_final: 0.7061 (m-10) REVERT: H 43 GLN cc_start: 0.5807 (pm20) cc_final: 0.5566 (pm20) REVERT: L 48 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8471 (mp) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.0621 time to fit residues: 3.7849 Evaluate side-chains 51 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 589 HIS ** 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 = 0.4754 r_free = 0.4754 target = 0.246736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.209733 restraints weight = 3821.968| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 2.57 r_work: 0.4283 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 3465 Z= 0.196 Angle : 0.717 8.479 4742 Z= 0.347 Chirality : 0.045 0.138 518 Planarity : 0.006 0.044 595 Dihedral : 6.879 54.680 604 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.54 % Allowed : 13.56 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -1.91 (0.41), residues: 415 helix: 0.29 (1.49), residues: 18 sheet: -1.76 (0.51), residues: 102 loop : -1.22 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 606 TYR 0.019 0.002 TYR L 50 PHE 0.015 0.002 PHE A 550 TRP 0.017 0.002 TRP A 487 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 3448) covalent geometry : angle 0.69305 / 0.34 ( 4701) SS BOND : bond 0.00341 / 0.17 ( 10) SS BOND : angle 0.98042 / 0.83 ( 20) hydrogen bonds : bond 0.03981 / 2.67 ( 81) hydrogen bonds : angle 7.74999 / 5.93 ( 219) link_BETA1-4 : bond 0.00929 / 0.46 ( 3) link_BETA1-4 : angle 2.12316 / 1.46 ( 9) link_NAG-ASN : bond 0.00252 / 0.13 ( 4) link_NAG-ASN : angle 3.16942 / 1.80 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1013.15 seconds wall clock time: 18 minutes 11.12 seconds (1091.12 seconds total)