Starting phenix.real_space_refine on Thu Jul 2 01:22:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iv5_35741/07_2026/8iv5_35741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv5_35741/07_2026/8iv5_35741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iv5_35741/07_2026/8iv5_35741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv5_35741/07_2026/8iv5_35741.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8iv5_35741/07_2026/8iv5_35741.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iv5_35741/07_2026/8iv5_35741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iv5_35741/07_2026/8iv5_35741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv5_35741/07_2026/8iv5_35741.map" } resolution = 3.77 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= 0.011 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 29 5.16 5 C 3221 2.51 5 N 857 2.21 5 O 989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5096 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 921 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "B" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "A" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} 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 chiralities: 3 Time building chain proxies: 1.19, per 1000 atoms: 0.23 Number of scatterers: 5096 At special positions: 0 Unit cell: (113.588, 73.132, 79.356, 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 29 16.00 O 989 8.00 N 857 7.00 C 3221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 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 C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN G 343 " Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 185.1 milliseconds 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 14 sheets defined 6.5% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'G' and resid 337 through 343 removed outlier: 3.832A pdb=" N VAL G 341 " --> pdb=" O PRO G 337 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE G 342 " --> pdb=" O PHE G 338 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN G 343 " --> pdb=" O GLY G 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 337 through 343' Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 403 through 407 removed outlier: 3.516A pdb=" N GLU G 406 " --> pdb=" O ARG G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 506 removed outlier: 3.520A pdb=" N GLN G 506 " --> pdb=" O VAL G 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.599A pdb=" N ASP B 82 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 83 " --> pdb=" O THR B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.028A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.812A pdb=" N ARG A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'G' and resid 354 through 358 removed outlier: 3.857A pdb=" N ASN G 354 " --> pdb=" O SER G 399 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER G 399 " --> pdb=" O ASN G 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA5, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.999A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.666A pdb=" N TYR L 49 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.614A pdb=" N VAL H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N MET H 34 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.519A pdb=" N MET H 85 " --> pdb=" O MET H 18 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER H 80 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP H 75 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.613A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B 72 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.905A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.963A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.727A pdb=" N GLU A 10 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 37 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.617A pdb=" N VAL A 18 " --> pdb=" O ILE A 83 " (cutoff:3.500A) 113 hydrogen bonds defined for protein. 264 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: 0.65 Time building geometry restraints manager: 0.54 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: 1619 1.34 - 1.46: 1311 1.46 - 1.58: 2252 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 5221 Sorted by residual: bond pdb=" C GLN G 506 " pdb=" N PRO G 507 " ideal model delta sigma weight residual 1.333 1.356 -0.022 1.01e-02 9.80e+03 4.88e+00 bond pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sigma weight residual 1.417 1.451 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" N ASN B 31 " pdb=" CA ASN B 31 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.25e+00 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.453 0.045 3.10e-02 1.04e+03 2.07e+00 bond pdb=" CA VAL H 48 " pdb=" CB VAL H 48 " ideal model delta sigma weight residual 1.545 1.532 0.013 9.10e-03 1.21e+04 1.94e+00 ... (remaining 5216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 6832 2.18 - 4.36: 225 4.36 - 6.55: 21 6.55 - 8.73: 2 8.73 - 10.91: 2 Bond angle restraints: 7082 Sorted by residual: angle pdb=" C SER B 40 " pdb=" N HIS B 41 " pdb=" CA HIS B 41 " ideal model delta sigma weight residual 122.82 128.23 -5.41 1.42e+00 4.96e-01 1.45e+01 angle pdb=" N GLY G 404 " pdb=" CA GLY G 404 " pdb=" C GLY G 404 " ideal model delta sigma weight residual 112.49 116.54 -4.05 1.21e+00 6.83e-01 1.12e+01 angle pdb=" C SER L 76 " pdb=" N ASN L 77 " pdb=" CA ASN L 77 " ideal model delta sigma weight residual 122.82 127.52 -4.70 1.42e+00 4.96e-01 1.10e+01 angle pdb=" C SER B 30 " pdb=" N ASN B 31 " pdb=" CA ASN B 31 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.86e+00 angle pdb=" C GLY A 66 " pdb=" N ARG A 67 " pdb=" CA ARG A 67 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.56e+00 ... (remaining 7077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 2653 15.62 - 31.25: 303 31.25 - 46.87: 65 46.87 - 62.49: 16 62.49 - 78.12: 4 Dihedral angle restraints: 3041 sinusoidal: 1190 harmonic: 1851 Sorted by residual: dihedral pdb=" CB CYS G 480 " pdb=" SG CYS G 480 " pdb=" SG CYS G 488 " pdb=" CB CYS G 488 " ideal model delta sinusoidal sigma weight residual -86.00 -133.64 47.64 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CA CYS G 480 " pdb=" C CYS G 480 " pdb=" N ASN G 481 " pdb=" CA ASN G 481 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA TYR A 60 " pdb=" C TYR A 60 " pdb=" N ASN A 61 " pdb=" CA ASN A 61 " ideal model delta harmonic sigma weight residual 180.00 155.27 24.73 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 3038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 563 0.057 - 0.113: 155 0.113 - 0.170: 39 0.170 - 0.227: 6 0.227 - 0.284: 1 Chirality restraints: 764 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA TYR L 94 " pdb=" N TYR L 94 " pdb=" C TYR L 94 " pdb=" CB TYR L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 761 not shown) Planarity restraints: 911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 94 " -0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO L 95 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 462 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO G 463 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 463 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 463 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO L 59 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.030 5.00e-02 4.00e+02 ... (remaining 908 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1629 2.82 - 3.34: 4043 3.34 - 3.86: 7954 3.86 - 4.38: 8799 4.38 - 4.90: 15817 Nonbonded interactions: 38242 Sorted by model distance: nonbonded pdb=" OD2 ASP G 398 " pdb=" OH TYR G 423 " model vdw 2.297 3.040 nonbonded pdb=" O SER B 91 " pdb=" OG SER B 91 " model vdw 2.307 3.040 nonbonded pdb=" OD1 ASP A 90 " pdb=" OH TYR A 94 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR G 345 " pdb=" O ASN B 92 " model vdw 2.327 3.040 nonbonded pdb=" OG SER B 63 " pdb=" OG SER B 74 " model vdw 2.332 3.040 ... (remaining 38237 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=0.83 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: 18.080 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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 : 0.007 0.068 5231 Z= 0.310 Angle : 0.893 10.910 7105 Z= 0.497 Chirality : 0.057 0.284 764 Planarity : 0.007 0.066 910 Dihedral : 13.898 78.115 1844 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.91 % Allowed : 9.80 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -3.73 (0.29), residues: 635 helix: -5.19 (0.23), residues: 20 sheet: -2.11 (0.31), residues: 238 loop : -2.64 (0.27), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 355 TYR 0.022 0.003 TYR L 49 PHE 0.020 0.002 PHE B 62 TRP 0.026 0.002 TRP G 436 HIS 0.003 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.31 ( 5221) covalent geometry : angle 0.87767 / 0.49 ( 7082) SS BOND : bond 0.00394 / 0.20 ( 7) SS BOND : angle 1.32590 / 0.80 ( 14) hydrogen bonds : bond 0.30574 / 20.48 ( 113) hydrogen bonds : angle 11.11698 / 7.91 ( 264) link_BETA1-4 : bond 0.00994 / 0.52 ( 2) link_BETA1-4 : angle 2.39677 / 1.36 ( 6) link_NAG-ASN : bond 0.00513 / 0.27 ( 1) link_NAG-ASN : angle 7.25245 / 3.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 466 ARG cc_start: 0.6802 (ptm160) cc_final: 0.5969 (ptm160) REVERT: G 472 ILE cc_start: 0.7949 (mm) cc_final: 0.7591 (mm) REVERT: G 493 GLN cc_start: 0.7198 (tt0) cc_final: 0.6725 (tm-30) REVERT: L 4 MET cc_start: 0.8176 (mmm) cc_final: 0.7958 (mmp) REVERT: L 19 VAL cc_start: 0.8552 (p) cc_final: 0.8208 (t) REVERT: L 26 SER cc_start: 0.7613 (m) cc_final: 0.7169 (m) REVERT: L 102 THR cc_start: 0.8308 (m) cc_final: 0.8091 (m) REVERT: H 35 ASP cc_start: 0.7719 (m-30) cc_final: 0.6548 (m-30) REVERT: H 50 GLN cc_start: 0.7769 (tt0) cc_final: 0.6865 (tt0) REVERT: H 54 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7885 (tptt) REVERT: H 73 SER cc_start: 0.7672 (m) cc_final: 0.7459 (p) REVERT: B 40 SER cc_start: 0.7934 (t) cc_final: 0.7720 (t) REVERT: B 61 ARG cc_start: 0.6137 (ptt-90) cc_final: 0.5591 (ptt-90) REVERT: B 70 ASP cc_start: 0.7105 (m-30) cc_final: 0.6342 (m-30) REVERT: B 105 GLU cc_start: 0.7443 (pt0) cc_final: 0.7240 (pt0) REVERT: A 10 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7311 (mm-30) REVERT: A 19 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7351 (tttp) REVERT: A 62 ASP cc_start: 0.7672 (m-30) cc_final: 0.7434 (m-30) REVERT: A 65 ARG cc_start: 0.7007 (ttp-110) cc_final: 0.6655 (mtm110) REVERT: A 87 LYS cc_start: 0.7568 (mttt) cc_final: 0.7239 (mtmt) outliers start: 5 outliers final: 5 residues processed: 158 average time/residue: 0.0907 time to fit residues: 17.6877 Evaluate side-chains 138 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain H residue 115 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 370 ASN ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 ASN G 460 ASN L 8 GLN L 37 GLN L 38 GLN L 77 ASN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN A 39 GLN A 52 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.102591 restraints weight = 7939.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.104905 restraints weight = 5394.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.106689 restraints weight = 4115.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107962 restraints weight = 3360.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108822 restraints weight = 2872.725| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5231 Z= 0.186 Angle : 0.619 6.845 7105 Z= 0.330 Chirality : 0.045 0.152 764 Planarity : 0.005 0.054 910 Dihedral : 6.246 32.691 712 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.27 % Allowed : 18.15 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -3.29 (0.31), residues: 635 helix: -4.74 (0.43), residues: 26 sheet: -1.80 (0.32), residues: 254 loop : -2.29 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.022 0.002 TYR L 49 PHE 0.016 0.001 PHE B 62 TRP 0.021 0.001 TRP G 436 HIS 0.003 0.001 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 ( 5221) covalent geometry : angle 0.60984 / 0.33 ( 7082) SS BOND : bond 0.00271 / 0.13 ( 7) SS BOND : angle 0.80015 / 0.52 ( 14) hydrogen bonds : bond 0.04461 / 3.02 ( 113) hydrogen bonds : angle 7.54084 / 5.26 ( 264) link_BETA1-4 : bond 0.00536 / 0.26 ( 2) link_BETA1-4 : angle 1.65405 / 0.98 ( 6) link_NAG-ASN : bond 0.00297 / 0.16 ( 1) link_NAG-ASN : angle 4.65596 / 2.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 417 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7834 (tttp) REVERT: G 466 ARG cc_start: 0.8388 (ptm160) cc_final: 0.7907 (ptm160) REVERT: G 472 ILE cc_start: 0.9240 (mm) cc_final: 0.9040 (mm) REVERT: G 511 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8930 (t) REVERT: L 104 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6475 (tt) REVERT: B 61 ARG cc_start: 0.8251 (ptt-90) cc_final: 0.7899 (ptt90) REVERT: A 65 ARG cc_start: 0.7550 (ttp-110) cc_final: 0.7151 (mtm110) outliers start: 18 outliers final: 14 residues processed: 151 average time/residue: 0.0875 time to fit residues: 16.4404 Evaluate side-chains 145 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 417 LYS Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 0.0470 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 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 = 0.3295 r_free = 0.3295 target = 0.119211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.100722 restraints weight = 7995.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.103295 restraints weight = 5259.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.105129 restraints weight = 3937.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.106440 restraints weight = 3176.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.107302 restraints weight = 2703.182| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5231 Z= 0.160 Angle : 0.593 6.183 7105 Z= 0.311 Chirality : 0.044 0.155 764 Planarity : 0.004 0.047 910 Dihedral : 5.684 30.766 709 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.81 % Allowed : 19.24 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -3.02 (0.31), residues: 635 helix: -4.34 (0.60), residues: 26 sheet: -1.50 (0.32), residues: 249 loop : -2.22 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 355 TYR 0.021 0.002 TYR A 80 PHE 0.013 0.001 PHE B 62 TRP 0.019 0.001 TRP G 436 HIS 0.002 0.001 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 5221) covalent geometry : angle 0.58578 / 0.31 ( 7082) SS BOND : bond 0.00309 / 0.18 ( 7) SS BOND : angle 0.66506 / 0.44 ( 14) hydrogen bonds : bond 0.03692 / 2.50 ( 113) hydrogen bonds : angle 6.75512 / 4.69 ( 264) link_BETA1-4 : bond 0.00498 / 0.25 ( 2) link_BETA1-4 : angle 1.36808 / 0.82 ( 6) link_NAG-ASN : bond 0.00317 / 0.17 ( 1) link_NAG-ASN : angle 4.00771 / 1.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 466 ARG cc_start: 0.8380 (ptm160) cc_final: 0.7765 (ptm160) REVERT: G 472 ILE cc_start: 0.9241 (mm) cc_final: 0.9017 (mm) REVERT: G 481 ASN cc_start: 0.7605 (t0) cc_final: 0.7396 (t0) REVERT: L 104 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6289 (tt) REVERT: B 61 ARG cc_start: 0.8178 (ptt-90) cc_final: 0.7791 (ptt90) REVERT: A 65 ARG cc_start: 0.7512 (ttp-110) cc_final: 0.7178 (mtp85) outliers start: 32 outliers final: 20 residues processed: 150 average time/residue: 0.0774 time to fit residues: 14.7829 Evaluate side-chains 148 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 0.0060 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 chunk 8 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 HIS ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 34 HIS ** 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 = 0.3316 r_free = 0.3316 target = 0.120828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.102801 restraints weight = 8014.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.105297 restraints weight = 5363.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106968 restraints weight = 4035.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.108296 restraints weight = 3287.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.109197 restraints weight = 2804.056| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5231 Z= 0.115 Angle : 0.554 6.529 7105 Z= 0.290 Chirality : 0.043 0.146 764 Planarity : 0.004 0.046 910 Dihedral : 5.244 28.089 709 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.90 % Allowed : 21.23 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.80 (0.31), residues: 635 helix: -4.16 (0.69), residues: 26 sheet: -1.36 (0.32), residues: 249 loop : -2.06 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 408 TYR 0.018 0.001 TYR A 80 PHE 0.017 0.001 PHE L 62 TRP 0.016 0.001 TRP G 436 HIS 0.002 0.000 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 5221) covalent geometry : angle 0.54819 / 0.29 ( 7082) SS BOND : bond 0.00541 / 0.29 ( 7) SS BOND : angle 0.79378 / 0.45 ( 14) hydrogen bonds : bond 0.03082 / 2.07 ( 113) hydrogen bonds : angle 6.19862 / 4.30 ( 264) link_BETA1-4 : bond 0.00439 / 0.22 ( 2) link_BETA1-4 : angle 1.49235 / 0.84 ( 6) link_NAG-ASN : bond 0.00319 / 0.17 ( 1) link_NAG-ASN : angle 3.35441 / 1.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 466 ARG cc_start: 0.8389 (ptm160) cc_final: 0.7822 (ptm160) REVERT: G 472 ILE cc_start: 0.9246 (mm) cc_final: 0.9039 (mm) REVERT: B 61 ARG cc_start: 0.8160 (ptt-90) cc_final: 0.7762 (ptt90) REVERT: B 90 GLN cc_start: 0.9215 (pp30) cc_final: 0.8970 (pp30) REVERT: A 80 TYR cc_start: 0.8435 (m-10) cc_final: 0.8110 (m-10) outliers start: 27 outliers final: 21 residues processed: 150 average time/residue: 0.0703 time to fit residues: 13.7131 Evaluate side-chains 148 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 0.0670 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.103067 restraints weight = 8117.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.105610 restraints weight = 5440.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.107382 restraints weight = 4100.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.108583 restraints weight = 3331.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109592 restraints weight = 2856.090| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5231 Z= 0.118 Angle : 0.556 6.336 7105 Z= 0.288 Chirality : 0.043 0.151 764 Planarity : 0.004 0.047 910 Dihedral : 5.078 26.490 709 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.72 % Allowed : 21.78 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.60 (0.32), residues: 635 helix: -4.07 (0.73), residues: 26 sheet: -1.13 (0.32), residues: 246 loop : -2.00 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 65 TYR 0.016 0.001 TYR G 449 PHE 0.010 0.001 PHE H 108 TRP 0.015 0.001 TRP G 436 HIS 0.001 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5221) covalent geometry : angle 0.54981 / 0.29 ( 7082) SS BOND : bond 0.00258 / 0.13 ( 7) SS BOND : angle 0.83520 / 0.47 ( 14) hydrogen bonds : bond 0.03090 / 2.13 ( 113) hydrogen bonds : angle 6.13576 / 4.25 ( 264) link_BETA1-4 : bond 0.00488 / 0.25 ( 2) link_BETA1-4 : angle 1.36741 / 0.76 ( 6) link_NAG-ASN : bond 0.00321 / 0.17 ( 1) link_NAG-ASN : angle 3.34546 / 1.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 466 ARG cc_start: 0.8392 (ptm160) cc_final: 0.7829 (ptm160) REVERT: G 472 ILE cc_start: 0.9249 (mm) cc_final: 0.9028 (mm) REVERT: L 107 LYS cc_start: 0.6349 (mtmm) cc_final: 0.5338 (mmtt) REVERT: B 61 ARG cc_start: 0.8148 (ptt-90) cc_final: 0.7703 (ptt90) REVERT: B 90 GLN cc_start: 0.9178 (pp30) cc_final: 0.8965 (pp30) outliers start: 26 outliers final: 22 residues processed: 142 average time/residue: 0.0688 time to fit residues: 12.6359 Evaluate side-chains 150 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.119589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.101483 restraints weight = 8136.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.103954 restraints weight = 5500.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.105674 restraints weight = 4165.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.106826 restraints weight = 3392.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.107760 restraints weight = 2924.231| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5231 Z= 0.174 Angle : 0.577 5.788 7105 Z= 0.299 Chirality : 0.043 0.152 764 Planarity : 0.004 0.050 910 Dihedral : 5.153 26.699 709 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.63 % Allowed : 22.87 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.49 (0.32), residues: 635 helix: -4.07 (0.72), residues: 26 sheet: -1.05 (0.31), residues: 260 loop : -1.94 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 65 TYR 0.017 0.002 TYR L 49 PHE 0.013 0.001 PHE B 62 TRP 0.010 0.001 TRP A 104 HIS 0.002 0.001 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 5221) covalent geometry : angle 0.56977 / 0.30 ( 7082) SS BOND : bond 0.00517 / 0.28 ( 7) SS BOND : angle 0.93013 / 0.53 ( 14) hydrogen bonds : bond 0.03233 / 2.21 ( 113) hydrogen bonds : angle 6.05607 / 4.21 ( 264) link_BETA1-4 : bond 0.00309 / 0.15 ( 2) link_BETA1-4 : angle 1.28859 / 0.74 ( 6) link_NAG-ASN : bond 0.00188 / 0.10 ( 1) link_NAG-ASN : angle 3.85604 / 1.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.176 Fit side-chains REVERT: G 466 ARG cc_start: 0.8432 (ptm160) cc_final: 0.7841 (ptm160) REVERT: G 472 ILE cc_start: 0.9250 (mm) cc_final: 0.9017 (mm) REVERT: L 107 LYS cc_start: 0.6488 (mtmm) cc_final: 0.5487 (mmtt) REVERT: B 61 ARG cc_start: 0.8229 (ptt-90) cc_final: 0.7657 (ptt-90) REVERT: A 65 ARG cc_start: 0.8487 (tpp80) cc_final: 0.7932 (ttm-80) outliers start: 31 outliers final: 24 residues processed: 147 average time/residue: 0.0741 time to fit residues: 13.9628 Evaluate side-chains 150 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.103709 restraints weight = 7891.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.106050 restraints weight = 5333.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.107870 restraints weight = 4051.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.109001 restraints weight = 3281.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.109987 restraints weight = 2811.738| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5231 Z= 0.154 Angle : 0.590 6.835 7105 Z= 0.306 Chirality : 0.044 0.151 764 Planarity : 0.004 0.049 910 Dihedral : 5.101 26.229 709 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.63 % Allowed : 23.23 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.37 (0.32), residues: 635 helix: -4.01 (0.73), residues: 26 sheet: -1.06 (0.31), residues: 261 loop : -1.78 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 355 TYR 0.020 0.001 TYR G 453 PHE 0.033 0.002 PHE H 70 TRP 0.012 0.001 TRP G 436 HIS 0.002 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 5221) covalent geometry : angle 0.58352 / 0.30 ( 7082) SS BOND : bond 0.00299 / 0.16 ( 7) SS BOND : angle 0.87952 / 0.49 ( 14) hydrogen bonds : bond 0.03145 / 2.17 ( 113) hydrogen bonds : angle 5.95584 / 4.13 ( 264) link_BETA1-4 : bond 0.00361 / 0.18 ( 2) link_BETA1-4 : angle 1.30512 / 0.74 ( 6) link_NAG-ASN : bond 0.00224 / 0.12 ( 1) link_NAG-ASN : angle 3.60971 / 1.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: G 466 ARG cc_start: 0.8437 (ptm160) cc_final: 0.7881 (ptm160) REVERT: G 472 ILE cc_start: 0.9246 (mm) cc_final: 0.9027 (mm) REVERT: L 107 LYS cc_start: 0.6480 (mtmm) cc_final: 0.5507 (mmtt) REVERT: B 61 ARG cc_start: 0.8260 (ptt-90) cc_final: 0.7683 (ptt-90) REVERT: A 65 ARG cc_start: 0.8503 (tpp80) cc_final: 0.8123 (tpp80) outliers start: 31 outliers final: 27 residues processed: 144 average time/residue: 0.0759 time to fit residues: 14.0387 Evaluate side-chains 151 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.102688 restraints weight = 7979.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.105126 restraints weight = 5363.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.106937 restraints weight = 4049.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.108160 restraints weight = 3270.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.109006 restraints weight = 2797.132| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5231 Z= 0.156 Angle : 0.585 6.516 7105 Z= 0.304 Chirality : 0.043 0.151 764 Planarity : 0.004 0.050 910 Dihedral : 5.113 26.019 709 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.63 % Allowed : 24.14 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.27 (0.32), residues: 635 helix: -3.94 (0.74), residues: 26 sheet: -1.03 (0.31), residues: 264 loop : -1.67 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 355 TYR 0.018 0.001 TYR G 453 PHE 0.024 0.001 PHE H 70 TRP 0.012 0.001 TRP G 436 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 5221) covalent geometry : angle 0.57795 / 0.30 ( 7082) SS BOND : bond 0.00346 / 0.19 ( 7) SS BOND : angle 1.06739 / 0.61 ( 14) hydrogen bonds : bond 0.03159 / 2.20 ( 113) hydrogen bonds : angle 5.88885 / 4.09 ( 264) link_BETA1-4 : bond 0.00349 / 0.17 ( 2) link_BETA1-4 : angle 1.30023 / 0.74 ( 6) link_NAG-ASN : bond 0.00220 / 0.12 ( 1) link_NAG-ASN : angle 3.62314 / 1.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: G 466 ARG cc_start: 0.8428 (ptm160) cc_final: 0.7832 (ptm160) REVERT: G 472 ILE cc_start: 0.9249 (mm) cc_final: 0.9001 (mm) REVERT: L 107 LYS cc_start: 0.6540 (mtmm) cc_final: 0.5513 (mmtt) REVERT: H 57 ASN cc_start: 0.8375 (m-40) cc_final: 0.8148 (p0) REVERT: B 61 ARG cc_start: 0.8230 (ptt-90) cc_final: 0.7936 (ptt90) REVERT: A 65 ARG cc_start: 0.8493 (tpp80) cc_final: 0.8105 (tpp80) outliers start: 31 outliers final: 28 residues processed: 139 average time/residue: 0.0779 time to fit residues: 13.8174 Evaluate side-chains 151 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.0050 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.0670 chunk 9 optimal weight: 0.2980 chunk 40 optimal weight: 0.0370 chunk 21 optimal weight: 0.0770 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 overall best weight: 0.0968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN A 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.125904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107959 restraints weight = 7877.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.110473 restraints weight = 5239.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112412 restraints weight = 3917.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.113695 restraints weight = 3131.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.114709 restraints weight = 2646.111| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (21 function evaluations) r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5231 Z= 0.096 Angle : 0.543 5.626 7105 Z= 0.286 Chirality : 0.042 0.145 764 Planarity : 0.004 0.051 910 Dihedral : 4.701 24.469 709 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.81 % Allowed : 26.13 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.02 (0.33), residues: 635 helix: -3.14 (0.81), residues: 32 sheet: -0.78 (0.32), residues: 252 loop : -1.58 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.016 0.001 TYR A 105 PHE 0.015 0.001 PHE H 70 TRP 0.009 0.001 TRP A 104 HIS 0.002 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 5221) covalent geometry : angle 0.53875 / 0.28 ( 7082) SS BOND : bond 0.00213 / 0.13 ( 7) SS BOND : angle 0.80677 / 0.42 ( 14) hydrogen bonds : bond 0.02805 / 1.94 ( 113) hydrogen bonds : angle 5.49007 / 3.80 ( 264) link_BETA1-4 : bond 0.00628 / 0.32 ( 2) link_BETA1-4 : angle 1.42749 / 0.78 ( 6) link_NAG-ASN : bond 0.00382 / 0.20 ( 1) link_NAG-ASN : angle 2.49677 / 1.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: G 466 ARG cc_start: 0.8314 (ptm160) cc_final: 0.7825 (ptm160) REVERT: G 472 ILE cc_start: 0.9250 (mm) cc_final: 0.9027 (mm) REVERT: L 107 LYS cc_start: 0.6363 (mtmm) cc_final: 0.5311 (mmtt) REVERT: B 61 ARG cc_start: 0.8175 (ptt-90) cc_final: 0.7598 (ptt90) REVERT: B 90 GLN cc_start: 0.9095 (pp30) cc_final: 0.8892 (pp30) REVERT: A 65 ARG cc_start: 0.8382 (tpp80) cc_final: 0.7909 (tpp80) REVERT: A 101 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8794 (t0) outliers start: 21 outliers final: 16 residues processed: 136 average time/residue: 0.0724 time to fit residues: 12.4874 Evaluate side-chains 132 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 101 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.120345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.102754 restraints weight = 8119.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105167 restraints weight = 5418.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.106940 restraints weight = 4067.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.108132 restraints weight = 3288.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.109134 restraints weight = 2809.593| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5231 Z= 0.198 Angle : 0.602 6.327 7105 Z= 0.313 Chirality : 0.045 0.175 764 Planarity : 0.004 0.054 910 Dihedral : 5.022 25.948 709 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.90 % Allowed : 26.50 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.06 (0.33), residues: 635 helix: -2.85 (0.96), residues: 26 sheet: -0.80 (0.32), residues: 258 loop : -1.69 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 355 TYR 0.021 0.002 TYR G 453 PHE 0.032 0.002 PHE H 70 TRP 0.011 0.001 TRP A 104 HIS 0.003 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 ( 5221) covalent geometry : angle 0.59493 / 0.31 ( 7082) SS BOND : bond 0.00334 / 0.17 ( 7) SS BOND : angle 1.09984 / 0.66 ( 14) hydrogen bonds : bond 0.03384 / 2.37 ( 113) hydrogen bonds : angle 5.81320 / 4.03 ( 264) link_BETA1-4 : bond 0.00271 / 0.14 ( 2) link_BETA1-4 : angle 1.15090 / 0.64 ( 6) link_NAG-ASN : bond 0.00128 / 0.07 ( 1) link_NAG-ASN : angle 3.74830 / 1.83 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: G 466 ARG cc_start: 0.8442 (ptm160) cc_final: 0.7828 (ptm160) REVERT: G 472 ILE cc_start: 0.9244 (mm) cc_final: 0.8992 (mm) REVERT: L 107 LYS cc_start: 0.6556 (mtmm) cc_final: 0.5497 (mmtt) REVERT: B 61 ARG cc_start: 0.8264 (ptt-90) cc_final: 0.7937 (ptt90) REVERT: A 65 ARG cc_start: 0.8552 (tpp80) cc_final: 0.8132 (tpp80) outliers start: 16 outliers final: 15 residues processed: 131 average time/residue: 0.0832 time to fit residues: 13.8388 Evaluate side-chains 134 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.0470 chunk 54 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.122131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.103991 restraints weight = 8091.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.106528 restraints weight = 5418.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.108215 restraints weight = 4068.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109613 restraints weight = 3306.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110489 restraints weight = 2799.078| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5231 Z= 0.152 Angle : 0.587 6.196 7105 Z= 0.306 Chirality : 0.044 0.184 764 Planarity : 0.004 0.052 910 Dihedral : 4.979 25.485 709 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.90 % Allowed : 27.40 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.03 (0.33), residues: 635 helix: -2.80 (0.97), residues: 26 sheet: -0.72 (0.33), residues: 251 loop : -1.72 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 454 TYR 0.018 0.001 TYR G 453 PHE 0.023 0.001 PHE H 70 TRP 0.008 0.001 TRP A 50 HIS 0.003 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 5221) covalent geometry : angle 0.58102 / 0.30 ( 7082) SS BOND : bond 0.00278 / 0.14 ( 7) SS BOND : angle 0.99135 / 0.56 ( 14) hydrogen bonds : bond 0.03201 / 2.25 ( 113) hydrogen bonds : angle 5.82764 / 4.03 ( 264) link_BETA1-4 : bond 0.00454 / 0.23 ( 2) link_BETA1-4 : angle 1.22053 / 0.68 ( 6) link_NAG-ASN : bond 0.00193 / 0.10 ( 1) link_NAG-ASN : angle 3.42603 / 1.69 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1394.61 seconds wall clock time: 24 minutes 52.90 seconds (1492.90 seconds total)