Starting phenix.real_space_refine on Fri Oct 10 12:42:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iv5_35741/10_2025/8iv5_35741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv5_35741/10_2025/8iv5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8iv5_35741/10_2025/8iv5_35741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv5_35741/10_2025/8iv5_35741.map" model { file = "/net/cci-nas-00/data/ceres_data/8iv5_35741/10_2025/8iv5_35741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv5_35741/10_2025/8iv5_35741.cif" } 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-2.0-5842/lib/python3.9/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.40, per 1000 atoms: 0.27 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: 0.45 Conformation dependent library (CDL) restraints added in 194.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.19 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: 0.67 Time building geometry restraints manager: 0.56 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 - 20.02: 2822 20.02 - 40.03: 237 40.03 - 60.05: 28 60.05 - 80.07: 11 80.07 - 100.08: 4 Dihedral angle restraints: 3102 sinusoidal: 1251 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 3099 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: 11.790 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: 0.020 Set scattering table: 0.010 Process input model: 6.440 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 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 : 15.145 100.082 1905 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 aren 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 covalent geometry : bond 0.00705 ( 5221) covalent geometry : angle 0.87767 ( 7082) SS BOND : bond 0.00394 ( 7) SS BOND : angle 1.32590 ( 14) hydrogen bonds : bond 0.30574 ( 113) hydrogen bonds : angle 11.11698 ( 264) link_BETA1-4 : bond 0.00994 ( 2) link_BETA1-4 : angle 2.39677 ( 6) link_NAG-ASN : bond 0.00513 ( 1) link_NAG-ASN : angle 7.25245 ( 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 : 0.189 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: 0.7614 (m) cc_final: 0.7169 (m) REVERT: L 102 THR cc_start: 0.8308 (m) cc_final: 0.8092 (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: 0.6864 (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: 0.7458 (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: 0.0949 time to fit residues: 18.3803 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 : 0.201 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3306 r_free = 0.3306 target = 0.120304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.102151 restraints weight = 7943.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.104603 restraints weight = 5367.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.106343 restraints weight = 4073.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.107535 restraints weight = 3329.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.108461 restraints weight = 2860.388| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 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 = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5231 Z= 0.188 Angle : 0.627 6.728 7105 Z= 0.331 Chirality : 0.045 0.151 764 Planarity : 0.005 0.054 910 Dihedral : 8.523 56.055 773 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.22 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 aren not related in a simple way. whole: -3.29 (0.31), residues: 635 helix: -4.73 (0.43), residues: 26 sheet: -1.80 (0.32), residues: 254 loop : -2.28 (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 0.002 TRP G 436 HIS 0.002 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 5221) covalent geometry : angle 0.61616 ( 7082) SS BOND : bond 0.00370 ( 7) SS BOND : angle 0.78755 ( 14) hydrogen bonds : bond 0.04465 ( 113) hydrogen bonds : angle 7.53986 ( 264) link_BETA1-4 : bond 0.00531 ( 2) link_BETA1-4 : angle 2.43393 ( 6) link_NAG-ASN : bond 0.00262 ( 1) link_NAG-ASN : angle 4.57523 ( 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 : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 417 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7852 (tttp) REVERT: G 466 ARG cc_start: 0.8388 (ptm160) cc_final: 0.7903 (ptm160) REVERT: G 472 ILE cc_start: 0.9241 (mm) cc_final: 0.9041 (mm) REVERT: L 104 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6471 (tt) REVERT: B 61 ARG cc_start: 0.8251 (ptt-90) cc_final: 0.7896 (ptt90) REVERT: A 65 ARG cc_start: 0.7544 (ttp-110) cc_final: 0.7153 (mtm110) outliers start: 18 outliers final: 13 residues processed: 151 average time/residue: 0.0862 time to fit residues: 16.1316 Evaluate side-chains 143 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 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 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 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: 0.7980 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.100997 restraints weight = 7970.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.103454 restraints weight = 5369.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.105169 restraints weight = 4048.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.106290 restraints weight = 3290.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.107187 restraints weight = 2835.378| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5231 Z= 0.163 Angle : 0.601 6.151 7105 Z= 0.314 Chirality : 0.045 0.157 764 Planarity : 0.004 0.048 910 Dihedral : 6.896 34.829 770 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.63 % Allowed : 19.42 % 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 aren not related in a simple way. whole: -3.06 (0.31), residues: 635 helix: -4.36 (0.59), residues: 26 sheet: -1.56 (0.32), residues: 249 loop : -2.23 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 355 TYR 0.022 0.002 TYR A 80 PHE 0.013 0.001 PHE B 62 TRP 0.018 0.001 TRP G 436 HIS 0.002 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 5221) covalent geometry : angle 0.59180 ( 7082) SS BOND : bond 0.00569 ( 7) SS BOND : angle 0.71532 ( 14) hydrogen bonds : bond 0.03689 ( 113) hydrogen bonds : angle 6.80918 ( 264) link_BETA1-4 : bond 0.00185 ( 2) link_BETA1-4 : angle 2.31457 ( 6) link_NAG-ASN : bond 0.00322 ( 1) link_NAG-ASN : angle 4.11863 ( 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 164 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 417 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7873 (tttp) REVERT: G 466 ARG cc_start: 0.8428 (ptm160) cc_final: 0.7897 (ptm160) REVERT: L 104 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6409 (tt) REVERT: B 61 ARG cc_start: 0.8236 (ptt-90) cc_final: 0.7898 (ptt90) REVERT: A 65 ARG cc_start: 0.7480 (ttp-110) cc_final: 0.7207 (mtp85) outliers start: 31 outliers final: 21 residues processed: 147 average time/residue: 0.0909 time to fit residues: 16.8418 Evaluate side-chains 149 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 417 LYS 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: 0.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.100405 restraints weight = 8055.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.102876 restraints weight = 5447.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.104616 restraints weight = 4114.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.105769 restraints weight = 3367.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.106622 restraints weight = 2897.490| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2430 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= 0.171 Angle : 0.591 5.641 7105 Z= 0.309 Chirality : 0.044 0.148 764 Planarity : 0.004 0.044 910 Dihedral : 6.104 33.617 770 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.54 % Allowed : 22.14 % Favored : 73.32 % 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 aren not related in a simple way. whole: -2.88 (0.31), residues: 635 helix: -4.11 (0.70), residues: 26 sheet: -1.41 (0.32), residues: 249 loop : -2.13 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 408 TYR 0.019 0.002 TYR G 449 PHE 0.017 0.001 PHE L 62 TRP 0.018 0.001 TRP G 436 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 5221) covalent geometry : angle 0.58184 ( 7082) SS BOND : bond 0.00327 ( 7) SS BOND : angle 0.81970 ( 14) hydrogen bonds : bond 0.03405 ( 113) hydrogen bonds : angle 6.31393 ( 264) link_BETA1-4 : bond 0.00230 ( 2) link_BETA1-4 : angle 2.23618 ( 6) link_NAG-ASN : bond 0.00225 ( 1) link_NAG-ASN : angle 3.94957 ( 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 158 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: G 355 ARG cc_start: 0.9157 (ttt90) cc_final: 0.8943 (ttm-80) REVERT: G 466 ARG cc_start: 0.8424 (ptm160) cc_final: 0.7805 (ptm160) REVERT: B 61 ARG cc_start: 0.8248 (ptt-90) cc_final: 0.7793 (ptt90) REVERT: A 80 TYR cc_start: 0.8478 (m-10) cc_final: 0.8161 (m-10) outliers start: 25 outliers final: 19 residues processed: 146 average time/residue: 0.0836 time to fit residues: 15.3777 Evaluate side-chains 143 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 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 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.100463 restraints weight = 8129.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.103038 restraints weight = 5432.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104688 restraints weight = 4069.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.105989 restraints weight = 3320.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.106819 restraints weight = 2825.002| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5231 Z= 0.166 Angle : 0.597 6.463 7105 Z= 0.307 Chirality : 0.044 0.150 764 Planarity : 0.004 0.044 910 Dihedral : 5.930 33.347 770 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 6.17 % Allowed : 21.96 % Favored : 71.87 % 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 aren not related in a simple way. whole: -2.64 (0.32), residues: 635 helix: -4.02 (0.72), residues: 26 sheet: -1.17 (0.32), residues: 261 loop : -2.04 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 65 TYR 0.017 0.002 TYR G 449 PHE 0.012 0.001 PHE B 62 TRP 0.017 0.001 TRP G 436 HIS 0.002 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5221) covalent geometry : angle 0.58819 ( 7082) SS BOND : bond 0.00453 ( 7) SS BOND : angle 0.92671 ( 14) hydrogen bonds : bond 0.03253 ( 113) hydrogen bonds : angle 6.23128 ( 264) link_BETA1-4 : bond 0.00339 ( 2) link_BETA1-4 : angle 2.01468 ( 6) link_NAG-ASN : bond 0.00201 ( 1) link_NAG-ASN : angle 3.88447 ( 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 164 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 466 ARG cc_start: 0.8427 (ptm160) cc_final: 0.7820 (ptm160) REVERT: L 107 LYS cc_start: 0.6413 (mtmm) cc_final: 0.5403 (mmtt) REVERT: B 61 ARG cc_start: 0.8200 (ptt-90) cc_final: 0.7697 (ptt90) outliers start: 34 outliers final: 25 residues processed: 147 average time/residue: 0.0847 time to fit residues: 15.8550 Evaluate side-chains 150 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 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 72 THR 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 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 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.119503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.101342 restraints weight = 8099.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.103890 restraints weight = 5446.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.105622 restraints weight = 4096.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.106789 restraints weight = 3324.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.107795 restraints weight = 2859.443| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5231 Z= 0.151 Angle : 0.581 6.424 7105 Z= 0.301 Chirality : 0.044 0.147 764 Planarity : 0.004 0.047 910 Dihedral : 5.737 33.129 770 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 6.35 % Allowed : 22.50 % 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 aren not related in a simple way. whole: -2.46 (0.32), residues: 635 helix: -4.02 (0.72), residues: 26 sheet: -1.13 (0.31), residues: 265 loop : -1.83 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.016 0.001 TYR G 449 PHE 0.032 0.002 PHE H 70 TRP 0.012 0.001 TRP A 104 HIS 0.002 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 5221) covalent geometry : angle 0.57263 ( 7082) SS BOND : bond 0.00297 ( 7) SS BOND : angle 0.89335 ( 14) hydrogen bonds : bond 0.03257 ( 113) hydrogen bonds : angle 6.13148 ( 264) link_BETA1-4 : bond 0.00391 ( 2) link_BETA1-4 : angle 1.88537 ( 6) link_NAG-ASN : bond 0.00256 ( 1) link_NAG-ASN : angle 3.73638 ( 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 165 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7722 (mp10) REVERT: G 466 ARG cc_start: 0.8415 (ptm160) cc_final: 0.7837 (ptm160) REVERT: L 107 LYS cc_start: 0.6463 (mtmm) cc_final: 0.5477 (mmtt) REVERT: B 61 ARG cc_start: 0.8251 (ptt-90) cc_final: 0.7683 (ptt90) outliers start: 35 outliers final: 28 residues processed: 148 average time/residue: 0.0767 time to fit residues: 14.5772 Evaluate side-chains 155 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 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 72 THR 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 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 30 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: 0.0770 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN A 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.101281 restraints weight = 8005.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.103722 restraints weight = 5332.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.105482 restraints weight = 4000.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.106639 restraints weight = 3221.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107564 restraints weight = 2753.155| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5231 Z= 0.158 Angle : 0.590 7.491 7105 Z= 0.306 Chirality : 0.044 0.147 764 Planarity : 0.004 0.046 910 Dihedral : 5.710 33.106 770 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.99 % Allowed : 23.59 % Favored : 70.42 % 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 aren not related in a simple way. whole: -2.40 (0.32), residues: 635 helix: -3.97 (0.73), residues: 26 sheet: -1.12 (0.31), residues: 265 loop : -1.76 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.020 0.002 TYR G 453 PHE 0.018 0.001 PHE H 70 TRP 0.014 0.001 TRP G 436 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 5221) covalent geometry : angle 0.58143 ( 7082) SS BOND : bond 0.00360 ( 7) SS BOND : angle 1.08380 ( 14) hydrogen bonds : bond 0.03218 ( 113) hydrogen bonds : angle 6.03099 ( 264) link_BETA1-4 : bond 0.00343 ( 2) link_BETA1-4 : angle 1.80633 ( 6) link_NAG-ASN : bond 0.00235 ( 1) link_NAG-ASN : angle 3.78509 ( 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 163 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: G 408 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8399 (ttp80) REVERT: G 414 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7686 (mp10) REVERT: G 466 ARG cc_start: 0.8424 (ptm160) cc_final: 0.7839 (ptm160) REVERT: L 107 LYS cc_start: 0.6540 (mtmm) cc_final: 0.5554 (mmtt) REVERT: B 61 ARG cc_start: 0.8259 (ptt-90) cc_final: 0.7644 (ptt90) outliers start: 33 outliers final: 30 residues processed: 146 average time/residue: 0.0745 time to fit residues: 14.0497 Evaluate side-chains 156 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 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 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 89 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 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 30 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: 0.6980 chunk 39 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3282 r_free = 0.3282 target = 0.118337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.100851 restraints weight = 8076.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.103319 restraints weight = 5361.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.105073 restraints weight = 3995.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.106303 restraints weight = 3211.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.107146 restraints weight = 2720.516| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5231 Z= 0.190 Angle : 0.614 7.062 7105 Z= 0.318 Chirality : 0.045 0.149 764 Planarity : 0.004 0.048 910 Dihedral : 5.828 32.920 770 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 6.72 % Allowed : 23.96 % Favored : 69.33 % 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 aren not related in a simple way. whole: -2.33 (0.32), residues: 635 helix: -3.91 (0.74), residues: 26 sheet: -1.10 (0.31), residues: 266 loop : -1.69 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 65 TYR 0.021 0.002 TYR G 453 PHE 0.017 0.002 PHE L 62 TRP 0.015 0.001 TRP G 436 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 5221) covalent geometry : angle 0.60475 ( 7082) SS BOND : bond 0.00344 ( 7) SS BOND : angle 1.12749 ( 14) hydrogen bonds : bond 0.03305 ( 113) hydrogen bonds : angle 6.09121 ( 264) link_BETA1-4 : bond 0.00320 ( 2) link_BETA1-4 : angle 1.76750 ( 6) link_NAG-ASN : bond 0.00167 ( 1) link_NAG-ASN : angle 4.05056 ( 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 159 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: G 408 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8392 (ttp80) REVERT: G 414 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7702 (mp10) REVERT: G 466 ARG cc_start: 0.8461 (ptm160) cc_final: 0.7872 (ptm160) REVERT: L 107 LYS cc_start: 0.6582 (mtmm) cc_final: 0.5587 (mmtt) REVERT: B 61 ARG cc_start: 0.8317 (ptt-90) cc_final: 0.8013 (ptt90) outliers start: 37 outliers final: 32 residues processed: 141 average time/residue: 0.0837 time to fit residues: 15.0230 Evaluate side-chains 154 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 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 14 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 89 LEU 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 30 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: 0.8980 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 9 optimal weight: 0.0020 chunk 40 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN A 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.120690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.102753 restraints weight = 7955.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.105256 restraints weight = 5344.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107088 restraints weight = 4010.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.108354 restraints weight = 3234.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.109257 restraints weight = 2742.540| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- 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 = 0.33 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 = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5231 Z= 0.137 Angle : 0.590 6.853 7105 Z= 0.307 Chirality : 0.044 0.152 764 Planarity : 0.004 0.048 910 Dihedral : 5.574 32.993 770 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.81 % Allowed : 24.86 % Favored : 69.33 % 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 aren not related in a simple way. whole: -2.13 (0.33), residues: 635 helix: -3.79 (0.77), residues: 26 sheet: -0.94 (0.32), residues: 255 loop : -1.57 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 65 TYR 0.017 0.001 TYR A 105 PHE 0.022 0.001 PHE L 62 TRP 0.015 0.001 TRP A 104 HIS 0.001 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5221) covalent geometry : angle 0.58264 ( 7082) SS BOND : bond 0.00237 ( 7) SS BOND : angle 0.91629 ( 14) hydrogen bonds : bond 0.03069 ( 113) hydrogen bonds : angle 5.88216 ( 264) link_BETA1-4 : bond 0.00420 ( 2) link_BETA1-4 : angle 1.81159 ( 6) link_NAG-ASN : bond 0.00280 ( 1) link_NAG-ASN : angle 3.49355 ( 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 151 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 408 ARG cc_start: 0.8622 (ttp80) cc_final: 0.8411 (ttp80) REVERT: G 414 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7567 (mp10) REVERT: G 466 ARG cc_start: 0.8399 (ptm160) cc_final: 0.7830 (ptm160) REVERT: G 467 ASP cc_start: 0.8009 (t0) cc_final: 0.7770 (t0) REVERT: L 47 MET cc_start: 0.7049 (mmm) cc_final: 0.6676 (mmm) REVERT: L 107 LYS cc_start: 0.6593 (mtmm) cc_final: 0.5516 (mmtt) REVERT: B 61 ARG cc_start: 0.8248 (ptt-90) cc_final: 0.7974 (ptt90) outliers start: 32 outliers final: 29 residues processed: 137 average time/residue: 0.0794 time to fit residues: 13.8088 Evaluate side-chains 148 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 14 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 89 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 115 VAL Chi-restraints excluded: chain B residue 14 THR 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 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN A 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.118106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.100395 restraints weight = 8035.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.102843 restraints weight = 5400.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.104620 restraints weight = 4068.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.105854 restraints weight = 3284.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106553 restraints weight = 2793.209| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3195 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= 0.202 Angle : 0.635 6.564 7105 Z= 0.328 Chirality : 0.045 0.163 764 Planarity : 0.004 0.048 910 Dihedral : 5.869 32.992 770 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.35 % Allowed : 24.86 % Favored : 68.78 % 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 aren not related in a simple way. whole: -2.26 (0.32), residues: 635 helix: -3.78 (0.77), residues: 26 sheet: -1.00 (0.32), residues: 256 loop : -1.69 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 65 TYR 0.022 0.002 TYR G 453 PHE 0.036 0.002 PHE H 70 TRP 0.016 0.001 TRP A 104 HIS 0.002 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 5221) covalent geometry : angle 0.62693 ( 7082) SS BOND : bond 0.00302 ( 7) SS BOND : angle 1.03584 ( 14) hydrogen bonds : bond 0.03454 ( 113) hydrogen bonds : angle 6.08472 ( 264) link_BETA1-4 : bond 0.00282 ( 2) link_BETA1-4 : angle 1.68894 ( 6) link_NAG-ASN : bond 0.00149 ( 1) link_NAG-ASN : angle 4.18519 ( 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 156 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 408 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8417 (ttp80) REVERT: G 414 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: G 466 ARG cc_start: 0.8453 (ptm160) cc_final: 0.7825 (ptm160) REVERT: G 467 ASP cc_start: 0.8070 (t0) cc_final: 0.7829 (t0) REVERT: L 107 LYS cc_start: 0.6683 (mtmm) cc_final: 0.5605 (mmtt) REVERT: H 57 ASN cc_start: 0.8452 (m-40) cc_final: 0.8245 (p0) REVERT: B 61 ARG cc_start: 0.8310 (ptt-90) cc_final: 0.7980 (ptt90) outliers start: 35 outliers final: 32 residues processed: 139 average time/residue: 0.0802 time to fit residues: 14.3797 Evaluate side-chains 153 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 414 GLN Chi-restraints excluded: chain G residue 449 TYR 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 14 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 89 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 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 30 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 28 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 54 optimal weight: 0.0470 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 5 optimal weight: 0.0670 overall best weight: 0.2332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 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 = 0.3338 r_free = 0.3338 target = 0.122774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.104956 restraints weight = 8035.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107547 restraints weight = 5349.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.109311 restraints weight = 3989.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110679 restraints weight = 3216.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111434 restraints weight = 2707.005| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5231 Z= 0.106 Angle : 0.576 5.857 7105 Z= 0.300 Chirality : 0.044 0.182 764 Planarity : 0.004 0.047 910 Dihedral : 5.340 32.963 770 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.99 % Allowed : 27.04 % Favored : 68.97 % 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 aren not related in a simple way. whole: -2.13 (0.32), residues: 635 helix: -3.74 (0.79), residues: 26 sheet: -0.88 (0.32), residues: 257 loop : -1.63 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 65 TYR 0.016 0.001 TYR A 105 PHE 0.015 0.001 PHE H 70 TRP 0.014 0.001 TRP A 104 HIS 0.002 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 5221) covalent geometry : angle 0.56963 ( 7082) SS BOND : bond 0.00207 ( 7) SS BOND : angle 0.81399 ( 14) hydrogen bonds : bond 0.03007 ( 113) hydrogen bonds : angle 5.80555 ( 264) link_BETA1-4 : bond 0.00538 ( 2) link_BETA1-4 : angle 1.87453 ( 6) link_NAG-ASN : bond 0.00347 ( 1) link_NAG-ASN : angle 2.95308 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.48 seconds wall clock time: 24 minutes 58.86 seconds (1498.86 seconds total)