Starting phenix.real_space_refine on Thu Jul 24 04:57:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iv5_35741/07_2025/8iv5_35741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv5_35741/07_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_35741/07_2025/8iv5_35741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv5_35741/07_2025/8iv5_35741.map" model { file = "/net/cci-nas-00/data/ceres_data/8iv5_35741/07_2025/8iv5_35741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv5_35741/07_2025/8iv5_35741.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.20, per 1000 atoms: 1.22 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: 1.34 Conformation dependent library (CDL) restraints added in 683.5 milliseconds 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 14 sheets defined 6.5% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 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: 1.21 Time building geometry restraints manager: 1.52 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: 9.500 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.640 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.310 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.002 TRP G 436 HIS 0.003 0.001 HIS L 91 PHE 0.020 0.002 PHE B 62 TYR 0.022 0.003 TYR L 49 ARG 0.003 0.001 ARG G 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 1) link_NAG-ASN : angle 7.25245 ( 3) link_BETA1-4 : bond 0.00994 ( 2) link_BETA1-4 : angle 2.39677 ( 6) hydrogen bonds : bond 0.30574 ( 113) hydrogen bonds : angle 11.11698 ( 264) SS BOND : bond 0.00394 ( 7) SS BOND : angle 1.32590 ( 14) covalent geometry : bond 0.00705 ( 5221) covalent geometry : angle 0.87767 ( 7082) *********************** 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 : 0.539 Fit side-chains revert: symmetry clash 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: 0.7171 (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: 0.6547 (m-30) REVERT: H 50 GLN cc_start: 0.7769 (tt0) cc_final: 0.6865 (tt0) REVERT: H 54 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7885 (tptt) REVERT: H 73 SER cc_start: 0.7672 (m) cc_final: 0.7458 (p) REVERT: B 40 SER cc_start: 0.7934 (t) cc_final: 0.7721 (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: 0.6324 (m-30) REVERT: B 105 GLU cc_start: 0.7443 (pt0) cc_final: 0.7241 (pt0) REVERT: A 10 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7310 (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: 0.2042 time to fit residues: 39.5918 Evaluate side-chains 137 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 51 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 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 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 = 0.3311 r_free = 0.3311 target = 0.120481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.102316 restraints weight = 7942.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104678 restraints weight = 5363.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106552 restraints weight = 4087.248| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5231 Z= 0.205 Angle : 0.637 7.012 7105 Z= 0.336 Chirality : 0.045 0.160 764 Planarity : 0.005 0.053 910 Dihedral : 8.670 57.620 773 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.27 % Allowed : 18.33 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.31), residues: 635 helix: -4.73 (0.43), residues: 26 sheet: -1.82 (0.32), residues: 254 loop : -2.31 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 436 HIS 0.002 0.001 HIS B 41 PHE 0.017 0.002 PHE B 62 TYR 0.023 0.002 TYR L 49 ARG 0.003 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 1) link_NAG-ASN : angle 4.75230 ( 3) link_BETA1-4 : bond 0.00477 ( 2) link_BETA1-4 : angle 2.37919 ( 6) hydrogen bonds : bond 0.04580 ( 113) hydrogen bonds : angle 7.56338 ( 264) SS BOND : bond 0.00265 ( 7) SS BOND : angle 0.86992 ( 14) covalent geometry : bond 0.00477 ( 5221) covalent geometry : angle 0.62583 ( 7082) *********************** 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 159 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 417 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7857 (tttp) REVERT: G 466 ARG cc_start: 0.8402 (ptm160) cc_final: 0.7924 (ptm160) REVERT: G 472 ILE cc_start: 0.9251 (mm) cc_final: 0.9039 (mm) REVERT: L 104 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6467 (tt) REVERT: B 61 ARG cc_start: 0.8280 (ptt-90) cc_final: 0.8020 (ptt-90) REVERT: A 65 ARG cc_start: 0.7561 (ttp-110) cc_final: 0.7340 (ttm110) outliers start: 18 outliers final: 15 residues processed: 151 average time/residue: 0.1858 time to fit residues: 34.9191 Evaluate side-chains 144 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 417 LYS Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 57 optimal weight: 0.0570 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.120684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.102582 restraints weight = 7939.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.104936 restraints weight = 5369.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.106527 restraints weight = 4067.345| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5231 Z= 0.140 Angle : 0.584 6.537 7105 Z= 0.306 Chirality : 0.044 0.156 764 Planarity : 0.004 0.047 910 Dihedral : 6.497 35.177 770 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.44 % Allowed : 19.78 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.31), residues: 635 helix: -4.32 (0.61), residues: 26 sheet: -1.50 (0.32), residues: 249 loop : -2.19 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 436 HIS 0.002 0.001 HIS L 91 PHE 0.011 0.001 PHE L 62 TYR 0.023 0.001 TYR A 80 ARG 0.004 0.000 ARG G 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 1) link_NAG-ASN : angle 3.76810 ( 3) link_BETA1-4 : bond 0.00375 ( 2) link_BETA1-4 : angle 2.36232 ( 6) hydrogen bonds : bond 0.03538 ( 113) hydrogen bonds : angle 6.67190 ( 264) SS BOND : bond 0.00427 ( 7) SS BOND : angle 0.58864 ( 14) covalent geometry : bond 0.00324 ( 5221) covalent geometry : angle 0.57559 ( 7082) *********************** 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 170 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: G 466 ARG cc_start: 0.8397 (ptm160) cc_final: 0.7845 (ptm160) REVERT: G 472 ILE cc_start: 0.9258 (mm) cc_final: 0.9051 (mm) REVERT: G 481 ASN cc_start: 0.7560 (t0) cc_final: 0.7358 (t0) REVERT: L 104 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6280 (tt) REVERT: B 61 ARG cc_start: 0.8174 (ptt-90) cc_final: 0.7809 (ptt90) REVERT: B 90 GLN cc_start: 0.9338 (pp30) cc_final: 0.9117 (pp30) REVERT: B 93 THR cc_start: 0.9547 (OUTLIER) cc_final: 0.9336 (m) outliers start: 30 outliers final: 18 residues processed: 155 average time/residue: 0.1786 time to fit residues: 35.0634 Evaluate side-chains 150 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain H residue 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 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.118978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.100640 restraints weight = 8187.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.103042 restraints weight = 5519.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.104767 restraints weight = 4195.856| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5231 Z= 0.177 Angle : 0.605 6.303 7105 Z= 0.312 Chirality : 0.044 0.150 764 Planarity : 0.004 0.049 910 Dihedral : 6.156 33.919 770 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.90 % Allowed : 21.42 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.31), residues: 635 helix: -4.15 (0.68), residues: 26 sheet: -1.39 (0.32), residues: 248 loop : -2.11 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 436 HIS 0.002 0.001 HIS B 41 PHE 0.015 0.001 PHE B 62 TYR 0.017 0.002 TYR G 449 ARG 0.004 0.000 ARG G 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 1) link_NAG-ASN : angle 4.04494 ( 3) link_BETA1-4 : bond 0.00404 ( 2) link_BETA1-4 : angle 2.18005 ( 6) hydrogen bonds : bond 0.03366 ( 113) hydrogen bonds : angle 6.36028 ( 264) SS BOND : bond 0.00309 ( 7) SS BOND : angle 0.90759 ( 14) covalent geometry : bond 0.00418 ( 5221) covalent geometry : angle 0.59593 ( 7082) *********************** 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 157 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 408 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8405 (ttp80) REVERT: G 466 ARG cc_start: 0.8426 (ptm160) cc_final: 0.7831 (ptm160) REVERT: G 472 ILE cc_start: 0.9246 (mm) cc_final: 0.9029 (mm) REVERT: B 61 ARG cc_start: 0.8268 (ptt-90) cc_final: 0.7825 (ptt90) outliers start: 27 outliers final: 25 residues processed: 142 average time/residue: 0.1845 time to fit residues: 33.0075 Evaluate side-chains 148 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 402 ILE Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 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 37 GLN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 93 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.100846 restraints weight = 8079.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103337 restraints weight = 5465.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.104921 restraints weight = 4137.137| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5231 Z= 0.172 Angle : 0.598 6.402 7105 Z= 0.308 Chirality : 0.044 0.151 764 Planarity : 0.004 0.047 910 Dihedral : 5.979 33.563 770 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.63 % Allowed : 21.78 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.32), residues: 635 helix: -4.05 (0.72), residues: 26 sheet: -1.18 (0.32), residues: 261 loop : -2.09 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 436 HIS 0.002 0.001 HIS L 91 PHE 0.016 0.001 PHE L 62 TYR 0.017 0.002 TYR G 449 ARG 0.007 0.001 ARG A 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 1) link_NAG-ASN : angle 3.97049 ( 3) link_BETA1-4 : bond 0.00431 ( 2) link_BETA1-4 : angle 2.01022 ( 6) hydrogen bonds : bond 0.03252 ( 113) hydrogen bonds : angle 6.16324 ( 264) SS BOND : bond 0.00327 ( 7) SS BOND : angle 0.92354 ( 14) covalent geometry : bond 0.00405 ( 5221) covalent geometry : angle 0.58901 ( 7082) *********************** 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 159 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: G 408 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8406 (ttp80) REVERT: G 466 ARG cc_start: 0.8433 (ptm160) cc_final: 0.7841 (ptm160) REVERT: G 472 ILE cc_start: 0.9257 (mm) cc_final: 0.9012 (mm) REVERT: L 107 LYS cc_start: 0.6453 (mtmm) cc_final: 0.5436 (mmtt) REVERT: B 61 ARG cc_start: 0.8221 (ptt-90) cc_final: 0.7731 (ptt90) outliers start: 31 outliers final: 26 residues processed: 144 average time/residue: 0.1799 time to fit residues: 32.8354 Evaluate side-chains 153 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 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 93 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 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 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 = 0.3284 r_free = 0.3284 target = 0.118338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.100426 restraints weight = 8037.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.102878 restraints weight = 5398.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.104533 restraints weight = 4079.478| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5231 Z= 0.171 Angle : 0.591 6.495 7105 Z= 0.306 Chirality : 0.044 0.152 764 Planarity : 0.004 0.047 910 Dihedral : 5.883 33.306 770 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 6.35 % Allowed : 22.32 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.32), residues: 635 helix: -4.04 (0.71), residues: 26 sheet: -1.05 (0.32), residues: 261 loop : -2.02 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 436 HIS 0.002 0.001 HIS L 91 PHE 0.013 0.001 PHE B 62 TYR 0.017 0.002 TYR A 80 ARG 0.007 0.000 ARG A 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 1) link_NAG-ASN : angle 3.97310 ( 3) link_BETA1-4 : bond 0.00442 ( 2) link_BETA1-4 : angle 1.92332 ( 6) hydrogen bonds : bond 0.03258 ( 113) hydrogen bonds : angle 6.14989 ( 264) SS BOND : bond 0.00396 ( 7) SS BOND : angle 0.92276 ( 14) covalent geometry : bond 0.00405 ( 5221) covalent geometry : angle 0.58219 ( 7082) *********************** 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 169 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: G 408 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8403 (ttp80) REVERT: G 414 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: G 466 ARG cc_start: 0.8427 (ptm160) cc_final: 0.7821 (ptm160) REVERT: G 472 ILE cc_start: 0.9257 (mm) cc_final: 0.9015 (mm) REVERT: L 107 LYS cc_start: 0.6523 (mtmm) cc_final: 0.5499 (mmtt) REVERT: B 61 ARG cc_start: 0.8211 (ptt-90) cc_final: 0.7688 (ptt90) REVERT: B 90 GLN cc_start: 0.9242 (pp30) cc_final: 0.9040 (pp30) outliers start: 35 outliers final: 29 residues processed: 152 average time/residue: 0.1828 time to fit residues: 35.4735 Evaluate side-chains 159 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 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 77 SER Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 50 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 0.0470 chunk 29 optimal weight: 5.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.101950 restraints weight = 8000.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.104398 restraints weight = 5406.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.106156 restraints weight = 4087.525| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5231 Z= 0.136 Angle : 0.575 7.467 7105 Z= 0.298 Chirality : 0.044 0.150 764 Planarity : 0.004 0.048 910 Dihedral : 5.634 33.595 770 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.26 % Allowed : 23.05 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.32), residues: 635 helix: -3.99 (0.73), residues: 26 sheet: -0.96 (0.32), residues: 261 loop : -1.87 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 436 HIS 0.002 0.001 HIS L 91 PHE 0.035 0.001 PHE H 70 TYR 0.018 0.001 TYR G 453 ARG 0.007 0.000 ARG A 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 1) link_NAG-ASN : angle 3.58780 ( 3) link_BETA1-4 : bond 0.00347 ( 2) link_BETA1-4 : angle 1.88476 ( 6) hydrogen bonds : bond 0.03100 ( 113) hydrogen bonds : angle 5.92345 ( 264) SS BOND : bond 0.00425 ( 7) SS BOND : angle 0.86037 ( 14) covalent geometry : bond 0.00321 ( 5221) covalent geometry : angle 0.56675 ( 7082) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: G 466 ARG cc_start: 0.8382 (ptm160) cc_final: 0.7792 (ptm160) REVERT: G 472 ILE cc_start: 0.9260 (mm) cc_final: 0.9018 (mm) REVERT: L 107 LYS cc_start: 0.6480 (mtmm) cc_final: 0.5532 (mmtt) REVERT: H 107 ASP cc_start: 0.8318 (t0) cc_final: 0.8114 (t0) REVERT: B 61 ARG cc_start: 0.8196 (ptt-90) cc_final: 0.7672 (ptt90) REVERT: B 90 GLN cc_start: 0.9201 (pp30) cc_final: 0.8776 (pp30) outliers start: 29 outliers final: 25 residues processed: 145 average time/residue: 0.1733 time to fit residues: 31.8328 Evaluate side-chains 151 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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** G 437 ASN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.119367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100947 restraints weight = 7979.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.103547 restraints weight = 5306.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.105404 restraints weight = 3956.720| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5231 Z= 0.157 Angle : 0.588 6.995 7105 Z= 0.306 Chirality : 0.044 0.150 764 Planarity : 0.004 0.049 910 Dihedral : 5.677 33.513 770 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 6.35 % Allowed : 23.96 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.32), residues: 635 helix: -3.93 (0.74), residues: 26 sheet: -0.92 (0.32), residues: 261 loop : -1.77 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 436 HIS 0.002 0.001 HIS L 91 PHE 0.022 0.002 PHE L 62 TYR 0.020 0.002 TYR A 80 ARG 0.007 0.000 ARG A 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 1) link_NAG-ASN : angle 3.81633 ( 3) link_BETA1-4 : bond 0.00351 ( 2) link_BETA1-4 : angle 1.77149 ( 6) hydrogen bonds : bond 0.03167 ( 113) hydrogen bonds : angle 5.89358 ( 264) SS BOND : bond 0.00337 ( 7) SS BOND : angle 1.08074 ( 14) covalent geometry : bond 0.00372 ( 5221) covalent geometry : angle 0.57944 ( 7082) *********************** 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 160 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 408 ARG cc_start: 0.8685 (ttp80) cc_final: 0.8457 (ttp80) REVERT: G 414 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: G 466 ARG cc_start: 0.8385 (ptm160) cc_final: 0.7756 (ptm160) REVERT: G 472 ILE cc_start: 0.9258 (mm) cc_final: 0.9006 (mm) REVERT: L 107 LYS cc_start: 0.6569 (mtmm) cc_final: 0.5510 (mmtt) REVERT: H 107 ASP cc_start: 0.8472 (t0) cc_final: 0.8262 (t0) REVERT: B 61 ARG cc_start: 0.8213 (ptt-90) cc_final: 0.7620 (ptt90) REVERT: B 90 GLN cc_start: 0.9211 (pp30) cc_final: 0.8991 (pp30) outliers start: 35 outliers final: 30 residues processed: 144 average time/residue: 0.1649 time to fit residues: 30.4576 Evaluate side-chains 155 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 14 SER 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 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.118085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.099715 restraints weight = 7984.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.102203 restraints weight = 5292.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.104017 restraints weight = 3975.428| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5231 Z= 0.188 Angle : 0.614 6.872 7105 Z= 0.318 Chirality : 0.044 0.151 764 Planarity : 0.004 0.049 910 Dihedral : 5.815 33.397 770 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 6.17 % Allowed : 24.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.33), residues: 635 helix: -3.80 (0.78), residues: 26 sheet: -0.93 (0.32), residues: 263 loop : -1.72 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.002 0.001 HIS L 91 PHE 0.021 0.001 PHE H 70 TYR 0.023 0.002 TYR A 80 ARG 0.008 0.001 ARG A 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 1) link_NAG-ASN : angle 4.07357 ( 3) link_BETA1-4 : bond 0.00290 ( 2) link_BETA1-4 : angle 1.74743 ( 6) hydrogen bonds : bond 0.03301 ( 113) hydrogen bonds : angle 5.91122 ( 264) SS BOND : bond 0.00360 ( 7) SS BOND : angle 1.12219 ( 14) covalent geometry : bond 0.00448 ( 5221) covalent geometry : angle 0.60467 ( 7082) *********************** 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 156 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: G 408 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8482 (ttp80) REVERT: G 414 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: G 466 ARG cc_start: 0.8427 (ptm160) cc_final: 0.7758 (ptm160) REVERT: G 467 ASP cc_start: 0.8118 (t0) cc_final: 0.7893 (t0) REVERT: G 472 ILE cc_start: 0.9257 (mm) cc_final: 0.9023 (mm) REVERT: L 107 LYS cc_start: 0.6643 (mtmm) cc_final: 0.5574 (mmtt) REVERT: H 107 ASP cc_start: 0.8492 (t0) cc_final: 0.8286 (t0) REVERT: B 61 ARG cc_start: 0.8246 (ptt-90) cc_final: 0.7970 (ptt90) REVERT: B 90 GLN cc_start: 0.9218 (pp30) cc_final: 0.8998 (pp30) outliers start: 34 outliers final: 29 residues processed: 141 average time/residue: 0.1705 time to fit residues: 30.8784 Evaluate side-chains 151 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 14 SER 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 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 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.0020 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 overall best weight: 0.3788 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.120942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.102999 restraints weight = 7955.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.105452 restraints weight = 5362.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107105 restraints weight = 4049.495| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5231 Z= 0.123 Angle : 0.580 6.282 7105 Z= 0.301 Chirality : 0.044 0.161 764 Planarity : 0.004 0.048 910 Dihedral : 5.508 33.341 770 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.17 % Allowed : 26.32 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.33), residues: 635 helix: -3.77 (0.78), residues: 26 sheet: -0.85 (0.32), residues: 263 loop : -1.66 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 436 HIS 0.001 0.000 HIS L 91 PHE 0.015 0.001 PHE H 70 TYR 0.017 0.001 TYR A 105 ARG 0.004 0.000 ARG H 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 1) link_NAG-ASN : angle 3.44544 ( 3) link_BETA1-4 : bond 0.00498 ( 2) link_BETA1-4 : angle 1.81871 ( 6) hydrogen bonds : bond 0.03015 ( 113) hydrogen bonds : angle 5.69995 ( 264) SS BOND : bond 0.00275 ( 7) SS BOND : angle 0.87907 ( 14) covalent geometry : bond 0.00286 ( 5221) covalent geometry : angle 0.57326 ( 7082) ********************** 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 144 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 466 ARG cc_start: 0.8378 (ptm160) cc_final: 0.7824 (ptm160) REVERT: G 467 ASP cc_start: 0.8000 (t0) cc_final: 0.7769 (t0) REVERT: G 472 ILE cc_start: 0.9257 (mm) cc_final: 0.9026 (mm) REVERT: L 47 MET cc_start: 0.6941 (mmm) cc_final: 0.6677 (mmm) REVERT: L 107 LYS cc_start: 0.6539 (mtmm) cc_final: 0.5446 (mmtt) REVERT: H 107 ASP cc_start: 0.8336 (t0) cc_final: 0.8131 (t0) REVERT: B 61 ARG cc_start: 0.8234 (ptt-90) cc_final: 0.7700 (ptt90) REVERT: B 90 GLN cc_start: 0.9139 (pp30) cc_final: 0.8760 (pp30) outliers start: 23 outliers final: 22 residues processed: 133 average time/residue: 0.1735 time to fit residues: 29.3505 Evaluate side-chains 141 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 14 SER 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 48 VAL Chi-restraints excluded: chain H residue 115 VAL 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 93 THR 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 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 8 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3322 r_free = 0.3322 target = 0.121388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.103330 restraints weight = 7963.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.105691 restraints weight = 5410.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.107482 restraints weight = 4128.315| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5231 Z= 0.128 Angle : 0.579 6.356 7105 Z= 0.300 Chirality : 0.044 0.181 764 Planarity : 0.004 0.050 910 Dihedral : 5.370 32.462 770 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.54 % Allowed : 26.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.33), residues: 635 helix: -3.36 (0.78), residues: 32 sheet: -0.80 (0.32), residues: 263 loop : -1.62 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.002 0.000 HIS L 91 PHE 0.030 0.001 PHE A 64 TYR 0.017 0.001 TYR G 453 ARG 0.004 0.000 ARG A 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 1) link_NAG-ASN : angle 3.42209 ( 3) link_BETA1-4 : bond 0.00461 ( 2) link_BETA1-4 : angle 1.59609 ( 6) hydrogen bonds : bond 0.03123 ( 113) hydrogen bonds : angle 5.69796 ( 264) SS BOND : bond 0.00303 ( 7) SS BOND : angle 0.89011 ( 14) covalent geometry : bond 0.00302 ( 5221) covalent geometry : angle 0.57214 ( 7082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2581.93 seconds wall clock time: 45 minutes 18.98 seconds (2718.98 seconds total)