Starting phenix.real_space_refine on Thu Mar 6 05:31:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lae_62925/03_2025/9lae_62925.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lae_62925/03_2025/9lae_62925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lae_62925/03_2025/9lae_62925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lae_62925/03_2025/9lae_62925.map" model { file = "/net/cci-nas-00/data/ceres_data/9lae_62925/03_2025/9lae_62925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lae_62925/03_2025/9lae_62925.cif" } resolution = 3.46 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= 0.014 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 28 5.16 5 C 3168 2.51 5 N 815 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 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5000 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: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 913 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.03, per 1000 atoms: 1.41 Number of scatterers: 5000 At special positions: 0 Unit cell: (94.138, 80.134, 104.252, 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 28 16.00 O 989 8.00 N 815 7.00 C 3168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, 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 391 " - pdb=" SG CYS G 525 " distance=2.06 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 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 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 NAG-ASN " NAG G 601 " - " ASN G 343 " Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 684.6 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: 1172 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 13 sheets defined 5.9% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'G' and resid 364 through 370 removed outlier: 4.357A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR G 369 " --> pdb=" O TYR G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 389 removed outlier: 4.042A pdb=" N ASN G 388 " --> pdb=" O THR G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.274A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.771A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.850A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.845A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.785A pdb=" N SER A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 354 through 358 removed outlier: 4.003A pdb=" N ASN G 394 " --> pdb=" O GLU G 516 " (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 'L' and resid 4 through 7 removed outlier: 3.961A pdb=" N SER L 7 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.170A pdb=" N MET L 11 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS L 104 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA L 13 " --> pdb=" O LYS L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.568A pdb=" N TRP L 34 " --> pdb=" O PHE L 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.552A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.570A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.529A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.561A pdb=" N LYS B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.611A pdb=" N VAL B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'A' and resid 9 through 12 removed outlier: 7.109A pdb=" N GLU A 10 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N TRP A 47 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR A 40 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU A 45 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 9 through 12 removed outlier: 7.109A pdb=" N GLU A 10 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR A 109 " --> pdb=" O ARG A 98 " (cutoff:3.500A) 153 hydrogen bonds defined for protein. 366 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: 1.99 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 804 1.30 - 1.44: 1548 1.44 - 1.58: 2735 1.58 - 1.72: 0 1.72 - 1.86: 40 Bond restraints: 5127 Sorted by residual: bond pdb=" C PHE G 392 " pdb=" O PHE G 392 " ideal model delta sigma weight residual 1.234 1.161 0.073 1.25e-02 6.40e+03 3.39e+01 bond pdb=" CA PHE G 347 " pdb=" C PHE G 347 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.45e-02 4.76e+03 2.75e+01 bond pdb=" CA PHE G 347 " pdb=" CB PHE G 347 " ideal model delta sigma weight residual 1.530 1.450 0.080 1.61e-02 3.86e+03 2.47e+01 bond pdb=" CA PHE G 392 " pdb=" C PHE G 392 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.24e-02 6.50e+03 1.68e+01 bond pdb=" C PHE G 347 " pdb=" O PHE G 347 " ideal model delta sigma weight residual 1.235 1.184 0.051 1.38e-02 5.25e+03 1.37e+01 ... (remaining 5122 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 6858 2.31 - 4.63: 88 4.63 - 6.94: 14 6.94 - 9.25: 2 9.25 - 11.56: 2 Bond angle restraints: 6964 Sorted by residual: angle pdb=" N PHE G 392 " pdb=" CA PHE G 392 " pdb=" C PHE G 392 " ideal model delta sigma weight residual 108.96 97.40 11.56 1.49e+00 4.50e-01 6.02e+01 angle pdb=" N VAL G 341 " pdb=" CA VAL G 341 " pdb=" C VAL G 341 " ideal model delta sigma weight residual 113.71 108.51 5.20 9.50e-01 1.11e+00 2.99e+01 angle pdb=" CA PHE G 392 " pdb=" C PHE G 392 " pdb=" N THR G 393 " ideal model delta sigma weight residual 115.38 122.62 -7.24 1.45e+00 4.76e-01 2.49e+01 angle pdb=" N VAL G 503 " pdb=" CA VAL G 503 " pdb=" C VAL G 503 " ideal model delta sigma weight residual 112.98 107.06 5.92 1.25e+00 6.40e-01 2.25e+01 angle pdb=" CA PHE G 392 " pdb=" C PHE G 392 " pdb=" O PHE G 392 " ideal model delta sigma weight residual 121.45 117.00 4.45 1.07e+00 8.73e-01 1.73e+01 ... (remaining 6959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2717 17.82 - 35.64: 243 35.64 - 53.45: 43 53.45 - 71.27: 6 71.27 - 89.09: 4 Dihedral angle restraints: 3013 sinusoidal: 1154 harmonic: 1859 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 93.00 163.34 -70.34 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CA CYS G 361 " pdb=" C CYS G 361 " pdb=" N VAL G 362 " pdb=" CA VAL G 362 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " pdb=" CB CYS G 361 " ideal model delta sinusoidal sigma weight residual 93.00 131.49 -38.49 1 1.00e+01 1.00e-02 2.09e+01 ... (remaining 3010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 510 0.044 - 0.089: 181 0.089 - 0.133: 51 0.133 - 0.177: 7 0.177 - 0.221: 1 Chirality restraints: 750 Sorted by residual: chirality pdb=" CA PHE G 392 " pdb=" N PHE G 392 " pdb=" C PHE G 392 " pdb=" CB PHE G 392 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA PHE G 347 " pdb=" N PHE G 347 " pdb=" C PHE G 347 " pdb=" CB PHE G 347 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA PRO G 463 " pdb=" N PRO G 463 " pdb=" C PRO G 463 " pdb=" CB PRO G 463 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 747 not shown) Planarity restraints: 889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG G 346 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C ARG G 346 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG G 346 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE G 347 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 58 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 59 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 389 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ASP G 389 " 0.029 2.00e-02 2.50e+03 pdb=" O ASP G 389 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU G 390 " -0.010 2.00e-02 2.50e+03 ... (remaining 886 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 121 2.68 - 3.23: 4582 3.23 - 3.79: 7182 3.79 - 4.34: 10120 4.34 - 4.90: 17729 Nonbonded interactions: 39734 Sorted by model distance: nonbonded pdb=" OG SER G 477 " pdb=" OD1 ASP A 99 " model vdw 2.120 3.040 nonbonded pdb=" OG SER G 477 " pdb=" O TYR A 105 " model vdw 2.215 3.040 nonbonded pdb=" O VAL L 25 " pdb=" OG1 THR L 68 " model vdw 2.217 3.040 nonbonded pdb=" N PHE G 392 " pdb=" O PHE G 392 " model vdw 2.234 2.496 nonbonded pdb=" O SER G 438 " pdb=" OG SER G 438 " model vdw 2.248 3.040 ... (remaining 39729 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=0.67 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 94.040 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 22.870 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:4.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 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 : 0.006 0.080 5127 Z= 0.388 Angle : 0.729 11.563 6964 Z= 0.429 Chirality : 0.048 0.221 750 Planarity : 0.004 0.045 888 Dihedral : 13.670 89.090 1817 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.03 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.66 (0.28), residues: 635 helix: -4.06 (0.70), residues: 26 sheet: -1.75 (0.31), residues: 215 loop : -2.84 (0.26), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.002 0.001 HIS H 99 PHE 0.021 0.002 PHE G 392 TYR 0.021 0.002 TYR G 505 ARG 0.002 0.000 ARG B 18 *********************** 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 135 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 346 ARG cc_start: 0.8146 (ttt180) cc_final: 0.7267 (ttm-80) REVERT: G 408 ARG cc_start: 0.7815 (mtp180) cc_final: 0.7572 (mtm180) REVERT: G 459 SER cc_start: 0.8141 (m) cc_final: 0.7780 (p) REVERT: G 472 ILE cc_start: 0.6195 (mp) cc_final: 0.5869 (mm) REVERT: L 51 SER cc_start: 0.8358 (t) cc_final: 0.8114 (p) REVERT: H 31 THR cc_start: 0.8922 (t) cc_final: 0.8620 (p) REVERT: H 63 SER cc_start: 0.8424 (m) cc_final: 0.8065 (p) REVERT: H 108 MET cc_start: 0.8338 (mtt) cc_final: 0.8043 (mtt) REVERT: H 113 GLN cc_start: 0.6904 (mt0) cc_final: 0.6088 (pt0) REVERT: B 23 CYS cc_start: 0.5494 (t) cc_final: 0.4655 (t) REVERT: B 37 GLN cc_start: 0.7868 (tt0) cc_final: 0.7667 (tt0) REVERT: A 38 LYS cc_start: 0.6928 (tttt) cc_final: 0.6695 (tttm) REVERT: A 80 TYR cc_start: 0.6538 (m-80) cc_final: 0.6192 (m-80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2321 time to fit residues: 39.3922 Evaluate side-chains 120 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 388 ASN G 450 ASN A 3 GLN A 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.147828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119920 restraints weight = 6458.493| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.14 r_work: 0.3198 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 5127 Z= 0.435 Angle : 0.674 10.546 6964 Z= 0.359 Chirality : 0.048 0.150 750 Planarity : 0.005 0.046 888 Dihedral : 6.125 81.030 730 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 3.11 % Allowed : 12.61 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.15 (0.29), residues: 635 helix: -4.52 (0.66), residues: 20 sheet: -1.46 (0.31), residues: 234 loop : -2.45 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 436 HIS 0.002 0.001 HIS L 33 PHE 0.016 0.002 PHE L 46 TYR 0.024 0.002 TYR G 369 ARG 0.002 0.000 ARG G 466 *********************** 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 134 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.711 Fit side-chains REVERT: G 346 ARG cc_start: 0.8510 (ttt180) cc_final: 0.8051 (ttm-80) REVERT: G 442 ASP cc_start: 0.9096 (m-30) cc_final: 0.8784 (m-30) REVERT: G 459 SER cc_start: 0.8870 (m) cc_final: 0.8639 (p) REVERT: G 484 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7048 (tm-30) REVERT: H 113 GLN cc_start: 0.7851 (mt0) cc_final: 0.7239 (pt0) REVERT: B 79 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7237 (mm110) REVERT: A 19 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7966 (ptmt) REVERT: A 80 TYR cc_start: 0.7369 (m-80) cc_final: 0.6906 (m-80) outliers start: 17 outliers final: 10 residues processed: 126 average time/residue: 0.3171 time to fit residues: 50.0672 Evaluate side-chains 122 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 19 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115458 restraints weight = 6603.880| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.24 r_work: 0.3212 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5127 Z= 0.249 Angle : 0.585 8.851 6964 Z= 0.311 Chirality : 0.045 0.148 750 Planarity : 0.004 0.048 888 Dihedral : 5.784 83.313 730 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.20 % Allowed : 14.08 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.53 (0.30), residues: 635 helix: -4.37 (0.67), residues: 21 sheet: -0.85 (0.32), residues: 248 loop : -2.17 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 436 HIS 0.001 0.001 HIS L 88 PHE 0.025 0.001 PHE L 46 TYR 0.020 0.001 TYR G 369 ARG 0.001 0.000 ARG G 403 *********************** 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 142 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.452 Fit side-chains REVERT: G 346 ARG cc_start: 0.8271 (ttt180) cc_final: 0.8060 (ttm-80) REVERT: G 442 ASP cc_start: 0.8936 (m-30) cc_final: 0.8722 (m-30) REVERT: H 113 GLN cc_start: 0.7696 (mt0) cc_final: 0.7222 (pt0) REVERT: B 79 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7278 (mm110) REVERT: A 19 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7723 (ptmt) REVERT: A 80 TYR cc_start: 0.7313 (m-80) cc_final: 0.7034 (m-80) outliers start: 23 outliers final: 13 residues processed: 138 average time/residue: 0.2053 time to fit residues: 36.3585 Evaluate side-chains 124 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 477 SER Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 388 ASN A 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.131363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.102757 restraints weight = 6803.636| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.15 r_work: 0.3194 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5127 Z= 0.335 Angle : 0.612 10.734 6964 Z= 0.322 Chirality : 0.046 0.145 750 Planarity : 0.005 0.045 888 Dihedral : 5.966 88.256 730 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.39 % Allowed : 16.45 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.44 (0.30), residues: 635 helix: -4.16 (0.71), residues: 21 sheet: -0.81 (0.31), residues: 258 loop : -2.13 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 436 HIS 0.002 0.001 HIS L 88 PHE 0.032 0.002 PHE L 46 TYR 0.018 0.002 TYR G 369 ARG 0.002 0.000 ARG G 466 *********************** 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 137 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.682 Fit side-chains REVERT: G 386 LYS cc_start: 0.8232 (mmpt) cc_final: 0.7923 (tttp) REVERT: G 442 ASP cc_start: 0.8976 (m-30) cc_final: 0.8756 (m-30) REVERT: G 484 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7069 (tm-30) REVERT: H 113 GLN cc_start: 0.7702 (mt0) cc_final: 0.7242 (pt0) REVERT: A 19 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7711 (ptmt) REVERT: A 80 TYR cc_start: 0.7276 (m-80) cc_final: 0.7029 (m-80) outliers start: 24 outliers final: 17 residues processed: 131 average time/residue: 0.3107 time to fit residues: 51.6137 Evaluate side-chains 130 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 477 SER Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 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 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.103767 restraints weight = 6751.566| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.04 r_work: 0.2903 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5127 Z= 0.287 Angle : 0.601 10.284 6964 Z= 0.315 Chirality : 0.045 0.144 750 Planarity : 0.004 0.047 888 Dihedral : 5.884 88.021 730 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.39 % Allowed : 16.82 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.19 (0.31), residues: 635 helix: -4.02 (0.72), residues: 21 sheet: -0.51 (0.32), residues: 248 loop : -2.03 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 436 HIS 0.002 0.001 HIS L 88 PHE 0.026 0.001 PHE L 46 TYR 0.016 0.001 TYR G 369 ARG 0.001 0.000 ARG G 466 *********************** 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 140 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.998 Fit side-chains REVERT: G 442 ASP cc_start: 0.9098 (m-30) cc_final: 0.8853 (m-30) REVERT: H 113 GLN cc_start: 0.7818 (mt0) cc_final: 0.7305 (pt0) REVERT: A 19 LYS cc_start: 0.8482 (ptmt) cc_final: 0.7831 (ptmt) REVERT: A 80 TYR cc_start: 0.7343 (m-80) cc_final: 0.6854 (m-80) REVERT: A 85 SER cc_start: 0.7666 (m) cc_final: 0.7283 (t) outliers start: 24 outliers final: 16 residues processed: 134 average time/residue: 0.2844 time to fit residues: 48.4720 Evaluate side-chains 127 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 477 SER Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.0070 chunk 15 optimal weight: 0.5980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN A 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.132367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.104051 restraints weight = 6689.457| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.14 r_work: 0.3215 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5127 Z= 0.278 Angle : 0.593 10.460 6964 Z= 0.310 Chirality : 0.045 0.148 750 Planarity : 0.004 0.041 888 Dihedral : 5.738 83.570 730 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 4.75 % Allowed : 17.18 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.31), residues: 635 helix: -3.73 (0.78), residues: 21 sheet: -0.41 (0.32), residues: 248 loop : -1.99 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 436 HIS 0.002 0.001 HIS L 88 PHE 0.023 0.001 PHE L 46 TYR 0.017 0.001 TYR A 27 ARG 0.001 0.000 ARG G 466 *********************** 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 142 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.946 Fit side-chains REVERT: G 442 ASP cc_start: 0.9007 (m-30) cc_final: 0.8782 (m-30) REVERT: H 113 GLN cc_start: 0.7740 (mt0) cc_final: 0.7286 (pt0) REVERT: A 19 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8107 (ptmt) REVERT: A 80 TYR cc_start: 0.7148 (m-80) cc_final: 0.6901 (m-80) REVERT: A 85 SER cc_start: 0.7618 (m) cc_final: 0.7382 (t) outliers start: 26 outliers final: 18 residues processed: 134 average time/residue: 0.3379 time to fit residues: 59.1982 Evaluate side-chains 133 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 477 SER Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.129923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.101838 restraints weight = 6756.509| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.10 r_work: 0.3246 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 5127 Z= 0.286 Angle : 0.605 10.478 6964 Z= 0.315 Chirality : 0.045 0.147 750 Planarity : 0.004 0.039 888 Dihedral : 5.682 80.937 730 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.57 % Allowed : 17.55 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.95 (0.31), residues: 635 helix: -3.39 (0.89), residues: 21 sheet: -0.28 (0.32), residues: 246 loop : -1.95 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 436 HIS 0.002 0.001 HIS L 88 PHE 0.029 0.001 PHE L 46 TYR 0.012 0.001 TYR G 453 ARG 0.001 0.000 ARG G 466 *********************** 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 141 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.557 Fit side-chains REVERT: G 442 ASP cc_start: 0.8994 (m-30) cc_final: 0.8767 (m-30) REVERT: H 84 SER cc_start: 0.9020 (p) cc_final: 0.8777 (t) REVERT: H 113 GLN cc_start: 0.7789 (mt0) cc_final: 0.7335 (pt0) REVERT: A 19 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8110 (ptmt) REVERT: A 80 TYR cc_start: 0.7164 (m-80) cc_final: 0.6917 (m-80) outliers start: 25 outliers final: 18 residues processed: 133 average time/residue: 0.2026 time to fit residues: 34.2637 Evaluate side-chains 131 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 477 SER Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 0.0040 chunk 1 optimal weight: 0.4980 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN A 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.132496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.103992 restraints weight = 6810.358| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.15 r_work: 0.3307 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5127 Z= 0.203 Angle : 0.579 11.317 6964 Z= 0.301 Chirality : 0.044 0.177 750 Planarity : 0.004 0.040 888 Dihedral : 5.465 79.920 730 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.39 % Allowed : 18.46 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.71 (0.31), residues: 635 helix: -3.29 (0.92), residues: 20 sheet: -0.06 (0.32), residues: 244 loop : -1.83 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 93 HIS 0.001 0.000 HIS L 88 PHE 0.024 0.001 PHE L 46 TYR 0.019 0.001 TYR A 27 ARG 0.002 0.000 ARG H 72 *********************** 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 136 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.887 Fit side-chains REVERT: G 438 SER cc_start: 0.9031 (t) cc_final: 0.8802 (t) REVERT: G 442 ASP cc_start: 0.8967 (m-30) cc_final: 0.8508 (m-30) REVERT: L 64 SER cc_start: 0.8130 (t) cc_final: 0.7905 (p) REVERT: L 102 GLU cc_start: 0.7375 (tt0) cc_final: 0.6942 (tp30) REVERT: H 84 SER cc_start: 0.8972 (p) cc_final: 0.8707 (t) REVERT: H 108 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8246 (mtt) REVERT: H 113 GLN cc_start: 0.7765 (mt0) cc_final: 0.7328 (pt0) REVERT: A 19 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7803 (ptmt) REVERT: A 80 TYR cc_start: 0.7129 (m-80) cc_final: 0.6709 (m-80) outliers start: 24 outliers final: 14 residues processed: 127 average time/residue: 0.2343 time to fit residues: 38.8116 Evaluate side-chains 125 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN A 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.129495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.100795 restraints weight = 6735.410| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.21 r_work: 0.2902 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 5127 Z= 0.300 Angle : 0.618 11.207 6964 Z= 0.321 Chirality : 0.045 0.179 750 Planarity : 0.004 0.040 888 Dihedral : 5.632 79.940 730 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.84 % Allowed : 19.74 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.78 (0.31), residues: 635 helix: -3.39 (0.88), residues: 21 sheet: -0.16 (0.32), residues: 248 loop : -1.84 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 436 HIS 0.002 0.001 HIS L 88 PHE 0.030 0.001 PHE L 46 TYR 0.013 0.001 TYR G 453 ARG 0.001 0.000 ARG H 38 *********************** 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 132 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.580 Fit side-chains REVERT: G 442 ASP cc_start: 0.9119 (m-30) cc_final: 0.8856 (m-30) REVERT: H 84 SER cc_start: 0.9035 (p) cc_final: 0.8793 (t) REVERT: H 113 GLN cc_start: 0.7844 (mt0) cc_final: 0.7305 (pt0) REVERT: A 19 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8089 (ptmt) REVERT: A 80 TYR cc_start: 0.7254 (m-80) cc_final: 0.7003 (m-80) outliers start: 21 outliers final: 17 residues processed: 122 average time/residue: 0.2002 time to fit residues: 31.2015 Evaluate side-chains 129 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 55 optimal weight: 0.0980 chunk 5 optimal weight: 0.0010 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 487 ASN A 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.133152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.104515 restraints weight = 6758.723| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.16 r_work: 0.2957 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5127 Z= 0.203 Angle : 0.576 10.152 6964 Z= 0.298 Chirality : 0.044 0.164 750 Planarity : 0.004 0.042 888 Dihedral : 5.391 79.665 730 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.84 % Allowed : 19.93 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.63 (0.32), residues: 635 helix: -3.33 (0.90), residues: 21 sheet: -0.14 (0.32), residues: 257 loop : -1.71 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 93 HIS 0.001 0.000 HIS L 88 PHE 0.022 0.001 PHE L 46 TYR 0.020 0.001 TYR A 27 ARG 0.001 0.000 ARG G 403 ********************** 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 131 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.325 Fit side-chains REVERT: G 438 SER cc_start: 0.9178 (t) cc_final: 0.8930 (t) REVERT: G 442 ASP cc_start: 0.9068 (m-30) cc_final: 0.8578 (m-30) REVERT: L 64 SER cc_start: 0.8084 (t) cc_final: 0.7814 (p) REVERT: L 102 GLU cc_start: 0.7482 (tt0) cc_final: 0.6920 (tp30) REVERT: H 84 SER cc_start: 0.9022 (p) cc_final: 0.8741 (t) REVERT: H 113 GLN cc_start: 0.7847 (mt0) cc_final: 0.7283 (pt0) REVERT: A 19 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8086 (ptmt) outliers start: 21 outliers final: 14 residues processed: 123 average time/residue: 0.2598 time to fit residues: 41.2335 Evaluate side-chains 124 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.127742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098660 restraints weight = 6838.670| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.21 r_work: 0.2875 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 5127 Z= 0.405 Angle : 0.676 12.058 6964 Z= 0.350 Chirality : 0.047 0.186 750 Planarity : 0.005 0.049 888 Dihedral : 5.845 79.971 730 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.02 % Allowed : 20.11 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.81 (0.31), residues: 635 helix: -3.40 (0.86), residues: 21 sheet: -0.19 (0.32), residues: 246 loop : -1.85 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 436 HIS 0.003 0.001 HIS L 88 PHE 0.036 0.002 PHE L 46 TYR 0.015 0.002 TYR B 49 ARG 0.002 0.000 ARG G 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4339.07 seconds wall clock time: 80 minutes 13.30 seconds (4813.30 seconds total)