Starting phenix.real_space_refine on Wed Mar 5 17:38:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k45_22660/03_2025/7k45_22660.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k45_22660/03_2025/7k45_22660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k45_22660/03_2025/7k45_22660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k45_22660/03_2025/7k45_22660.map" model { file = "/net/cci-nas-00/data/ceres_data/7k45_22660/03_2025/7k45_22660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k45_22660/03_2025/7k45_22660.cif" } resolution = 3.7 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= 0.015 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 16 5.16 5 C 1960 2.51 5 N 529 2.21 5 O 533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 3038 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 849 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "L" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 730 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1431 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.32, per 1000 atoms: 2.41 Number of scatterers: 3038 At special positions: 0 Unit cell: (70.35, 55.65, 100.8, 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 16 16.00 O 533 8.00 N 529 7.00 C 1960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.10 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 405.0 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 10 sheets defined 15.3% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.745A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.815A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.227A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.295A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.052A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA4, first strand: chain 'H' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.738A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 126 hydrogen bonds defined for protein. 285 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: 1.27 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 933 1.33 - 1.47: 940 1.47 - 1.60: 1225 1.60 - 1.73: 2 1.73 - 1.86: 18 Bond restraints: 3118 Sorted by residual: bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.611 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.479 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C5 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.413 1.474 -0.061 2.00e-02 2.50e+03 9.37e+00 bond pdb=" NE1 TRP H 50 " pdb=" CE2 TRP H 50 " ideal model delta sigma weight residual 1.370 1.337 0.033 1.10e-02 8.26e+03 8.78e+00 bond pdb=" CB ASN B 422 " pdb=" CG ASN B 422 " ideal model delta sigma weight residual 1.516 1.446 0.070 2.50e-02 1.60e+03 7.94e+00 ... (remaining 3113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 3463 1.63 - 3.26: 641 3.26 - 4.89: 116 4.89 - 6.53: 36 6.53 - 8.16: 11 Bond angle restraints: 4267 Sorted by residual: angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 120.03 128.19 -8.16 9.90e-01 1.02e+00 6.79e+01 angle pdb=" C ILE L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 120.21 126.95 -6.74 9.60e-01 1.09e+00 4.93e+01 angle pdb=" C SER B 383 " pdb=" N PRO B 384 " pdb=" CA PRO B 384 " ideal model delta sigma weight residual 119.56 126.42 -6.86 1.02e+00 9.61e-01 4.53e+01 angle pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.56 126.33 -6.77 1.02e+00 9.61e-01 4.41e+01 angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.87 126.70 -6.83 1.04e+00 9.25e-01 4.31e+01 ... (remaining 4262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 1752 16.65 - 33.30: 55 33.30 - 49.94: 10 49.94 - 66.59: 4 66.59 - 83.24: 1 Dihedral angle restraints: 1822 sinusoidal: 618 harmonic: 1204 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 121.87 -28.87 1 1.00e+01 1.00e-02 1.19e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 66.25 26.75 1 1.00e+01 1.00e-02 1.03e+01 dihedral pdb=" C TYR L 92 " pdb=" N TYR L 92 " pdb=" CA TYR L 92 " pdb=" CB TYR L 92 " ideal model delta harmonic sigma weight residual -122.60 -115.16 -7.44 0 2.50e+00 1.60e-01 8.85e+00 ... (remaining 1819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 306 0.068 - 0.136: 127 0.136 - 0.204: 28 0.204 - 0.272: 5 0.272 - 0.340: 4 Chirality restraints: 470 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.64e+01 chirality pdb=" C2 NAG A 2 " pdb=" C1 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" N2 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.83 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C2 NAG A 1 " pdb=" C1 NAG A 1 " pdb=" C3 NAG A 1 " pdb=" N2 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.82 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 467 not shown) Planarity restraints: 561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 92 " -0.030 2.00e-02 2.50e+03 1.51e-02 4.56e+00 pdb=" CG TYR L 92 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR L 92 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR L 92 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR L 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR L 92 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR L 92 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 92 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 50 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.49e+00 pdb=" CG TRP H 50 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP H 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP H 50 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP H 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 50 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 50 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 50 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 50 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 50 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.023 2.00e-02 2.50e+03 1.32e-02 4.34e+00 pdb=" CG TRP H 47 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.017 2.00e-02 2.50e+03 ... (remaining 558 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 1766 3.03 - 3.50: 2712 3.50 - 3.97: 4880 3.97 - 4.43: 5575 4.43 - 4.90: 9162 Nonbonded interactions: 24095 Sorted by model distance: nonbonded pdb=" N LYS B 462 " pdb=" O LYS B 462 " model vdw 2.568 2.496 nonbonded pdb=" N GLU L 80 " pdb=" O GLU L 80 " model vdw 2.592 2.496 nonbonded pdb=" CB GLN H 6 " pdb=" OE1 GLN H 6 " model vdw 2.598 2.752 nonbonded pdb=" N GLY B 502 " pdb=" O GLY B 502 " model vdw 2.601 2.496 nonbonded pdb=" N SER B 373 " pdb=" N PHE B 374 " model vdw 2.605 2.560 ... (remaining 24090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.940 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 18.080 Find NCS groups from input model: 0.030 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 0.014 0.092 3118 Z= 0.969 Angle : 1.416 8.157 4267 Z= 0.963 Chirality : 0.079 0.340 470 Planarity : 0.006 0.039 560 Dihedral : 9.350 83.236 1037 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.92 (0.41), residues: 411 helix: -4.00 (0.49), residues: 33 sheet: 1.14 (0.43), residues: 150 loop : 1.17 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.008 TRP H 50 HIS 0.002 0.001 HIS H 65 PHE 0.013 0.003 PHE H 64 TYR 0.030 0.004 TYR L 92 ARG 0.004 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: B 369 TYR cc_start: 0.7080 (t80) cc_final: 0.6653 (t80) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2456 time to fit residues: 23.6794 Evaluate side-chains 44 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.1980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.1980 overall best weight: 0.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN B 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.104434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.094537 restraints weight = 7257.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.097152 restraints weight = 3953.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.098943 restraints weight = 2501.280| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3118 Z= 0.234 Angle : 0.644 6.838 4267 Z= 0.347 Chirality : 0.047 0.141 470 Planarity : 0.005 0.037 560 Dihedral : 4.933 21.952 502 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.64 % Allowed : 13.36 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.50 (0.40), residues: 411 helix: -3.64 (0.67), residues: 27 sheet: 0.64 (0.40), residues: 154 loop : 0.81 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.004 0.003 HIS H 65 PHE 0.011 0.002 PHE B 497 TYR 0.027 0.002 TYR L 92 ARG 0.004 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 37 TYR cc_start: 0.8658 (m-10) cc_final: 0.7856 (m-80) REVERT: L 72 PHE cc_start: 0.6843 (m-80) cc_final: 0.6586 (m-80) REVERT: B 369 TYR cc_start: 0.6709 (t80) cc_final: 0.6373 (t80) outliers start: 9 outliers final: 6 residues processed: 62 average time/residue: 0.1770 time to fit residues: 13.0648 Evaluate side-chains 48 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 35 GLN B 370 ASN B 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.099603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.090345 restraints weight = 7260.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.092520 restraints weight = 4373.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.094076 restraints weight = 2974.843| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3118 Z= 0.455 Angle : 0.720 7.565 4267 Z= 0.392 Chirality : 0.048 0.136 470 Planarity : 0.005 0.035 560 Dihedral : 5.406 25.779 502 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 5.67 % Allowed : 12.15 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.07 (0.39), residues: 411 helix: -3.28 (0.95), residues: 20 sheet: 0.21 (0.40), residues: 152 loop : 0.39 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 36 HIS 0.007 0.004 HIS H 65 PHE 0.012 0.002 PHE B 486 TYR 0.037 0.002 TYR L 92 ARG 0.005 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7681 (m-30) cc_final: 0.7297 (m-30) REVERT: L 72 PHE cc_start: 0.7246 (m-80) cc_final: 0.6808 (m-10) REVERT: B 369 TYR cc_start: 0.6760 (t80) cc_final: 0.6338 (t80) outliers start: 14 outliers final: 11 residues processed: 54 average time/residue: 0.1544 time to fit residues: 10.3028 Evaluate side-chains 51 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 5 optimal weight: 0.1980 chunk 23 optimal weight: 0.0000 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.100578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.091441 restraints weight = 7243.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.093675 restraints weight = 4307.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.095196 restraints weight = 2883.210| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3118 Z= 0.330 Angle : 0.659 6.854 4267 Z= 0.357 Chirality : 0.047 0.138 470 Planarity : 0.005 0.039 560 Dihedral : 5.318 26.220 502 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.86 % Allowed : 13.77 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.05 (0.40), residues: 411 helix: -3.04 (1.05), residues: 20 sheet: 0.02 (0.39), residues: 152 loop : 0.36 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 436 HIS 0.004 0.003 HIS H 65 PHE 0.017 0.002 PHE B 392 TYR 0.027 0.002 TYR L 92 ARG 0.003 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7620 (m-30) cc_final: 0.7190 (m-30) outliers start: 12 outliers final: 11 residues processed: 46 average time/residue: 0.1547 time to fit residues: 8.7990 Evaluate side-chains 48 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.0870 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 36 optimal weight: 0.0770 chunk 4 optimal weight: 0.4980 chunk 32 optimal weight: 0.2980 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.098584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.088835 restraints weight = 7321.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.091294 restraints weight = 4173.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.092980 restraints weight = 2711.477| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3118 Z= 0.255 Angle : 0.601 5.863 4267 Z= 0.324 Chirality : 0.046 0.139 470 Planarity : 0.004 0.038 560 Dihedral : 5.052 27.702 502 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 5.26 % Allowed : 12.96 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.13 (0.41), residues: 411 helix: -2.90 (1.10), residues: 20 sheet: -0.08 (0.39), residues: 155 loop : 0.32 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.003 0.002 HIS H 65 PHE 0.015 0.001 PHE B 392 TYR 0.023 0.002 TYR L 92 ARG 0.003 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7837 (m-30) cc_final: 0.7317 (m-30) REVERT: L 102 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7187 (mp10) outliers start: 13 outliers final: 11 residues processed: 50 average time/residue: 0.1558 time to fit residues: 9.5828 Evaluate side-chains 52 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 0.0970 chunk 35 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 22 optimal weight: 0.0170 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.099424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.089456 restraints weight = 7515.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.091991 restraints weight = 4210.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.093691 restraints weight = 2718.245| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3118 Z= 0.202 Angle : 0.564 6.009 4267 Z= 0.302 Chirality : 0.045 0.141 470 Planarity : 0.004 0.039 560 Dihedral : 4.793 28.432 502 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.86 % Allowed : 14.57 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.04 (0.41), residues: 411 helix: -2.83 (1.09), residues: 20 sheet: 0.06 (0.40), residues: 154 loop : 0.33 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS H 65 PHE 0.013 0.001 PHE B 392 TYR 0.021 0.001 TYR L 92 ARG 0.002 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7851 (m-30) cc_final: 0.7391 (m-30) REVERT: L 37 TYR cc_start: 0.8728 (m-10) cc_final: 0.8056 (m-80) REVERT: L 102 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.6904 (mp10) outliers start: 12 outliers final: 8 residues processed: 53 average time/residue: 0.2051 time to fit residues: 12.7587 Evaluate side-chains 50 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 22 optimal weight: 0.0020 chunk 39 optimal weight: 0.0870 chunk 6 optimal weight: 0.1980 chunk 35 optimal weight: 0.2980 chunk 19 optimal weight: 0.0980 overall best weight: 0.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN B 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.101531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.091536 restraints weight = 7224.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.094052 restraints weight = 4139.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.095776 restraints weight = 2688.401| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3118 Z= 0.155 Angle : 0.560 7.962 4267 Z= 0.293 Chirality : 0.045 0.141 470 Planarity : 0.004 0.038 560 Dihedral : 4.549 28.049 502 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.05 % Allowed : 17.81 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.06 (0.41), residues: 411 helix: -2.81 (1.08), residues: 20 sheet: 0.14 (0.40), residues: 154 loop : 0.39 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.001 0.001 HIS H 65 PHE 0.022 0.001 PHE B 392 TYR 0.016 0.001 TYR L 92 ARG 0.005 0.000 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7753 (m-30) cc_final: 0.7423 (m-30) REVERT: L 37 TYR cc_start: 0.8613 (m-10) cc_final: 0.8046 (m-80) REVERT: L 102 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.6755 (mp10) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.1922 time to fit residues: 11.7737 Evaluate side-chains 50 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 471 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 0.0470 chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.096890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.086761 restraints weight = 7314.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.089194 restraints weight = 4257.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.090855 restraints weight = 2821.602| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3118 Z= 0.359 Angle : 0.642 7.684 4267 Z= 0.344 Chirality : 0.046 0.131 470 Planarity : 0.005 0.042 560 Dihedral : 5.045 30.788 502 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.67 % Allowed : 14.98 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.13 (0.41), residues: 411 helix: -2.92 (1.08), residues: 20 sheet: -0.01 (0.40), residues: 156 loop : 0.28 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 436 HIS 0.004 0.003 HIS H 65 PHE 0.016 0.002 PHE B 392 TYR 0.029 0.002 TYR L 92 ARG 0.004 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7923 (m-30) cc_final: 0.7404 (m-30) REVERT: L 102 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.7046 (mp10) outliers start: 14 outliers final: 11 residues processed: 52 average time/residue: 0.1677 time to fit residues: 10.6181 Evaluate side-chains 50 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.0010 chunk 16 optimal weight: 0.0980 overall best weight: 0.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.099321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.089628 restraints weight = 7416.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.091971 restraints weight = 4308.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.093600 restraints weight = 2860.264| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3118 Z= 0.202 Angle : 0.581 7.624 4267 Z= 0.308 Chirality : 0.045 0.137 470 Planarity : 0.004 0.040 560 Dihedral : 4.801 31.526 502 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.86 % Allowed : 16.19 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.09 (0.42), residues: 411 helix: -2.85 (1.08), residues: 20 sheet: 0.02 (0.41), residues: 149 loop : 0.28 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS H 65 PHE 0.016 0.001 PHE B 392 TYR 0.019 0.001 TYR L 92 ARG 0.004 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7845 (m-30) cc_final: 0.7434 (m-30) REVERT: L 102 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.6786 (mp10) outliers start: 12 outliers final: 8 residues processed: 51 average time/residue: 0.1856 time to fit residues: 11.2691 Evaluate side-chains 49 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.0270 chunk 12 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 16 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 overall best weight: 0.2038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.099250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.089422 restraints weight = 7198.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.091857 restraints weight = 4096.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093391 restraints weight = 2681.650| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3118 Z= 0.202 Angle : 0.574 7.493 4267 Z= 0.304 Chirality : 0.045 0.138 470 Planarity : 0.004 0.038 560 Dihedral : 4.730 31.784 502 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.64 % Allowed : 17.41 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.03 (0.42), residues: 411 helix: -2.84 (1.08), residues: 20 sheet: 0.03 (0.41), residues: 155 loop : 0.36 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS H 65 PHE 0.016 0.001 PHE B 392 TYR 0.020 0.001 TYR L 92 ARG 0.003 0.000 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7845 (m-30) cc_final: 0.7467 (m-30) REVERT: L 102 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.6771 (mp10) outliers start: 9 outliers final: 8 residues processed: 49 average time/residue: 0.2039 time to fit residues: 11.8878 Evaluate side-chains 47 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 1 optimal weight: 0.0270 chunk 14 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.096921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087181 restraints weight = 7404.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.089525 restraints weight = 4348.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.091091 restraints weight = 2887.927| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3118 Z= 0.351 Angle : 0.643 7.750 4267 Z= 0.343 Chirality : 0.046 0.133 470 Planarity : 0.005 0.041 560 Dihedral : 5.105 33.747 502 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.26 % Allowed : 15.79 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.10 (0.42), residues: 411 helix: -2.74 (1.22), residues: 14 sheet: -0.03 (0.41), residues: 154 loop : 0.22 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 436 HIS 0.004 0.003 HIS H 65 PHE 0.012 0.002 PHE B 392 TYR 0.026 0.002 TYR L 92 ARG 0.006 0.001 ARG L 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1722.62 seconds wall clock time: 30 minutes 22.30 seconds (1822.30 seconds total)