Starting phenix.real_space_refine on Tue Feb 11 01:06:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wm0_32596/02_2025/7wm0_32596.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wm0_32596/02_2025/7wm0_32596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wm0_32596/02_2025/7wm0_32596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wm0_32596/02_2025/7wm0_32596.map" model { file = "/net/cci-nas-00/data/ceres_data/7wm0_32596/02_2025/7wm0_32596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wm0_32596/02_2025/7wm0_32596.cif" } resolution = 3.35 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= 0.005 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 17 5.16 5 C 2146 2.51 5 N 573 2.21 5 O 640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3376 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1554 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Chain: "L" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" 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: 3.51, per 1000 atoms: 1.04 Number of scatterers: 3376 At special positions: 0 Unit cell: (71.994, 79.092, 70.98, 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 17 16.00 O 640 8.00 N 573 7.00 C 2146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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=2.01 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 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 B1301 " - " ASN B 343 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 417.2 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 10.4% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.113A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.814A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.373A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.373A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.805A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.664A pdb=" N THR H 124 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR H 94 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 126 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.561A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1016 1.34 - 1.46: 795 1.46 - 1.59: 1630 1.59 - 1.71: 0 1.71 - 1.83: 22 Bond restraints: 3463 Sorted by residual: bond pdb=" N ILE B 472 " pdb=" CA ILE B 472 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" N VAL L 88 " pdb=" CA VAL L 88 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.14e-02 7.69e+03 1.18e+01 bond pdb=" N LYS B 444 " pdb=" CA LYS B 444 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N ILE B 402 " pdb=" CA ILE B 402 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" N ASN H 54 " pdb=" CA ASN H 54 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.10e-02 8.26e+03 9.66e+00 ... (remaining 3458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 3960 1.62 - 3.23: 630 3.23 - 4.85: 96 4.85 - 6.47: 15 6.47 - 8.09: 6 Bond angle restraints: 4707 Sorted by residual: angle pdb=" N SER B 366 " pdb=" CA SER B 366 " pdb=" C SER B 366 " ideal model delta sigma weight residual 111.71 105.91 5.80 1.15e+00 7.56e-01 2.54e+01 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 109.85 116.70 -6.85 1.58e+00 4.01e-01 1.88e+01 angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 112.90 108.75 4.15 9.60e-01 1.09e+00 1.87e+01 angle pdb=" C VAL B 407 " pdb=" N ARG B 408 " pdb=" CA ARG B 408 " ideal model delta sigma weight residual 120.38 126.29 -5.91 1.37e+00 5.33e-01 1.86e+01 angle pdb=" N TYR B 369 " pdb=" CA TYR B 369 " pdb=" C TYR B 369 " ideal model delta sigma weight residual 112.89 108.02 4.87 1.24e+00 6.50e-01 1.54e+01 ... (remaining 4702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 1807 13.97 - 27.95: 173 27.95 - 41.92: 53 41.92 - 55.90: 11 55.90 - 69.87: 7 Dihedral angle restraints: 2051 sinusoidal: 810 harmonic: 1241 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 93.00 126.08 -33.08 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" C ARG B 466 " pdb=" N ARG B 466 " pdb=" CA ARG B 466 " pdb=" CB ARG B 466 " ideal model delta harmonic sigma weight residual -122.60 -114.01 -8.59 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" C TYR B 365 " pdb=" N TYR B 365 " pdb=" CA TYR B 365 " pdb=" CB TYR B 365 " ideal model delta harmonic sigma weight residual -122.60 -114.17 -8.43 0 2.50e+00 1.60e-01 1.14e+01 ... (remaining 2048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 340 0.067 - 0.133: 117 0.133 - 0.200: 39 0.200 - 0.267: 8 0.267 - 0.333: 2 Chirality restraints: 506 Sorted by residual: chirality pdb=" CA ILE L 2 " pdb=" N ILE L 2 " pdb=" C ILE L 2 " pdb=" CB ILE L 2 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ARG B 466 " pdb=" N ARG B 466 " pdb=" C ARG B 466 " pdb=" CB ARG B 466 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA TYR H 115 " pdb=" N TYR H 115 " pdb=" C TYR H 115 " pdb=" CB TYR H 115 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 503 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.355 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG B1301 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " -0.137 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 353 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C TRP B 353 " -0.047 2.00e-02 2.50e+03 pdb=" O TRP B 353 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 354 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 116 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C GLY H 116 " 0.037 2.00e-02 2.50e+03 pdb=" O GLY H 116 " -0.014 2.00e-02 2.50e+03 pdb=" N MET H 117 " -0.013 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.90: 1446 2.90 - 3.40: 3021 3.40 - 3.90: 5401 3.90 - 4.40: 6057 4.40 - 4.90: 10403 Nonbonded interactions: 26328 Sorted by model distance: nonbonded pdb=" OD1 ASP H 62 " pdb=" N SER H 63 " model vdw 2.405 3.120 nonbonded pdb=" OD1 ASP H 118 " pdb=" N VAL H 119 " model vdw 2.423 3.120 nonbonded pdb=" NH1 ARG L 59 " pdb=" O PHE L 67 " model vdw 2.452 3.120 nonbonded pdb=" O SER H 130 " pdb=" OG SER H 130 " model vdw 2.456 3.040 nonbonded pdb=" NE2 GLN L 95 " pdb=" O PRO L 100 " model vdw 2.457 3.120 ... (remaining 26323 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 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: 2.710 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.790 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5482 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 : 0.009 0.044 3463 Z= 0.597 Angle : 1.223 8.086 4707 Z= 0.850 Chirality : 0.078 0.333 506 Planarity : 0.013 0.304 611 Dihedral : 12.602 69.871 1247 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.28 % Allowed : 6.89 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -2.87 (0.38), residues: 424 helix: -4.69 (0.22), residues: 39 sheet: -1.16 (0.45), residues: 142 loop : -1.89 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 353 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.002 PHE B 515 TYR 0.012 0.002 TYR B 396 ARG 0.003 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ASP cc_start: 0.8174 (m-30) cc_final: 0.7972 (m-30) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1627 time to fit residues: 16.8871 Evaluate side-chains 55 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.0060 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN H 13 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.169825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.153388 restraints weight = 7628.597| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 4.28 r_work: 0.4193 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3463 Z= 0.273 Angle : 0.678 7.693 4707 Z= 0.351 Chirality : 0.046 0.163 506 Planarity : 0.005 0.034 611 Dihedral : 6.043 52.043 499 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.20 % Allowed : 11.57 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.39), residues: 424 helix: -4.66 (0.42), residues: 20 sheet: -0.64 (0.47), residues: 131 loop : -1.23 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 436 HIS 0.007 0.002 HIS H 35 PHE 0.025 0.002 PHE B 464 TYR 0.013 0.002 TYR B 421 ARG 0.005 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: B 380 TYR cc_start: 0.6375 (m-80) cc_final: 0.6167 (m-10) REVERT: H 90 ASP cc_start: 0.7449 (t70) cc_final: 0.7204 (t0) REVERT: H 102 MET cc_start: 0.7380 (mtm) cc_final: 0.6801 (mtm) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.1349 time to fit residues: 12.0611 Evaluate side-chains 60 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.0070 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.0870 chunk 12 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN H 74 ASN L 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.165966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.151874 restraints weight = 7454.471| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 4.07 r_work: 0.4133 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3463 Z= 0.213 Angle : 0.620 6.636 4707 Z= 0.321 Chirality : 0.044 0.157 506 Planarity : 0.004 0.032 611 Dihedral : 6.173 57.336 499 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.68 % Allowed : 13.22 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.49 (0.39), residues: 424 helix: -4.48 (0.60), residues: 20 sheet: -0.15 (0.47), residues: 131 loop : -1.17 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 436 HIS 0.006 0.002 HIS B 505 PHE 0.011 0.002 PHE B 400 TYR 0.020 0.002 TYR B 508 ARG 0.003 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 380 TYR cc_start: 0.6431 (m-80) cc_final: 0.6208 (m-10) REVERT: H 90 ASP cc_start: 0.7463 (t70) cc_final: 0.7144 (t0) REVERT: H 102 MET cc_start: 0.6986 (mtm) cc_final: 0.6684 (mtm) outliers start: 17 outliers final: 12 residues processed: 78 average time/residue: 0.1596 time to fit residues: 15.3897 Evaluate side-chains 65 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.170930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.157442 restraints weight = 7621.534| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 3.81 r_work: 0.4310 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3463 Z= 0.199 Angle : 0.625 7.966 4707 Z= 0.318 Chirality : 0.043 0.142 506 Planarity : 0.004 0.031 611 Dihedral : 6.262 58.392 499 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.96 % Allowed : 16.25 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.31 (0.40), residues: 424 helix: -4.72 (0.46), residues: 26 sheet: 0.04 (0.47), residues: 134 loop : -0.95 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.008 0.001 PHE B 464 TYR 0.034 0.002 TYR B 508 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 362 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8539 (m) REVERT: B 380 TYR cc_start: 0.6525 (m-80) cc_final: 0.6265 (m-80) REVERT: B 501 TYR cc_start: 0.4442 (OUTLIER) cc_final: 0.4122 (m-10) REVERT: H 90 ASP cc_start: 0.7329 (t70) cc_final: 0.7055 (t0) REVERT: H 102 MET cc_start: 0.7020 (mtm) cc_final: 0.6772 (mtm) outliers start: 18 outliers final: 15 residues processed: 70 average time/residue: 0.1421 time to fit residues: 12.3793 Evaluate side-chains 69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 14 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS H 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.165861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.153163 restraints weight = 7479.012| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 3.61 r_work: 0.4254 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3463 Z= 0.259 Angle : 0.685 9.306 4707 Z= 0.351 Chirality : 0.044 0.148 506 Planarity : 0.005 0.037 611 Dihedral : 6.536 48.796 499 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.51 % Allowed : 17.36 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.43 (0.40), residues: 424 helix: -4.79 (0.40), residues: 26 sheet: 0.12 (0.49), residues: 132 loop : -1.13 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.002 PHE B 377 TYR 0.043 0.002 TYR B 508 ARG 0.005 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.405 Fit side-chains REVERT: B 449 TYR cc_start: 0.6716 (t80) cc_final: 0.6383 (t80) REVERT: B 501 TYR cc_start: 0.4688 (OUTLIER) cc_final: 0.4315 (m-10) REVERT: H 102 MET cc_start: 0.6879 (mtm) cc_final: 0.6678 (mtm) outliers start: 20 outliers final: 14 residues processed: 80 average time/residue: 0.1788 time to fit residues: 17.2149 Evaluate side-chains 69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 27 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.156386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.143329 restraints weight = 7540.501| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 3.98 r_work: 0.4026 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.6948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3463 Z= 0.283 Angle : 0.713 8.817 4707 Z= 0.370 Chirality : 0.045 0.144 506 Planarity : 0.004 0.033 611 Dihedral : 6.661 42.536 499 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 6.61 % Allowed : 19.56 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.50 (0.40), residues: 424 helix: -4.93 (0.31), residues: 26 sheet: 0.14 (0.49), residues: 131 loop : -1.20 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 436 HIS 0.005 0.001 HIS B 505 PHE 0.014 0.002 PHE H 29 TYR 0.021 0.002 TYR B 508 ARG 0.004 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.391 Fit side-chains REVERT: B 448 ASN cc_start: 0.6289 (t0) cc_final: 0.5997 (t0) REVERT: B 481 ASN cc_start: 0.6528 (OUTLIER) cc_final: 0.6101 (p0) REVERT: B 501 TYR cc_start: 0.4898 (OUTLIER) cc_final: 0.4419 (m-10) outliers start: 24 outliers final: 19 residues processed: 83 average time/residue: 0.1222 time to fit residues: 12.9893 Evaluate side-chains 82 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.0000 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN L 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.157075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.144357 restraints weight = 7386.518| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 3.93 r_work: 0.4042 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.7210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3463 Z= 0.224 Angle : 0.680 7.397 4707 Z= 0.351 Chirality : 0.044 0.137 506 Planarity : 0.004 0.031 611 Dihedral : 6.339 39.667 499 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 6.34 % Allowed : 22.59 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.52 (0.39), residues: 424 helix: -4.95 (0.30), residues: 26 sheet: 0.12 (0.49), residues: 131 loop : -1.22 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 436 HIS 0.004 0.001 HIS B 505 PHE 0.011 0.002 PHE L 67 TYR 0.018 0.002 TYR B 508 ARG 0.004 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.392 Fit side-chains REVERT: B 378 LYS cc_start: 0.7755 (mmtm) cc_final: 0.7266 (pttt) REVERT: B 448 ASN cc_start: 0.6451 (t0) cc_final: 0.6221 (t0) outliers start: 23 outliers final: 19 residues processed: 82 average time/residue: 0.1280 time to fit residues: 13.5308 Evaluate side-chains 80 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 23 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN L 31 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.155984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.143550 restraints weight = 7446.491| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 3.97 r_work: 0.4027 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.7531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3463 Z= 0.248 Angle : 0.694 7.336 4707 Z= 0.356 Chirality : 0.045 0.162 506 Planarity : 0.004 0.033 611 Dihedral : 6.467 40.042 499 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 6.34 % Allowed : 23.69 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.50 (0.39), residues: 424 helix: -4.95 (0.27), residues: 26 sheet: 0.34 (0.51), residues: 119 loop : -1.26 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 436 HIS 0.003 0.001 HIS B 505 PHE 0.011 0.002 PHE B 374 TYR 0.020 0.002 TYR B 508 ARG 0.005 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: B 448 ASN cc_start: 0.6877 (t0) cc_final: 0.6494 (t0) outliers start: 23 outliers final: 20 residues processed: 82 average time/residue: 0.1274 time to fit residues: 13.2391 Evaluate side-chains 82 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 55 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.0370 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 14 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN L 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.157620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.147390 restraints weight = 7178.108| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 3.14 r_work: 0.4114 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.7630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3463 Z= 0.212 Angle : 0.685 7.684 4707 Z= 0.351 Chirality : 0.044 0.152 506 Planarity : 0.004 0.033 611 Dihedral : 6.231 38.792 499 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.79 % Allowed : 24.52 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.47 (0.39), residues: 424 helix: -4.91 (0.29), residues: 26 sheet: 0.37 (0.51), residues: 119 loop : -1.24 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 436 HIS 0.002 0.001 HIS B 505 PHE 0.012 0.002 PHE B 374 TYR 0.018 0.002 TYR B 508 ARG 0.004 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: B 448 ASN cc_start: 0.6605 (t0) cc_final: 0.6286 (t0) outliers start: 21 outliers final: 19 residues processed: 76 average time/residue: 0.1246 time to fit residues: 12.1520 Evaluate side-chains 77 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 31 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 15 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN L 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.157089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.147287 restraints weight = 7266.169| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 3.08 r_work: 0.4084 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.7706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3463 Z= 0.224 Angle : 0.689 9.263 4707 Z= 0.351 Chirality : 0.044 0.150 506 Planarity : 0.004 0.032 611 Dihedral : 6.271 39.322 499 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 6.34 % Allowed : 23.42 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.56 (0.39), residues: 424 helix: -4.88 (0.29), residues: 26 sheet: 0.49 (0.53), residues: 113 loop : -1.37 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 436 HIS 0.002 0.001 HIS B 505 PHE 0.012 0.001 PHE B 374 TYR 0.016 0.002 TYR B 508 ARG 0.004 0.000 ARG B 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: B 448 ASN cc_start: 0.6867 (t0) cc_final: 0.6570 (t0) outliers start: 23 outliers final: 21 residues processed: 76 average time/residue: 0.1272 time to fit residues: 12.2861 Evaluate side-chains 76 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 31 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 0.0570 chunk 36 optimal weight: 0.0370 chunk 27 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.0980 chunk 30 optimal weight: 0.2980 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN H 74 ASN L 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.158910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.148781 restraints weight = 7290.235| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 3.15 r_work: 0.4127 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.7768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3463 Z= 0.188 Angle : 0.665 9.085 4707 Z= 0.339 Chirality : 0.044 0.145 506 Planarity : 0.004 0.032 611 Dihedral : 6.012 38.594 499 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.41 % Allowed : 25.34 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.54 (0.39), residues: 424 helix: -4.83 (0.31), residues: 26 sheet: 0.48 (0.53), residues: 111 loop : -1.34 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.003 0.001 HIS L 31 PHE 0.009 0.001 PHE B 374 TYR 0.013 0.001 TYR B 508 ARG 0.003 0.000 ARG B 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2264.49 seconds wall clock time: 40 minutes 58.43 seconds (2458.43 seconds total)