Starting phenix.real_space_refine on Tue Feb 11 00:13:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wt9_32772/02_2025/7wt9_32772.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wt9_32772/02_2025/7wt9_32772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wt9_32772/02_2025/7wt9_32772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wt9_32772/02_2025/7wt9_32772.map" model { file = "/net/cci-nas-00/data/ceres_data/7wt9_32772/02_2025/7wt9_32772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wt9_32772/02_2025/7wt9_32772.cif" } resolution = 4.3 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= 0.001 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 2117 2.51 5 N 564 2.21 5 O 646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 3343 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 900 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "A" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Time building chain proxies: 3.13, per 1000 atoms: 0.94 Number of scatterers: 3343 At special positions: 0 Unit cell: (63.44, 80.08, 105.04, 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 646 8.00 N 564 7.00 C 2117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " 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 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 933.2 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: 792 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 10.0% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.734A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 372 removed outlier: 3.525A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 removed outlier: 3.716A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.116A pdb=" N ILE A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.562A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.790A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 395 through 397 Processing sheet with id=AA4, first strand: chain 'E' and resid 400 through 402 removed outlier: 3.579A pdb=" N PHE E 400 " --> pdb=" O VAL E 510 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'A' and resid 10 through 11 Processing sheet with id=AA8, first strand: chain 'A' and resid 22 through 24 removed outlier: 3.510A pdb=" N THR A 72 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER A 63 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.515A pdb=" N GLN A 38 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 85 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 97 " --> pdb=" O GLN A 90 " (cutoff:3.500A) 58 hydrogen bonds defined for protein. 156 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: 0.76 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1078 1.35 - 1.47: 865 1.47 - 1.59: 1460 1.59 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3423 Sorted by residual: bond pdb=" N VAL E 445 " pdb=" CA VAL E 445 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.07e+00 bond pdb=" N LYS E 444 " pdb=" CA LYS E 444 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.60e+00 bond pdb=" C SER A 7 " pdb=" N PRO A 8 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.33e+00 bond pdb=" N SER E 446 " pdb=" CA SER E 446 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.19e+00 bond pdb=" N ASN E 448 " pdb=" CA ASN E 448 " ideal model delta sigma weight residual 1.460 1.486 -0.027 1.28e-02 6.10e+03 4.37e+00 ... (remaining 3418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 4495 3.18 - 6.36: 137 6.36 - 9.54: 18 9.54 - 12.72: 3 12.72 - 15.90: 1 Bond angle restraints: 4654 Sorted by residual: angle pdb=" C GLY A 68 " pdb=" N THR A 69 " pdb=" CA THR A 69 " ideal model delta sigma weight residual 123.91 131.91 -8.00 1.66e+00 3.63e-01 2.32e+01 angle pdb=" CA GLN E 409 " pdb=" CB GLN E 409 " pdb=" CG GLN E 409 " ideal model delta sigma weight residual 114.10 123.38 -9.28 2.00e+00 2.50e-01 2.15e+01 angle pdb=" CA LEU E 518 " pdb=" CB LEU E 518 " pdb=" CG LEU E 518 " ideal model delta sigma weight residual 116.30 132.20 -15.90 3.50e+00 8.16e-02 2.06e+01 angle pdb=" CB MET A 4 " pdb=" CG MET A 4 " pdb=" SD MET A 4 " ideal model delta sigma weight residual 112.70 124.79 -12.09 3.00e+00 1.11e-01 1.62e+01 angle pdb=" CB GLU E 340 " pdb=" CG GLU E 340 " pdb=" CD GLU E 340 " ideal model delta sigma weight residual 112.60 119.08 -6.48 1.70e+00 3.46e-01 1.46e+01 ... (remaining 4649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 1826 17.01 - 34.02: 162 34.02 - 51.04: 38 51.04 - 68.05: 4 68.05 - 85.06: 4 Dihedral angle restraints: 2034 sinusoidal: 787 harmonic: 1247 Sorted by residual: dihedral pdb=" CB CYS E 336 " pdb=" SG CYS E 336 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual 93.00 175.66 -82.66 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual -86.00 -13.69 -72.31 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CA GLU H 98 " pdb=" C GLU H 98 " pdb=" N VAL H 99 " pdb=" CA VAL H 99 " ideal model delta harmonic sigma weight residual -180.00 -142.14 -37.86 0 5.00e+00 4.00e-02 5.73e+01 ... (remaining 2031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 442 0.100 - 0.200: 58 0.200 - 0.300: 4 0.300 - 0.400: 1 0.400 - 0.500: 2 Chirality restraints: 507 Sorted by residual: chirality pdb=" CB THR H 114 " pdb=" CA THR H 114 " pdb=" OG1 THR H 114 " pdb=" CG2 THR H 114 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" CB ILE E 402 " pdb=" CA ILE E 402 " pdb=" CG1 ILE E 402 " pdb=" CG2 ILE E 402 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CB VAL E 341 " pdb=" CA VAL E 341 " pdb=" CG1 VAL E 341 " pdb=" CG2 VAL E 341 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 504 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 35 " -0.015 2.00e-02 2.50e+03 2.46e-02 1.52e+01 pdb=" CG TRP A 35 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 35 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A 35 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 35 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 35 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 35 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 35 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 35 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 35 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 50 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.16e+00 pdb=" C ASP A 50 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP A 50 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 51 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 351 " 0.014 2.00e-02 2.50e+03 1.93e-02 7.43e+00 pdb=" CG TYR E 351 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR E 351 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR E 351 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR E 351 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 351 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 351 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 351 " -0.001 2.00e-02 2.50e+03 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 974 2.82 - 3.34: 2792 3.34 - 3.86: 5460 3.86 - 4.38: 5736 4.38 - 4.90: 9882 Nonbonded interactions: 24844 Sorted by model distance: nonbonded pdb=" O TYR A 86 " pdb=" OG1 THR A 102 " model vdw 2.304 3.040 nonbonded pdb=" OG1 THR A 74 " pdb=" OD1 ASN A 76 " model vdw 2.318 3.040 nonbonded pdb=" OG SER H 56 " pdb=" OG1 THR E 415 " model vdw 2.339 3.040 nonbonded pdb=" OG1 THR E 376 " pdb=" NZ LYS E 378 " model vdw 2.358 3.120 nonbonded pdb=" O ALA A 25 " pdb=" OG1 THR A 69 " model vdw 2.392 3.040 ... (remaining 24839 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.760 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 3423 Z= 0.378 Angle : 1.266 15.900 4654 Z= 0.676 Chirality : 0.071 0.500 507 Planarity : 0.009 0.069 604 Dihedral : 13.288 85.060 1224 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.27 % Allowed : 1.36 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.35), residues: 424 helix: -3.94 (0.49), residues: 33 sheet: -2.31 (0.46), residues: 100 loop : -2.14 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.006 TRP A 35 HIS 0.001 0.000 HIS E 505 PHE 0.045 0.003 PHE E 400 TYR 0.047 0.003 TYR E 351 ARG 0.005 0.001 ARG E 493 *********************** 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 114 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.379 Fit side-chains REVERT: H 82 MET cc_start: 0.7811 (mpp) cc_final: 0.7220 (mpp) REVERT: H 106 MET cc_start: 0.6874 (ptm) cc_final: 0.6641 (ptm) REVERT: E 389 ASP cc_start: 0.8174 (m-30) cc_final: 0.7776 (p0) REVERT: E 460 ASN cc_start: 0.8024 (t0) cc_final: 0.7194 (p0) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.1428 time to fit residues: 20.0116 Evaluate side-chains 85 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 100 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 = 0.3692 r_free = 0.3692 target = 0.099141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.083755 restraints weight = 12079.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.085912 restraints weight = 7447.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.087442 restraints weight = 5254.746| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3423 Z= 0.218 Angle : 0.651 10.373 4654 Z= 0.343 Chirality : 0.045 0.175 507 Planarity : 0.005 0.047 604 Dihedral : 5.741 28.452 475 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.27 % Allowed : 3.80 % Favored : 95.92 % 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: -3.05 (0.36), residues: 424 helix: -3.04 (0.71), residues: 33 sheet: -1.98 (0.43), residues: 125 loop : -1.96 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 35 HIS 0.002 0.001 HIS E 519 PHE 0.024 0.002 PHE A 71 TYR 0.025 0.002 TYR E 380 ARG 0.002 0.000 ARG H 97 *********************** 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 91 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: H 78 LEU cc_start: 0.8550 (tp) cc_final: 0.8339 (tp) REVERT: H 82 MET cc_start: 0.8060 (mpp) cc_final: 0.7451 (mpp) REVERT: E 389 ASP cc_start: 0.8715 (m-30) cc_final: 0.8025 (p0) REVERT: E 460 ASN cc_start: 0.8566 (t0) cc_final: 0.7818 (p0) REVERT: E 461 LEU cc_start: 0.8984 (tp) cc_final: 0.8728 (mt) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1705 time to fit residues: 18.4398 Evaluate side-chains 67 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.096889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.082212 restraints weight = 11710.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.084202 restraints weight = 7223.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.085600 restraints weight = 5071.178| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3423 Z= 0.248 Angle : 0.654 9.761 4654 Z= 0.343 Chirality : 0.045 0.148 507 Planarity : 0.005 0.045 604 Dihedral : 5.655 28.557 475 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.27 % Allowed : 5.98 % Favored : 93.75 % 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: -2.96 (0.37), residues: 424 helix: -2.78 (0.71), residues: 32 sheet: -2.11 (0.41), residues: 127 loop : -1.80 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 35 HIS 0.001 0.000 HIS E 505 PHE 0.028 0.003 PHE E 392 TYR 0.022 0.002 TYR E 380 ARG 0.004 0.001 ARG E 457 *********************** 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 99 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.8679 (tp) cc_final: 0.8334 (tp) REVERT: H 82 MET cc_start: 0.8046 (mpp) cc_final: 0.7690 (mpp) REVERT: E 460 ASN cc_start: 0.8710 (t0) cc_final: 0.8054 (p0) REVERT: E 461 LEU cc_start: 0.9129 (tp) cc_final: 0.8922 (tp) REVERT: E 516 GLU cc_start: 0.7378 (pm20) cc_final: 0.7164 (pm20) REVERT: A 4 MET cc_start: 0.7670 (tpt) cc_final: 0.7395 (tpp) REVERT: A 53 ASN cc_start: 0.7684 (m110) cc_final: 0.7441 (m-40) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1681 time to fit residues: 19.5838 Evaluate side-chains 72 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 0.0770 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.096602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.081554 restraints weight = 11840.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.083696 restraints weight = 7048.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.085197 restraints weight = 4865.401| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3423 Z= 0.207 Angle : 0.632 8.845 4654 Z= 0.330 Chirality : 0.045 0.151 507 Planarity : 0.005 0.047 604 Dihedral : 5.476 29.168 475 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: -2.87 (0.37), residues: 424 helix: -2.56 (0.75), residues: 33 sheet: -2.02 (0.42), residues: 117 loop : -1.81 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 36 HIS 0.000 0.000 HIS E 505 PHE 0.018 0.002 PHE A 71 TYR 0.012 0.002 TYR A 49 ARG 0.006 0.001 ARG H 97 *********************** 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 90 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.8563 (tp) cc_final: 0.8158 (tp) REVERT: H 85 LEU cc_start: 0.8479 (mt) cc_final: 0.8223 (mt) REVERT: H 103 ASN cc_start: 0.7728 (t0) cc_final: 0.7524 (t0) REVERT: E 460 ASN cc_start: 0.8857 (t0) cc_final: 0.8158 (p0) REVERT: A 53 ASN cc_start: 0.7909 (m110) cc_final: 0.7636 (m-40) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1699 time to fit residues: 18.3806 Evaluate side-chains 70 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.1980 chunk 35 optimal weight: 0.2980 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.098331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.083577 restraints weight = 11515.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.085631 restraints weight = 6906.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.087091 restraints weight = 4764.956| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3423 Z= 0.175 Angle : 0.613 10.265 4654 Z= 0.313 Chirality : 0.045 0.149 507 Planarity : 0.004 0.047 604 Dihedral : 5.143 27.829 475 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.27 % Allowed : 4.62 % Favored : 95.11 % 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: -2.66 (0.38), residues: 424 helix: -2.42 (0.78), residues: 34 sheet: -1.91 (0.43), residues: 117 loop : -1.64 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 36 HIS 0.000 0.000 HIS E 519 PHE 0.014 0.002 PHE E 464 TYR 0.023 0.002 TYR E 380 ARG 0.002 0.000 ARG H 97 *********************** 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 94 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.7956 (mp0) cc_final: 0.7752 (mp0) REVERT: H 78 LEU cc_start: 0.8401 (tp) cc_final: 0.7988 (tp) REVERT: H 82 MET cc_start: 0.8117 (mpp) cc_final: 0.7454 (mpp) REVERT: H 85 LEU cc_start: 0.8783 (mt) cc_final: 0.7957 (mt) REVERT: E 460 ASN cc_start: 0.8772 (t0) cc_final: 0.8029 (p0) REVERT: A 71 PHE cc_start: 0.8445 (m-10) cc_final: 0.7597 (m-10) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1796 time to fit residues: 20.2457 Evaluate side-chains 72 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN A 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.095274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.080476 restraints weight = 12159.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.082476 restraints weight = 7505.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.083822 restraints weight = 5258.525| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3423 Z= 0.272 Angle : 0.674 9.804 4654 Z= 0.350 Chirality : 0.046 0.146 507 Planarity : 0.005 0.055 604 Dihedral : 5.587 29.538 475 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.27 % Allowed : 4.35 % Favored : 95.38 % 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: -2.89 (0.37), residues: 424 helix: -2.63 (0.75), residues: 34 sheet: -2.11 (0.40), residues: 129 loop : -1.72 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 36 HIS 0.000 0.000 HIS E 505 PHE 0.025 0.003 PHE E 392 TYR 0.021 0.002 TYR E 380 ARG 0.005 0.001 ARG E 493 *********************** 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 98 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 20 LEU cc_start: 0.9480 (mt) cc_final: 0.9208 (mp) REVERT: H 46 GLU cc_start: 0.8003 (mp0) cc_final: 0.7786 (mp0) REVERT: H 78 LEU cc_start: 0.8616 (tp) cc_final: 0.8300 (tp) REVERT: H 82 MET cc_start: 0.8230 (mpp) cc_final: 0.7760 (mpp) REVERT: H 85 LEU cc_start: 0.9025 (mt) cc_final: 0.8562 (mt) REVERT: E 417 ASN cc_start: 0.7957 (p0) cc_final: 0.7678 (p0) REVERT: A 3 GLN cc_start: 0.8067 (mp10) cc_final: 0.7783 (mp10) REVERT: A 70 ASP cc_start: 0.9233 (m-30) cc_final: 0.9007 (m-30) outliers start: 1 outliers final: 1 residues processed: 97 average time/residue: 0.1717 time to fit residues: 19.9277 Evaluate side-chains 72 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 ASN A 53 ASN ** A 89 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 = 0.3575 r_free = 0.3575 target = 0.093518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079364 restraints weight = 11845.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.081224 restraints weight = 7397.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082479 restraints weight = 5230.006| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3423 Z= 0.305 Angle : 0.733 10.694 4654 Z= 0.381 Chirality : 0.047 0.177 507 Planarity : 0.005 0.047 604 Dihedral : 5.796 28.797 475 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 0.27 % Allowed : 2.45 % Favored : 97.28 % 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: -3.09 (0.38), residues: 424 helix: -2.45 (0.82), residues: 34 sheet: -2.49 (0.40), residues: 130 loop : -1.74 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 353 HIS 0.001 0.000 HIS E 505 PHE 0.036 0.003 PHE E 392 TYR 0.024 0.002 TYR E 380 ARG 0.003 0.000 ARG E 493 *********************** 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 93 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: H 33 TYR cc_start: 0.7719 (m-10) cc_final: 0.7283 (m-10) REVERT: H 78 LEU cc_start: 0.8563 (tp) cc_final: 0.8263 (tp) REVERT: H 82 MET cc_start: 0.8233 (mpp) cc_final: 0.7844 (mpp) REVERT: H 85 LEU cc_start: 0.9144 (mt) cc_final: 0.8839 (mt) REVERT: E 460 ASN cc_start: 0.8914 (t0) cc_final: 0.8547 (p0) REVERT: A 3 GLN cc_start: 0.8160 (mp10) cc_final: 0.7858 (mp10) REVERT: A 70 ASP cc_start: 0.9300 (m-30) cc_final: 0.9068 (m-30) outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.1601 time to fit residues: 18.0679 Evaluate side-chains 75 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 0.0020 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 89 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 = 0.3619 r_free = 0.3619 target = 0.096413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.082350 restraints weight = 11730.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.084288 restraints weight = 7207.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.085669 restraints weight = 5054.543| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3423 Z= 0.193 Angle : 0.684 9.717 4654 Z= 0.350 Chirality : 0.046 0.159 507 Planarity : 0.005 0.050 604 Dihedral : 5.325 27.738 475 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -2.93 (0.38), residues: 424 helix: -2.39 (0.81), residues: 35 sheet: -2.24 (0.39), residues: 132 loop : -1.70 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.017 0.002 PHE E 392 TYR 0.029 0.002 TYR E 380 ARG 0.002 0.000 ARG H 97 *********************** 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 100 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8507 (pp) cc_final: 0.8010 (pp) REVERT: H 33 TYR cc_start: 0.7208 (m-10) cc_final: 0.6721 (m-10) REVERT: H 82 MET cc_start: 0.8108 (mpp) cc_final: 0.7893 (mpp) REVERT: H 85 LEU cc_start: 0.9081 (mt) cc_final: 0.8531 (mt) REVERT: E 353 TRP cc_start: 0.8744 (p-90) cc_final: 0.8541 (p-90) REVERT: E 417 ASN cc_start: 0.7828 (p0) cc_final: 0.7311 (p0) REVERT: E 418 ILE cc_start: 0.8606 (mp) cc_final: 0.8343 (mp) REVERT: E 421 TYR cc_start: 0.8268 (m-10) cc_final: 0.7819 (m-10) REVERT: E 460 ASN cc_start: 0.8742 (t0) cc_final: 0.8392 (p0) REVERT: E 489 TYR cc_start: 0.6052 (m-80) cc_final: 0.5793 (m-80) REVERT: A 3 GLN cc_start: 0.7967 (mp10) cc_final: 0.7706 (mp10) REVERT: A 53 ASN cc_start: 0.8071 (m110) cc_final: 0.7863 (m110) REVERT: A 70 ASP cc_start: 0.9232 (m-30) cc_final: 0.8997 (m-30) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1638 time to fit residues: 19.6553 Evaluate side-chains 80 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 0.0770 chunk 17 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.096344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.082247 restraints weight = 12205.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.084155 restraints weight = 7626.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.085496 restraints weight = 5384.675| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3423 Z= 0.210 Angle : 0.705 10.785 4654 Z= 0.360 Chirality : 0.046 0.152 507 Planarity : 0.004 0.049 604 Dihedral : 5.357 27.514 475 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -2.73 (0.38), residues: 424 helix: -2.35 (0.82), residues: 35 sheet: -1.91 (0.42), residues: 129 loop : -1.68 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 353 HIS 0.001 0.000 HIS E 519 PHE 0.020 0.002 PHE E 456 TYR 0.024 0.001 TYR E 380 ARG 0.005 0.000 ARG H 86 *********************** 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 91 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: H 33 TYR cc_start: 0.7208 (m-10) cc_final: 0.6788 (m-10) REVERT: H 78 LEU cc_start: 0.8702 (tp) cc_final: 0.8339 (tp) REVERT: E 417 ASN cc_start: 0.7798 (p0) cc_final: 0.7252 (p0) REVERT: E 418 ILE cc_start: 0.8568 (mp) cc_final: 0.8294 (mp) REVERT: E 421 TYR cc_start: 0.8362 (m-10) cc_final: 0.7886 (m-10) REVERT: E 460 ASN cc_start: 0.8708 (t0) cc_final: 0.8355 (p0) REVERT: A 3 GLN cc_start: 0.7949 (mp10) cc_final: 0.7733 (mp10) REVERT: A 27 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8499 (tm-30) REVERT: A 48 ILE cc_start: 0.8608 (tt) cc_final: 0.8373 (mp) REVERT: A 70 ASP cc_start: 0.9218 (m-30) cc_final: 0.8955 (m-30) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1651 time to fit residues: 18.1928 Evaluate side-chains 72 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 89 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 = 0.3584 r_free = 0.3584 target = 0.094428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.080331 restraints weight = 12251.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.082197 restraints weight = 7703.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083475 restraints weight = 5475.357| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3423 Z= 0.256 Angle : 0.716 10.756 4654 Z= 0.368 Chirality : 0.046 0.148 507 Planarity : 0.005 0.049 604 Dihedral : 5.563 28.147 475 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -2.74 (0.39), residues: 424 helix: -2.44 (0.81), residues: 35 sheet: -1.97 (0.43), residues: 129 loop : -1.65 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 353 HIS 0.001 0.000 HIS E 505 PHE 0.016 0.002 PHE E 464 TYR 0.027 0.002 TYR E 351 ARG 0.004 0.001 ARG H 86 ********************** 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 88 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.8773 (tp) cc_final: 0.8447 (tp) REVERT: H 82 MET cc_start: 0.8174 (mpp) cc_final: 0.6953 (mpp) REVERT: H 85 LEU cc_start: 0.8959 (mt) cc_final: 0.8510 (mt) REVERT: H 86 ARG cc_start: 0.7418 (mmp80) cc_final: 0.7175 (mmp-170) REVERT: H 106 MET cc_start: 0.7417 (ptm) cc_final: 0.6949 (ptm) REVERT: E 417 ASN cc_start: 0.7922 (p0) cc_final: 0.7485 (p0) REVERT: E 418 ILE cc_start: 0.8687 (mp) cc_final: 0.8466 (mp) REVERT: E 471 GLU cc_start: 0.7687 (pm20) cc_final: 0.7328 (pm20) REVERT: A 3 GLN cc_start: 0.8044 (mp10) cc_final: 0.7812 (mp10) REVERT: A 27 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8430 (tm-30) REVERT: A 70 ASP cc_start: 0.9244 (m-30) cc_final: 0.9027 (m-30) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1758 time to fit residues: 18.7229 Evaluate side-chains 69 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.0040 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.094818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080036 restraints weight = 12088.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.082053 restraints weight = 7394.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.083394 restraints weight = 5155.896| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3423 Z= 0.240 Angle : 0.723 10.728 4654 Z= 0.370 Chirality : 0.047 0.149 507 Planarity : 0.005 0.048 604 Dihedral : 5.607 28.009 475 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -2.77 (0.39), residues: 424 helix: -2.44 (0.81), residues: 35 sheet: -1.97 (0.43), residues: 128 loop : -1.69 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 353 HIS 0.001 0.000 HIS E 519 PHE 0.025 0.003 PHE E 456 TYR 0.024 0.002 TYR E 380 ARG 0.003 0.000 ARG E 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1602.65 seconds wall clock time: 29 minutes 49.26 seconds (1789.26 seconds total)