Starting phenix.real_space_refine on Wed Mar 5 19:15:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wt9_32772/03_2025/7wt9_32772.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wt9_32772/03_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_32772/03_2025/7wt9_32772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wt9_32772/03_2025/7wt9_32772.map" model { file = "/net/cci-nas-00/data/ceres_data/7wt9_32772/03_2025/7wt9_32772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wt9_32772/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.85, per 1000 atoms: 1.15 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: 0.72 Conformation dependent library (CDL) restraints added in 405.8 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: 0.44 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: 0.89 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: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.420 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- 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 : 0.385 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: 0.1497 time to fit residues: 21.0999 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 : 0.355 ------------------------------------------------------------------------------- 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: 0.7980 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.097786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.082461 restraints weight = 12224.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.084544 restraints weight = 7555.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.086027 restraints weight = 5368.816| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3423 Z= 0.246 Angle : 0.675 10.347 4654 Z= 0.356 Chirality : 0.046 0.167 507 Planarity : 0.005 0.046 604 Dihedral : 5.834 28.699 475 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % 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: -3.12 (0.36), residues: 424 helix: -3.00 (0.73), residues: 33 sheet: -2.06 (0.42), residues: 125 loop : -2.00 (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 0.025 0.003 PHE A 71 TYR 0.025 0.002 TYR E 380 ARG 0.003 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 : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.8608 (tp) cc_final: 0.8392 (tp) REVERT: H 82 MET cc_start: 0.8121 (mpp) cc_final: 0.7443 (mpp) REVERT: E 460 ASN cc_start: 0.8649 (t0) cc_final: 0.7920 (p0) REVERT: E 461 LEU cc_start: 0.9044 (tp) cc_final: 0.8789 (mt) REVERT: A 3 GLN cc_start: 0.7894 (mp10) cc_final: 0.7641 (mp10) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1598 time to fit residues: 17.4569 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 : 0.429 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 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 = 0.3617 r_free = 0.3617 target = 0.095805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.081555 restraints weight = 11821.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.083434 restraints weight = 7437.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.084744 restraints weight = 5324.203| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3423 Z= 0.269 Angle : 0.673 9.789 4654 Z= 0.353 Chirality : 0.045 0.144 507 Planarity : 0.005 0.046 604 Dihedral : 5.817 29.319 475 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.54 % Allowed : 5.98 % Favored : 93.48 % 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: -3.08 (0.37), residues: 424 helix: -2.86 (0.72), residues: 32 sheet: -2.25 (0.41), residues: 127 loop : -1.86 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 35 HIS 0.001 0.000 HIS E 505 PHE 0.030 0.003 PHE E 392 TYR 0.012 0.002 TYR E 396 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 98 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.8658 (tp) cc_final: 0.8401 (tp) REVERT: H 82 MET cc_start: 0.8190 (mpp) cc_final: 0.7843 (mpp) REVERT: H 85 LEU cc_start: 0.8579 (mt) cc_final: 0.8189 (mt) REVERT: E 355 ARG cc_start: 0.8087 (ptt180) cc_final: 0.7876 (ptp90) REVERT: E 460 ASN cc_start: 0.8796 (t0) cc_final: 0.8274 (p0) REVERT: E 461 LEU cc_start: 0.9129 (tp) cc_final: 0.8916 (tp) REVERT: A 50 ASP cc_start: 0.9157 (t0) cc_final: 0.8884 (t0) REVERT: A 53 ASN cc_start: 0.7900 (m110) cc_final: 0.7646 (m-40) outliers start: 2 outliers final: 0 residues processed: 97 average time/residue: 0.1742 time to fit residues: 20.0319 Evaluate side-chains 71 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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: 0.7980 chunk 21 optimal weight: 0.0370 chunk 18 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.095808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.081505 restraints weight = 11786.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.083416 restraints weight = 7273.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.084782 restraints weight = 5138.773| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3423 Z= 0.224 Angle : 0.647 8.921 4654 Z= 0.338 Chirality : 0.045 0.152 507 Planarity : 0.005 0.046 604 Dihedral : 5.595 29.034 475 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.27 % Allowed : 5.16 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.37), residues: 424 helix: -2.71 (0.75), residues: 33 sheet: -2.16 (0.42), residues: 119 loop : -1.90 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP H 36 HIS 0.001 0.000 HIS E 505 PHE 0.023 0.003 PHE E 392 TYR 0.013 0.002 TYR E 396 ARG 0.003 0.000 ARG H 38 *********************** 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: 1 poor density : 89 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.8573 (tp) cc_final: 0.8157 (tp) REVERT: H 85 LEU cc_start: 0.8908 (mt) cc_final: 0.8393 (mt) REVERT: H 86 ARG cc_start: 0.7471 (mmp80) cc_final: 0.7234 (mmp-170) REVERT: H 103 ASN cc_start: 0.7764 (t0) cc_final: 0.7560 (t0) REVERT: E 355 ARG cc_start: 0.8149 (ptt180) cc_final: 0.7914 (ptp90) REVERT: A 4 MET cc_start: 0.6987 (tpt) cc_final: 0.6492 (tpp) REVERT: A 50 ASP cc_start: 0.9086 (t0) cc_final: 0.8844 (t0) REVERT: A 53 ASN cc_start: 0.7944 (m110) cc_final: 0.7639 (m-40) REVERT: A 70 ASP cc_start: 0.9267 (m-30) cc_final: 0.9044 (m-30) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1676 time to fit residues: 18.1442 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 : 0.347 ------------------------------------------------------------------------------- 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: 0.0970 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** 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 = 0.3651 r_free = 0.3651 target = 0.098005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.083932 restraints weight = 11600.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.085891 restraints weight = 7244.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.087266 restraints weight = 5101.886| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3423 Z= 0.174 Angle : 0.624 10.386 4654 Z= 0.318 Chirality : 0.045 0.147 507 Planarity : 0.004 0.046 604 Dihedral : 5.209 27.174 475 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 4.89 % 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: -2.87 (0.37), residues: 424 helix: -2.74 (0.73), residues: 35 sheet: -1.99 (0.43), residues: 124 loop : -1.76 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 36 HIS 0.000 0.000 HIS E 519 PHE 0.011 0.002 PHE A 71 TYR 0.010 0.001 TYR E 473 ARG 0.001 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 91 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 20 LEU cc_start: 0.9490 (mt) cc_final: 0.9228 (mp) REVERT: H 46 GLU cc_start: 0.7986 (mp0) cc_final: 0.7710 (mp0) REVERT: H 78 LEU cc_start: 0.8430 (tp) cc_final: 0.8057 (tp) REVERT: H 82 MET cc_start: 0.8032 (mpp) cc_final: 0.7500 (mpp) REVERT: H 85 LEU cc_start: 0.8901 (mt) cc_final: 0.8157 (mt) REVERT: H 86 ARG cc_start: 0.7535 (mmp80) cc_final: 0.7203 (mmp-170) REVERT: E 460 ASN cc_start: 0.8976 (t0) cc_final: 0.8728 (t0) REVERT: A 50 ASP cc_start: 0.8972 (t0) cc_final: 0.8735 (t0) REVERT: A 71 PHE cc_start: 0.8437 (m-10) cc_final: 0.7652 (m-10) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1656 time to fit residues: 18.1702 Evaluate side-chains 74 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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: 0.9990 chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 19 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** 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 = 0.3615 r_free = 0.3615 target = 0.096109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.081653 restraints weight = 11872.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.083693 restraints weight = 7196.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085116 restraints weight = 4995.870| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3423 Z= 0.227 Angle : 0.646 9.876 4654 Z= 0.334 Chirality : 0.046 0.150 507 Planarity : 0.005 0.055 604 Dihedral : 5.343 27.673 475 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % 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: -3.01 (0.36), residues: 424 helix: -2.80 (0.72), residues: 35 sheet: -2.15 (0.41), residues: 120 loop : -1.85 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.019 0.002 PHE A 98 TYR 0.012 0.002 TYR E 473 ARG 0.005 0.001 ARG E 355 *********************** 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 95 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.8483 (tp) cc_final: 0.8127 (tp) REVERT: H 82 MET cc_start: 0.8196 (mpp) cc_final: 0.7908 (mpp) REVERT: H 85 LEU cc_start: 0.9049 (mt) cc_final: 0.8593 (mt) REVERT: H 86 ARG cc_start: 0.7698 (mmp80) cc_final: 0.7425 (mmp-170) REVERT: E 417 ASN cc_start: 0.7852 (p0) cc_final: 0.7311 (p0) REVERT: E 418 ILE cc_start: 0.8668 (mp) cc_final: 0.8428 (mp) REVERT: A 50 ASP cc_start: 0.8945 (t0) cc_final: 0.8726 (t0) REVERT: A 70 ASP cc_start: 0.9266 (m-30) cc_final: 0.9014 (m-30) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1619 time to fit residues: 18.6250 Evaluate side-chains 73 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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: 0.5980 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.093399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.079384 restraints weight = 11809.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.081219 restraints weight = 7374.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.082496 restraints weight = 5231.692| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3423 Z= 0.294 Angle : 0.730 9.284 4654 Z= 0.377 Chirality : 0.048 0.172 507 Planarity : 0.005 0.047 604 Dihedral : 5.722 27.282 475 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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: -3.17 (0.37), residues: 424 helix: -2.45 (0.83), residues: 34 sheet: -2.25 (0.39), residues: 133 loop : -1.98 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 436 HIS 0.001 0.000 HIS E 505 PHE 0.021 0.003 PHE E 464 TYR 0.017 0.002 TYR E 396 ARG 0.004 0.001 ARG H 97 *********************** 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 92 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 TYR cc_start: 0.7643 (m-10) cc_final: 0.7370 (m-10) REVERT: H 46 GLU cc_start: 0.8036 (mp0) cc_final: 0.7788 (mp0) REVERT: H 78 LEU cc_start: 0.8529 (tp) cc_final: 0.8172 (tp) REVERT: H 85 LEU cc_start: 0.9177 (mt) cc_final: 0.8768 (mt) REVERT: H 86 ARG cc_start: 0.7951 (mmp80) cc_final: 0.7601 (mmp-170) REVERT: H 103 ASN cc_start: 0.7824 (t0) cc_final: 0.7594 (t0) REVERT: A 4 MET cc_start: 0.7653 (tpt) cc_final: 0.7359 (tpp) REVERT: A 50 ASP cc_start: 0.9043 (t0) cc_final: 0.8810 (t0) REVERT: A 53 ASN cc_start: 0.7973 (m110) cc_final: 0.7737 (m-40) REVERT: A 70 ASP cc_start: 0.9216 (m-30) cc_final: 0.8944 (m-30) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1675 time to fit residues: 18.5673 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 : 0.381 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.096651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.081908 restraints weight = 11741.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.083874 restraints weight = 7326.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.085260 restraints weight = 5187.302| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3423 Z= 0.209 Angle : 0.688 9.897 4654 Z= 0.353 Chirality : 0.047 0.162 507 Planarity : 0.004 0.050 604 Dihedral : 5.407 26.405 475 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -3.06 (0.37), residues: 424 helix: -2.45 (0.81), residues: 35 sheet: -2.20 (0.40), residues: 132 loop : -1.89 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.021 0.002 PHE E 392 TYR 0.012 0.001 TYR E 473 ARG 0.003 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 96 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 TYR cc_start: 0.7763 (m-10) cc_final: 0.7407 (m-10) REVERT: H 36 TRP cc_start: 0.8206 (m-10) cc_final: 0.8003 (m-10) REVERT: H 86 ARG cc_start: 0.7965 (mmp80) cc_final: 0.7476 (mmp-170) REVERT: E 417 ASN cc_start: 0.7852 (p0) cc_final: 0.7396 (p0) REVERT: E 421 TYR cc_start: 0.8365 (m-10) cc_final: 0.8067 (m-10) REVERT: A 53 ASN cc_start: 0.7773 (m110) cc_final: 0.7477 (m-40) REVERT: A 70 ASP cc_start: 0.9247 (m-30) cc_final: 0.9003 (m-30) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1593 time to fit residues: 18.5952 Evaluate side-chains 77 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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: 0.6980 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 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 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 = 0.3592 r_free = 0.3592 target = 0.094720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.079896 restraints weight = 11959.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.081900 restraints weight = 7367.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.083223 restraints weight = 5157.753| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4864 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= 0.270 Angle : 0.743 10.805 4654 Z= 0.380 Chirality : 0.047 0.155 507 Planarity : 0.005 0.049 604 Dihedral : 5.653 26.765 475 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % 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: -3.16 (0.37), residues: 424 helix: -2.37 (0.82), residues: 35 sheet: -2.43 (0.40), residues: 128 loop : -1.90 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 353 HIS 0.002 0.001 HIS E 519 PHE 0.033 0.003 PHE E 456 TYR 0.019 0.002 TYR E 396 ARG 0.004 0.001 ARG H 38 *********************** 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 96 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 TYR cc_start: 0.7304 (m-10) cc_final: 0.6848 (m-10) REVERT: H 86 ARG cc_start: 0.8160 (mmp80) cc_final: 0.7895 (mmp80) REVERT: H 103 ASN cc_start: 0.7823 (t0) cc_final: 0.7601 (t0) REVERT: E 417 ASN cc_start: 0.7695 (p0) cc_final: 0.7385 (p0) REVERT: E 421 TYR cc_start: 0.8320 (m-10) cc_final: 0.7781 (m-10) REVERT: A 27 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8458 (tm-30) REVERT: A 53 ASN cc_start: 0.7931 (m110) cc_final: 0.7585 (m-40) REVERT: A 70 ASP cc_start: 0.9258 (m-30) cc_final: 0.9019 (m-30) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1561 time to fit residues: 18.3214 Evaluate side-chains 75 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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: 0.0050 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.0040 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 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 = 0.3615 r_free = 0.3615 target = 0.096017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.081444 restraints weight = 11916.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.083437 restraints weight = 7350.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.084807 restraints weight = 5161.445| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4800 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= 0.219 Angle : 0.721 10.000 4654 Z= 0.371 Chirality : 0.047 0.146 507 Planarity : 0.004 0.050 604 Dihedral : 5.524 26.163 475 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.27 % Allowed : 0.54 % 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: -3.04 (0.38), residues: 424 helix: -2.43 (0.80), residues: 35 sheet: -2.23 (0.42), residues: 125 loop : -1.87 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 36 HIS 0.001 0.000 HIS E 505 PHE 0.022 0.002 PHE E 392 TYR 0.028 0.002 TYR E 351 ARG 0.003 0.000 ARG E 408 ********************** 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 101 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 TYR cc_start: 0.7541 (m-10) cc_final: 0.7086 (m-10) REVERT: H 78 LEU cc_start: 0.8788 (tp) cc_final: 0.8491 (tp) REVERT: H 86 ARG cc_start: 0.8141 (mmp80) cc_final: 0.7876 (mmp80) REVERT: H 103 ASN cc_start: 0.7740 (t0) cc_final: 0.7513 (t0) REVERT: H 106 MET cc_start: 0.7247 (ptm) cc_final: 0.6915 (ptm) REVERT: E 417 ASN cc_start: 0.7811 (p0) cc_final: 0.7352 (p0) REVERT: E 418 ILE cc_start: 0.8626 (mp) cc_final: 0.8370 (mp) REVERT: E 421 TYR cc_start: 0.8356 (m-10) cc_final: 0.8043 (m-10) REVERT: E 423 TYR cc_start: 0.8520 (t80) cc_final: 0.8208 (t80) REVERT: A 27 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8418 (tm-30) REVERT: A 53 ASN cc_start: 0.8204 (m110) cc_final: 0.7826 (m-40) REVERT: A 70 ASP cc_start: 0.9236 (m-30) cc_final: 0.8954 (m-30) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.1476 time to fit residues: 17.9962 Evaluate side-chains 80 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 30 optimal weight: 0.5980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.096723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.082354 restraints weight = 12178.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.084296 restraints weight = 7656.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085654 restraints weight = 5454.377| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3423 Z= 0.209 Angle : 0.709 10.973 4654 Z= 0.363 Chirality : 0.046 0.148 507 Planarity : 0.004 0.050 604 Dihedral : 5.345 25.956 475 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -2.88 (0.38), residues: 424 helix: -2.30 (0.78), residues: 35 sheet: -2.08 (0.43), residues: 125 loop : -1.79 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.022 0.002 PHE E 456 TYR 0.010 0.001 TYR E 473 ARG 0.002 0.000 ARG E 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1652.35 seconds wall clock time: 29 minutes 32.19 seconds (1772.19 seconds total)