Starting phenix.real_space_refine on Wed Jul 23 13:02:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wt9_32772/07_2025/7wt9_32772.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wt9_32772/07_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_32772/07_2025/7wt9_32772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wt9_32772/07_2025/7wt9_32772.map" model { file = "/net/cci-nas-00/data/ceres_data/7wt9_32772/07_2025/7wt9_32772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wt9_32772/07_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-5711/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: 3.43, per 1000 atoms: 1.03 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: 1.11 Conformation dependent library (CDL) restraints added in 930.4 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: 0.73 Time building geometry restraints manager: 1.21 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.970 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- 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 3429 Z= 0.292 Angle : 1.292 15.900 4666 Z= 0.687 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 Details of bonding type rmsd hydrogen bonds : bond 0.25818 ( 58) hydrogen bonds : angle 11.14879 ( 156) SS BOND : bond 0.01015 ( 6) SS BOND : angle 5.25418 ( 12) covalent geometry : bond 0.00564 ( 3423) covalent geometry : angle 1.26607 ( 4654) *********************** 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 : 0.388 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: 0.1435 time to fit residues: 20.0388 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 : 0.383 ------------------------------------------------------------------------------- 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 3429 Z= 0.180 Angle : 0.690 10.347 4666 Z= 0.362 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 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 58) hydrogen bonds : angle 8.21893 ( 156) SS BOND : bond 0.00436 ( 6) SS BOND : angle 2.84972 ( 12) covalent geometry : bond 0.00380 ( 3423) covalent geometry : angle 0.67518 ( 4654) *********************** 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 : 1.197 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: 0.2237 time to fit residues: 25.0738 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 : 0.440 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.7980 chunk 27 optimal weight: 0.0470 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: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.098072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.083531 restraints weight = 11545.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.085541 restraints weight = 7135.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.086908 restraints weight = 5023.571| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3429 Z= 0.150 Angle : 0.644 9.797 4666 Z= 0.335 Chirality : 0.044 0.145 507 Planarity : 0.005 0.046 604 Dihedral : 5.533 28.199 475 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % 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: -2.95 (0.37), residues: 424 helix: -2.75 (0.72), residues: 32 sheet: -2.03 (0.42), residues: 125 loop : -1.85 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 35 HIS 0.001 0.000 HIS E 505 PHE 0.023 0.002 PHE E 392 TYR 0.011 0.001 TYR E 396 ARG 0.004 0.001 ARG E 509 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 58) hydrogen bonds : angle 7.50426 ( 156) SS BOND : bond 0.00444 ( 6) SS BOND : angle 2.75663 ( 12) covalent geometry : bond 0.00331 ( 3423) covalent geometry : angle 0.62959 ( 4654) *********************** 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 96 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.8493 (tp) cc_final: 0.8233 (tp) REVERT: H 82 MET cc_start: 0.8027 (mpp) cc_final: 0.7700 (mpp) REVERT: H 85 LEU cc_start: 0.8430 (mt) cc_final: 0.8124 (mt) REVERT: E 460 ASN cc_start: 0.8727 (t0) cc_final: 0.8046 (p0) REVERT: A 53 ASN cc_start: 0.7669 (m110) cc_final: 0.7398 (m110) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.4093 time to fit residues: 46.7821 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 : 0.996 ------------------------------------------------------------------------------- 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: 0.4980 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.097917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.082689 restraints weight = 11852.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.084892 restraints weight = 7034.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.086350 restraints weight = 4823.880| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3429 Z= 0.132 Angle : 0.637 8.794 4666 Z= 0.329 Chirality : 0.045 0.152 507 Planarity : 0.005 0.047 604 Dihedral : 5.416 28.121 475 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % 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: -2.88 (0.37), residues: 424 helix: -2.62 (0.73), residues: 33 sheet: -2.02 (0.43), residues: 117 loop : -1.82 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 36 HIS 0.000 0.000 HIS E 505 PHE 0.019 0.002 PHE E 392 TYR 0.024 0.002 TYR E 380 ARG 0.007 0.001 ARG E 355 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 58) hydrogen bonds : angle 7.52377 ( 156) SS BOND : bond 0.00387 ( 6) SS BOND : angle 2.84738 ( 12) covalent geometry : bond 0.00291 ( 3423) covalent geometry : angle 0.62074 ( 4654) *********************** 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 89 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 TYR cc_start: 0.6918 (m-10) cc_final: 0.6488 (m-10) REVERT: H 34 MET cc_start: 0.6519 (mmp) cc_final: 0.6075 (mmm) REVERT: H 78 LEU cc_start: 0.8417 (tp) cc_final: 0.8003 (tp) REVERT: H 85 LEU cc_start: 0.8839 (mt) cc_final: 0.8232 (mt) REVERT: H 103 ASN cc_start: 0.7637 (t0) cc_final: 0.7433 (t0) REVERT: E 460 ASN cc_start: 0.8763 (t0) cc_final: 0.8049 (p0) REVERT: A 53 ASN cc_start: 0.7904 (m110) cc_final: 0.7628 (m-40) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2241 time to fit residues: 23.9922 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 : 0.298 ------------------------------------------------------------------------------- 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: 0.9990 chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.097641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.082704 restraints weight = 11834.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.084829 restraints weight = 7089.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.086313 restraints weight = 4896.235| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 0.027 3429 Z= 0.143 Angle : 0.642 8.192 4666 Z= 0.329 Chirality : 0.045 0.148 507 Planarity : 0.005 0.044 604 Dihedral : 5.293 28.280 475 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % 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: -2.78 (0.38), residues: 424 helix: -2.54 (0.76), residues: 34 sheet: -2.02 (0.42), residues: 124 loop : -1.67 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 36 HIS 0.000 0.000 HIS E 519 PHE 0.025 0.002 PHE E 392 TYR 0.023 0.002 TYR E 380 ARG 0.003 0.001 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 58) hydrogen bonds : angle 7.06833 ( 156) SS BOND : bond 0.00402 ( 6) SS BOND : angle 3.17577 ( 12) covalent geometry : bond 0.00320 ( 3423) covalent geometry : angle 0.62204 ( 4654) *********************** 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 93 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8432 (tp30) cc_final: 0.8028 (mp0) REVERT: H 57 THR cc_start: 0.7917 (p) cc_final: 0.7714 (p) REVERT: H 78 LEU cc_start: 0.8502 (tp) cc_final: 0.8124 (tp) REVERT: H 82 MET cc_start: 0.8104 (mpp) cc_final: 0.7693 (mpp) REVERT: H 85 LEU cc_start: 0.8522 (mt) cc_final: 0.8306 (mt) REVERT: E 460 ASN cc_start: 0.8759 (t0) cc_final: 0.8038 (p0) REVERT: A 53 ASN cc_start: 0.7759 (m110) cc_final: 0.7547 (m-40) REVERT: A 71 PHE cc_start: 0.8487 (m-10) cc_final: 0.7653 (m-10) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.2734 time to fit residues: 31.0211 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 : 0.534 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.095884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.081810 restraints weight = 12054.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.083670 restraints weight = 7504.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.084982 restraints weight = 5330.374| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3429 Z= 0.165 Angle : 0.672 10.653 4666 Z= 0.343 Chirality : 0.046 0.146 507 Planarity : 0.004 0.043 604 Dihedral : 5.288 27.625 475 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.27 % Allowed : 4.08 % 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: -2.91 (0.37), residues: 424 helix: -2.58 (0.75), residues: 35 sheet: -2.17 (0.40), residues: 130 loop : -1.70 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.000 0.000 HIS E 519 PHE 0.018 0.002 PHE E 464 TYR 0.022 0.002 TYR E 380 ARG 0.003 0.001 ARG E 457 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 58) hydrogen bonds : angle 7.14362 ( 156) SS BOND : bond 0.00531 ( 6) SS BOND : angle 2.76518 ( 12) covalent geometry : bond 0.00366 ( 3423) covalent geometry : angle 0.65787 ( 4654) *********************** 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 94 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.8435 (tp) cc_final: 0.8052 (tp) REVERT: H 82 MET cc_start: 0.8056 (mpp) cc_final: 0.7741 (mpp) REVERT: H 85 LEU cc_start: 0.8941 (mt) cc_final: 0.8462 (mt) REVERT: H 86 ARG cc_start: 0.7541 (mmp80) cc_final: 0.7286 (mmp-170) REVERT: H 94 TYR cc_start: 0.8060 (m-10) cc_final: 0.7694 (m-10) REVERT: H 103 ASN cc_start: 0.7777 (t0) cc_final: 0.7489 (t0) REVERT: E 417 ASN cc_start: 0.7915 (p0) cc_final: 0.7352 (p0) REVERT: E 418 ILE cc_start: 0.8651 (mp) cc_final: 0.8365 (mp) REVERT: E 460 ASN cc_start: 0.8675 (t0) cc_final: 0.8276 (p0) REVERT: A 71 PHE cc_start: 0.8556 (m-10) cc_final: 0.7785 (m-10) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.2048 time to fit residues: 22.6475 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 : 0.531 ------------------------------------------------------------------------------- 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: 0.5980 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3598 r_free = 0.3598 target = 0.094992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.080879 restraints weight = 11825.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.082799 restraints weight = 7320.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.084142 restraints weight = 5160.778| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3429 Z= 0.174 Angle : 0.732 10.991 4666 Z= 0.374 Chirality : 0.046 0.174 507 Planarity : 0.004 0.042 604 Dihedral : 5.434 28.162 475 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % 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: -2.95 (0.37), residues: 424 helix: -2.65 (0.77), residues: 35 sheet: -2.23 (0.41), residues: 128 loop : -1.71 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 436 HIS 0.002 0.001 HIS E 519 PHE 0.016 0.002 PHE E 464 TYR 0.024 0.002 TYR E 380 ARG 0.003 0.001 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 58) hydrogen bonds : angle 7.02327 ( 156) SS BOND : bond 0.00363 ( 6) SS BOND : angle 4.63760 ( 12) covalent geometry : bond 0.00389 ( 3423) covalent geometry : angle 0.69364 ( 4654) *********************** 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 94 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.8438 (tp) cc_final: 0.8097 (tp) REVERT: H 82 MET cc_start: 0.8140 (mpp) cc_final: 0.7808 (mpp) REVERT: H 85 LEU cc_start: 0.9060 (mt) cc_final: 0.8352 (mt) REVERT: H 86 ARG cc_start: 0.7683 (mmp80) cc_final: 0.7344 (mmp-170) REVERT: H 106 MET cc_start: 0.7110 (ptm) cc_final: 0.6836 (ptm) REVERT: E 417 ASN cc_start: 0.7868 (p0) cc_final: 0.7509 (p0) REVERT: E 460 ASN cc_start: 0.8766 (t0) cc_final: 0.8433 (p0) REVERT: A 3 GLN cc_start: 0.8028 (mp10) cc_final: 0.7776 (mp10) REVERT: A 70 ASP cc_start: 0.9253 (m-30) cc_final: 0.8997 (m-30) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1733 time to fit residues: 19.5470 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 : 0.389 ------------------------------------------------------------------------------- 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: 0.0270 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN 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 = 0.3607 r_free = 0.3607 target = 0.095611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.081432 restraints weight = 11657.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.083374 restraints weight = 7116.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.084758 restraints weight = 4994.409| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3429 Z= 0.150 Angle : 0.702 9.753 4666 Z= 0.359 Chirality : 0.046 0.158 507 Planarity : 0.004 0.045 604 Dihedral : 5.309 27.717 475 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 0.27 % Allowed : 1.63 % Favored : 98.10 % 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: -2.95 (0.38), residues: 424 helix: -2.61 (0.76), residues: 35 sheet: -2.24 (0.41), residues: 128 loop : -1.71 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 353 HIS 0.001 0.000 HIS E 519 PHE 0.013 0.002 PHE E 464 TYR 0.023 0.002 TYR E 380 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 58) hydrogen bonds : angle 6.79715 ( 156) SS BOND : bond 0.00292 ( 6) SS BOND : angle 3.55948 ( 12) covalent geometry : bond 0.00341 ( 3423) covalent geometry : angle 0.67908 ( 4654) *********************** 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 97 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.8468 (tp) cc_final: 0.8118 (tp) REVERT: H 85 LEU cc_start: 0.9017 (mt) cc_final: 0.8357 (mt) REVERT: H 86 ARG cc_start: 0.7925 (mmp80) cc_final: 0.7435 (mmp-170) REVERT: E 417 ASN cc_start: 0.7706 (p0) cc_final: 0.7141 (p0) REVERT: E 418 ILE cc_start: 0.8532 (mp) cc_final: 0.8165 (mp) REVERT: E 421 TYR cc_start: 0.8505 (m-10) cc_final: 0.8299 (m-80) REVERT: E 460 ASN cc_start: 0.8776 (t0) cc_final: 0.8383 (p0) REVERT: E 489 TYR cc_start: 0.5960 (m-80) cc_final: 0.5713 (m-80) REVERT: A 3 GLN cc_start: 0.8030 (mp10) cc_final: 0.7788 (mp10) REVERT: A 53 ASN cc_start: 0.8009 (m110) cc_final: 0.7696 (m-40) REVERT: A 70 ASP cc_start: 0.9282 (m-30) cc_final: 0.9042 (m-30) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.2163 time to fit residues: 25.7979 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 : 0.469 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.0020 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.095397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.080485 restraints weight = 11835.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.082511 restraints weight = 7190.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.083947 restraints weight = 5028.132| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3429 Z= 0.161 Angle : 0.730 9.501 4666 Z= 0.374 Chirality : 0.046 0.148 507 Planarity : 0.004 0.045 604 Dihedral : 5.414 28.018 475 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: -3.02 (0.37), residues: 424 helix: -2.60 (0.75), residues: 35 sheet: -2.27 (0.41), residues: 127 loop : -1.78 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 36 HIS 0.001 0.000 HIS E 505 PHE 0.014 0.002 PHE E 464 TYR 0.021 0.002 TYR E 380 ARG 0.003 0.001 ARG E 457 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 58) hydrogen bonds : angle 7.01530 ( 156) SS BOND : bond 0.00343 ( 6) SS BOND : angle 3.31382 ( 12) covalent geometry : bond 0.00366 ( 3423) covalent geometry : angle 0.71146 ( 4654) *********************** 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 92 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 LEU cc_start: 0.9492 (mt) cc_final: 0.9287 (mt) REVERT: H 33 TYR cc_start: 0.7641 (m-10) cc_final: 0.7106 (m-10) REVERT: H 78 LEU cc_start: 0.8430 (tp) cc_final: 0.8075 (tp) REVERT: H 82 MET cc_start: 0.8402 (mpp) cc_final: 0.7581 (mpp) REVERT: H 85 LEU cc_start: 0.9098 (mt) cc_final: 0.8490 (mt) REVERT: H 86 ARG cc_start: 0.7898 (mmp80) cc_final: 0.7491 (mmp-170) REVERT: H 106 MET cc_start: 0.7209 (ptm) cc_final: 0.6877 (ptm) REVERT: E 417 ASN cc_start: 0.7748 (p0) cc_final: 0.7241 (p0) REVERT: E 418 ILE cc_start: 0.8561 (mp) cc_final: 0.8265 (mp) REVERT: E 421 TYR cc_start: 0.8482 (m-10) cc_final: 0.7873 (m-10) REVERT: E 460 ASN cc_start: 0.8773 (t0) cc_final: 0.8398 (p0) REVERT: A 3 GLN cc_start: 0.8110 (mp10) cc_final: 0.7863 (mp10) REVERT: A 53 ASN cc_start: 0.8261 (m110) cc_final: 0.7921 (m-40) REVERT: A 70 ASP cc_start: 0.9263 (m-30) cc_final: 0.9004 (m-30) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2427 time to fit residues: 26.4742 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 : 0.745 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.094794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.080458 restraints weight = 11834.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082424 restraints weight = 7297.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.083781 restraints weight = 5129.658| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3429 Z= 0.171 Angle : 0.732 9.441 4666 Z= 0.374 Chirality : 0.046 0.149 507 Planarity : 0.005 0.074 604 Dihedral : 5.454 28.094 475 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % 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: -3.09 (0.37), residues: 424 helix: -2.61 (0.75), residues: 35 sheet: -2.26 (0.41), residues: 128 loop : -1.87 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.015 0.002 PHE E 464 TYR 0.021 0.002 TYR E 380 ARG 0.004 0.000 ARG E 408 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 58) hydrogen bonds : angle 6.95544 ( 156) SS BOND : bond 0.00319 ( 6) SS BOND : angle 3.35015 ( 12) covalent geometry : bond 0.00387 ( 3423) covalent geometry : angle 0.71262 ( 4654) ********************** 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 94 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8244 (m-10) cc_final: 0.8005 (m-10) REVERT: H 82 MET cc_start: 0.8409 (mpp) cc_final: 0.7624 (mpp) REVERT: H 85 LEU cc_start: 0.9137 (mt) cc_final: 0.8908 (mt) REVERT: H 86 ARG cc_start: 0.7962 (mmp80) cc_final: 0.7508 (mmp-170) REVERT: H 103 ASN cc_start: 0.7912 (t0) cc_final: 0.7617 (t0) REVERT: E 417 ASN cc_start: 0.7721 (p0) cc_final: 0.7143 (p0) REVERT: E 418 ILE cc_start: 0.8568 (mp) cc_final: 0.8269 (mp) REVERT: E 421 TYR cc_start: 0.8497 (m-10) cc_final: 0.8287 (m-80) REVERT: E 460 ASN cc_start: 0.8788 (t0) cc_final: 0.8426 (p0) REVERT: A 3 GLN cc_start: 0.8067 (mp10) cc_final: 0.7811 (mp10) REVERT: A 70 ASP cc_start: 0.9241 (m-30) cc_final: 0.9036 (m-30) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1610 time to fit residues: 18.2287 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 : 0.388 ------------------------------------------------------------------------------- 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: 7.9990 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.094560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.080183 restraints weight = 11819.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.082178 restraints weight = 7248.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.083577 restraints weight = 5054.372| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3429 Z= 0.171 Angle : 0.774 11.023 4666 Z= 0.392 Chirality : 0.047 0.148 507 Planarity : 0.005 0.044 604 Dihedral : 5.486 28.290 475 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % 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: -3.07 (0.38), residues: 424 helix: -2.50 (0.80), residues: 33 sheet: -2.18 (0.42), residues: 132 loop : -1.92 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.000 0.000 HIS E 519 PHE 0.027 0.002 PHE E 456 TYR 0.026 0.002 TYR E 351 ARG 0.003 0.000 ARG E 408 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 58) hydrogen bonds : angle 6.97999 ( 156) SS BOND : bond 0.00362 ( 6) SS BOND : angle 4.69264 ( 12) covalent geometry : bond 0.00393 ( 3423) covalent geometry : angle 0.73721 ( 4654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2607.61 seconds wall clock time: 49 minutes 28.49 seconds (2968.49 seconds total)