Starting phenix.real_space_refine on Fri Dec 27 07:23:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t01_25574/12_2024/7t01_25574.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t01_25574/12_2024/7t01_25574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t01_25574/12_2024/7t01_25574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t01_25574/12_2024/7t01_25574.map" model { file = "/net/cci-nas-00/data/ceres_data/7t01_25574/12_2024/7t01_25574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t01_25574/12_2024/7t01_25574.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2136 2.51 5 N 555 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3343 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1595 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 924 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Time building chain proxies: 4.78, per 1000 atoms: 1.43 Number of scatterers: 3343 At special positions: 0 Unit cell: (68.85, 62.37, 101.25, 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 636 8.00 N 555 7.00 C 2136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 790 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 13.1% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.007A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.380A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.572A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.297A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.732A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.596A pdb=" N GLN H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR H 70 " --> pdb=" O THR H 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.602A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYR H 54 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL H 34 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL H 112 " --> pdb=" O HIS H 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.602A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYR H 54 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL H 34 " --> pdb=" O TYR H 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.714A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.722A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA L 50 " --> pdb=" O ARG L 53 " (cutoff:3.500A) 111 hydrogen bonds defined for protein. 255 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: 0.91 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1049 1.34 - 1.46: 894 1.46 - 1.59: 1469 1.59 - 1.71: 0 1.71 - 1.83: 20 Bond restraints: 3432 Sorted by residual: bond pdb=" C THR L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.75e+00 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.75e+00 bond pdb=" C LYS H 13 " pdb=" N PRO H 14 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.07e+00 bond pdb=" CB ILE L 48 " pdb=" CG2 ILE L 48 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 1.00e+00 ... (remaining 3427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 4592 2.62 - 5.24: 69 5.24 - 7.86: 10 7.86 - 10.48: 1 10.48 - 13.09: 1 Bond angle restraints: 4673 Sorted by residual: angle pdb=" CA LEU H 29 " pdb=" CB LEU H 29 " pdb=" CG LEU H 29 " ideal model delta sigma weight residual 116.30 129.39 -13.09 3.50e+00 8.16e-02 1.40e+01 angle pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " pdb=" CG TYR L 49 " ideal model delta sigma weight residual 113.90 120.52 -6.62 1.80e+00 3.09e-01 1.35e+01 angle pdb=" CA VAL L 29 " pdb=" CB VAL L 29 " pdb=" CG1 VAL L 29 " ideal model delta sigma weight residual 110.40 116.34 -5.94 1.70e+00 3.46e-01 1.22e+01 angle pdb=" N VAL L 29 " pdb=" CA VAL L 29 " pdb=" CB VAL L 29 " ideal model delta sigma weight residual 112.08 107.07 5.01 1.68e+00 3.54e-01 8.90e+00 angle pdb=" C TYR L 49 " pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " ideal model delta sigma weight residual 110.90 106.38 4.52 1.58e+00 4.01e-01 8.19e+00 ... (remaining 4668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 1810 14.74 - 29.48: 171 29.48 - 44.22: 29 44.22 - 58.96: 5 58.96 - 73.70: 4 Dihedral angle restraints: 2019 sinusoidal: 781 harmonic: 1238 Sorted by residual: dihedral pdb=" CA TYR H 54 " pdb=" C TYR H 54 " pdb=" N TRP H 55 " pdb=" CA TRP H 55 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA SER L 9 " pdb=" C SER L 9 " pdb=" N SER L 10 " pdb=" CA SER L 10 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA LEU L 78 " pdb=" C LEU L 78 " pdb=" N GLN L 79 " pdb=" CA GLN L 79 " ideal model delta harmonic sigma weight residual 180.00 153.01 26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 311 0.043 - 0.085: 143 0.085 - 0.128: 51 0.128 - 0.171: 8 0.171 - 0.214: 2 Chirality restraints: 515 Sorted by residual: chirality pdb=" CA THR L 94 " pdb=" N THR L 94 " pdb=" C THR L 94 " pdb=" CB THR L 94 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASER L 7 " pdb=" N SER L 7 " pdb=" C SER L 7 " pdb=" CB ASER L 7 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA PRO H 14 " pdb=" N PRO H 14 " pdb=" C PRO H 14 " pdb=" CB PRO H 14 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 512 not shown) Planarity restraints: 598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 49 " -0.025 2.00e-02 2.50e+03 2.08e-02 8.61e+00 pdb=" CG TYR L 49 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR L 49 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR L 49 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR L 49 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR L 49 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR L 49 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR L 49 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 29 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C VAL L 29 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL L 29 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE L 30 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 60 " -0.167 9.50e-02 1.11e+02 7.55e-02 4.40e+00 pdb=" NE ARG H 60 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG H 60 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG H 60 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG H 60 " -0.000 2.00e-02 2.50e+03 ... (remaining 595 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 1135 2.85 - 3.36: 3020 3.36 - 3.87: 5498 3.87 - 4.39: 6364 4.39 - 4.90: 10848 Nonbonded interactions: 26865 Sorted by model distance: nonbonded pdb=" OD2 ASP H 74 " pdb=" OG SER H 76 " model vdw 2.335 3.040 nonbonded pdb=" O ALA L 25 " pdb=" OG1 THR L 69 " model vdw 2.379 3.040 nonbonded pdb=" ND2 ASN A 394 " pdb=" OE2 GLU A 516 " model vdw 2.419 3.120 nonbonded pdb=" OG SER A 438 " pdb=" OD2 ASP A 442 " model vdw 2.485 3.040 nonbonded pdb=" NH1 ARG H 60 " pdb=" OG1 THR L 94 " model vdw 2.508 3.120 ... (remaining 26860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.830 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: 0.030 Set scattering table: 0.040 Process input model: 15.060 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.004 0.039 3432 Z= 0.241 Angle : 0.870 13.094 4673 Z= 0.469 Chirality : 0.054 0.214 515 Planarity : 0.008 0.075 598 Dihedral : 12.300 73.703 1220 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.08 (0.38), residues: 422 helix: -3.82 (0.72), residues: 19 sheet: -0.35 (0.44), residues: 125 loop : -0.63 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 436 HIS 0.002 0.001 HIS H 99 PHE 0.020 0.002 PHE L 83 TYR 0.047 0.005 TYR L 49 ARG 0.017 0.003 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8549 (m) cc_final: 0.8312 (p) REVERT: A 362 VAL cc_start: 0.8512 (t) cc_final: 0.8165 (p) REVERT: A 421 TYR cc_start: 0.8398 (m-10) cc_final: 0.7723 (m-10) REVERT: A 425 LEU cc_start: 0.8830 (mt) cc_final: 0.8604 (mt) REVERT: A 442 ASP cc_start: 0.8082 (m-30) cc_final: 0.7821 (m-30) REVERT: A 454 ARG cc_start: 0.9020 (ttm-80) cc_final: 0.8736 (ttm110) REVERT: A 456 PHE cc_start: 0.7839 (m-80) cc_final: 0.7590 (m-80) REVERT: H 61 TYR cc_start: 0.8953 (m-80) cc_final: 0.8675 (m-80) REVERT: L 2 MET cc_start: 0.8511 (tpt) cc_final: 0.8181 (tpt) REVERT: L 14 SER cc_start: 0.8801 (m) cc_final: 0.8560 (m) REVERT: L 22 THR cc_start: 0.7998 (p) cc_final: 0.7726 (p) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.8147 time to fit residues: 142.9543 Evaluate side-chains 149 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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: 0.2980 chunk 31 optimal weight: 0.1980 chunk 17 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3432 Z= 0.258 Angle : 0.763 10.125 4673 Z= 0.378 Chirality : 0.049 0.187 515 Planarity : 0.004 0.031 598 Dihedral : 6.525 24.130 465 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.68 % Allowed : 20.11 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.37), residues: 422 helix: -2.21 (1.28), residues: 18 sheet: -0.13 (0.46), residues: 119 loop : -0.71 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 436 HIS 0.002 0.001 HIS H 99 PHE 0.020 0.002 PHE L 83 TYR 0.012 0.002 TYR L 49 ARG 0.005 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8439 (m) cc_final: 0.8225 (p) REVERT: A 362 VAL cc_start: 0.8644 (t) cc_final: 0.8438 (p) REVERT: A 425 LEU cc_start: 0.8884 (mt) cc_final: 0.8615 (mt) REVERT: A 442 ASP cc_start: 0.8230 (m-30) cc_final: 0.7866 (m-30) REVERT: A 454 ARG cc_start: 0.9093 (ttm-80) cc_final: 0.8719 (ttm110) REVERT: A 456 PHE cc_start: 0.7844 (m-80) cc_final: 0.7583 (m-80) REVERT: A 489 TYR cc_start: 0.7740 (m-80) cc_final: 0.7504 (m-10) REVERT: A 528 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8588 (mmtp) REVERT: H 24 PHE cc_start: 0.8806 (p90) cc_final: 0.8587 (p90) REVERT: H 27 PHE cc_start: 0.8714 (p90) cc_final: 0.8418 (p90) REVERT: H 61 TYR cc_start: 0.8927 (m-80) cc_final: 0.8618 (m-80) REVERT: L 2 MET cc_start: 0.8287 (tpt) cc_final: 0.8052 (tpt) REVERT: L 3 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7272 (mm-40) REVERT: L 18 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7993 (ttm170) REVERT: L 55 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8433 (tm-30) REVERT: L 61 ARG cc_start: 0.8782 (ptt-90) cc_final: 0.8555 (ptt-90) outliers start: 10 outliers final: 3 residues processed: 157 average time/residue: 0.8175 time to fit residues: 133.5628 Evaluate side-chains 143 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN L 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3432 Z= 0.411 Angle : 0.774 10.636 4673 Z= 0.389 Chirality : 0.051 0.208 515 Planarity : 0.005 0.042 598 Dihedral : 6.347 24.121 465 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 6.17 % Allowed : 23.32 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.05 (0.38), residues: 422 helix: -2.38 (1.23), residues: 18 sheet: -0.07 (0.46), residues: 122 loop : -0.88 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 55 HIS 0.003 0.001 HIS H 99 PHE 0.020 0.002 PHE H 96 TYR 0.014 0.002 TYR A 421 ARG 0.003 0.001 ARG H 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 VAL cc_start: 0.8684 (t) cc_final: 0.8465 (p) REVERT: A 421 TYR cc_start: 0.8504 (m-10) cc_final: 0.8231 (m-10) REVERT: A 425 LEU cc_start: 0.8934 (mt) cc_final: 0.8725 (mt) REVERT: A 442 ASP cc_start: 0.8346 (m-30) cc_final: 0.7983 (m-30) REVERT: A 454 ARG cc_start: 0.9162 (ttm-80) cc_final: 0.8881 (ttm-80) REVERT: A 456 PHE cc_start: 0.7947 (m-80) cc_final: 0.7697 (m-80) REVERT: A 489 TYR cc_start: 0.7823 (m-80) cc_final: 0.7554 (m-10) REVERT: H 61 TYR cc_start: 0.8988 (m-80) cc_final: 0.8775 (m-80) REVERT: H 119 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8719 (p) REVERT: L 2 MET cc_start: 0.8352 (tpt) cc_final: 0.7893 (tpt) REVERT: L 27 GLN cc_start: 0.7224 (mm110) cc_final: 0.6592 (mm-40) REVERT: L 55 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8502 (tm-30) REVERT: L 90 GLN cc_start: 0.8753 (pp30) cc_final: 0.8344 (pp30) outliers start: 23 outliers final: 9 residues processed: 163 average time/residue: 0.8932 time to fit residues: 150.9519 Evaluate side-chains 146 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.0670 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3432 Z= 0.388 Angle : 0.771 11.531 4673 Z= 0.385 Chirality : 0.050 0.208 515 Planarity : 0.005 0.047 598 Dihedral : 6.231 25.564 465 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.70 % Allowed : 26.54 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.39), residues: 422 helix: -2.25 (1.69), residues: 12 sheet: -0.32 (0.47), residues: 116 loop : -0.94 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 55 HIS 0.004 0.002 HIS A 519 PHE 0.037 0.003 PHE H 27 TYR 0.014 0.002 TYR L 87 ARG 0.007 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8225 (p) REVERT: A 425 LEU cc_start: 0.8922 (mt) cc_final: 0.8651 (mt) REVERT: A 442 ASP cc_start: 0.8357 (m-30) cc_final: 0.7982 (m-30) REVERT: A 454 ARG cc_start: 0.9178 (ttm-80) cc_final: 0.8799 (ttm-80) REVERT: A 456 PHE cc_start: 0.7963 (m-80) cc_final: 0.7701 (m-80) REVERT: A 489 TYR cc_start: 0.7770 (m-80) cc_final: 0.7536 (m-10) REVERT: H 55 TRP cc_start: 0.8639 (p90) cc_final: 0.8346 (p90) REVERT: H 80 VAL cc_start: 0.9086 (t) cc_final: 0.8876 (t) REVERT: H 81 VAL cc_start: 0.9210 (m) cc_final: 0.8933 (p) REVERT: H 106 ASP cc_start: 0.7979 (m-30) cc_final: 0.7750 (m-30) REVERT: L 2 MET cc_start: 0.8311 (tpt) cc_final: 0.7934 (tpt) REVERT: L 18 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8313 (ptm160) REVERT: L 27 GLN cc_start: 0.7185 (mm110) cc_final: 0.6616 (mm-40) REVERT: L 55 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8622 (tm-30) REVERT: L 82 ASP cc_start: 0.7985 (m-30) cc_final: 0.7584 (m-30) REVERT: L 90 GLN cc_start: 0.8809 (pp30) cc_final: 0.8345 (pp30) outliers start: 25 outliers final: 11 residues processed: 153 average time/residue: 0.9029 time to fit residues: 143.1679 Evaluate side-chains 165 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.0870 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3432 Z= 0.245 Angle : 0.749 11.179 4673 Z= 0.367 Chirality : 0.049 0.189 515 Planarity : 0.005 0.044 598 Dihedral : 5.825 24.955 465 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.90 % Allowed : 28.95 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.28 (0.39), residues: 422 helix: -2.60 (1.19), residues: 19 sheet: -0.65 (0.47), residues: 124 loop : -0.80 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 38 HIS 0.003 0.001 HIS H 99 PHE 0.039 0.002 PHE H 27 TYR 0.017 0.001 TYR A 421 ARG 0.006 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8318 (t) REVERT: A 355 ARG cc_start: 0.8590 (tpp-160) cc_final: 0.8302 (tpp-160) REVERT: A 390 LEU cc_start: 0.8678 (mm) cc_final: 0.8420 (mp) REVERT: A 409 GLN cc_start: 0.8931 (mt0) cc_final: 0.8679 (tt0) REVERT: A 421 TYR cc_start: 0.8525 (m-10) cc_final: 0.8033 (m-80) REVERT: A 425 LEU cc_start: 0.8857 (mt) cc_final: 0.8625 (mt) REVERT: A 442 ASP cc_start: 0.8326 (m-30) cc_final: 0.7961 (m-30) REVERT: A 454 ARG cc_start: 0.9147 (ttm-80) cc_final: 0.8803 (ttm-80) REVERT: A 456 PHE cc_start: 0.7813 (m-80) cc_final: 0.7545 (m-10) REVERT: H 81 VAL cc_start: 0.9162 (m) cc_final: 0.8874 (p) REVERT: H 106 ASP cc_start: 0.7984 (m-30) cc_final: 0.7692 (m-30) REVERT: L 2 MET cc_start: 0.8349 (tpt) cc_final: 0.8001 (tpt) REVERT: L 3 GLN cc_start: 0.8039 (mp10) cc_final: 0.7666 (mm110) REVERT: L 18 ARG cc_start: 0.8475 (ttm170) cc_final: 0.8273 (ptm160) REVERT: L 27 GLN cc_start: 0.7251 (mm110) cc_final: 0.6646 (mm-40) REVERT: L 55 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8501 (tm-30) outliers start: 22 outliers final: 11 residues processed: 159 average time/residue: 0.8426 time to fit residues: 139.2896 Evaluate side-chains 158 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.0170 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3432 Z= 0.365 Angle : 0.794 12.057 4673 Z= 0.387 Chirality : 0.050 0.199 515 Planarity : 0.005 0.045 598 Dihedral : 5.978 25.767 465 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 7.51 % Allowed : 30.83 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.28 (0.40), residues: 422 helix: -2.69 (1.17), residues: 19 sheet: -0.72 (0.47), residues: 127 loop : -0.74 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 38 HIS 0.001 0.000 HIS H 99 PHE 0.027 0.002 PHE H 27 TYR 0.019 0.002 TYR A 380 ARG 0.005 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8363 (t) REVERT: A 355 ARG cc_start: 0.8586 (tpp-160) cc_final: 0.8299 (tpp-160) REVERT: A 392 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8799 (m-80) REVERT: A 409 GLN cc_start: 0.8975 (mt0) cc_final: 0.8675 (tt0) REVERT: A 421 TYR cc_start: 0.8529 (m-10) cc_final: 0.8160 (m-80) REVERT: A 425 LEU cc_start: 0.8904 (mt) cc_final: 0.8691 (mt) REVERT: A 442 ASP cc_start: 0.8362 (m-30) cc_final: 0.7988 (m-30) REVERT: A 454 ARG cc_start: 0.9185 (ttm-80) cc_final: 0.8857 (ttm-80) REVERT: A 456 PHE cc_start: 0.7857 (m-80) cc_final: 0.7572 (m-80) REVERT: H 80 VAL cc_start: 0.9088 (t) cc_final: 0.8870 (t) REVERT: H 81 VAL cc_start: 0.9174 (m) cc_final: 0.8900 (p) REVERT: H 106 ASP cc_start: 0.8000 (m-30) cc_final: 0.7729 (m-30) REVERT: L 2 MET cc_start: 0.8451 (tpt) cc_final: 0.8108 (tpt) REVERT: L 18 ARG cc_start: 0.8412 (ttm170) cc_final: 0.8158 (ptm160) REVERT: L 27 GLN cc_start: 0.7367 (mm110) cc_final: 0.6870 (mm-40) REVERT: L 55 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8501 (tm-30) REVERT: L 90 GLN cc_start: 0.8830 (pp30) cc_final: 0.8424 (pp30) outliers start: 28 outliers final: 16 residues processed: 161 average time/residue: 0.8719 time to fit residues: 145.8065 Evaluate side-chains 168 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 7 optimal weight: 0.3980 chunk 27 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3432 Z= 0.290 Angle : 0.792 12.372 4673 Z= 0.382 Chirality : 0.050 0.188 515 Planarity : 0.005 0.046 598 Dihedral : 5.831 24.946 465 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.09 % Allowed : 33.24 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.41 (0.40), residues: 422 helix: -2.60 (1.22), residues: 19 sheet: -0.75 (0.48), residues: 127 loop : -0.89 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 38 HIS 0.003 0.001 HIS A 519 PHE 0.025 0.002 PHE H 27 TYR 0.025 0.002 TYR A 380 ARG 0.009 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8328 (t) REVERT: A 355 ARG cc_start: 0.8587 (tpp-160) cc_final: 0.8328 (tpp-160) REVERT: A 392 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8769 (m-80) REVERT: A 409 GLN cc_start: 0.8922 (mt0) cc_final: 0.8503 (tt0) REVERT: A 421 TYR cc_start: 0.8535 (m-10) cc_final: 0.8197 (m-80) REVERT: A 442 ASP cc_start: 0.8328 (m-30) cc_final: 0.7969 (m-30) REVERT: H 106 ASP cc_start: 0.7990 (m-30) cc_final: 0.7705 (m-30) REVERT: L 2 MET cc_start: 0.8467 (tpt) cc_final: 0.8129 (tpt) REVERT: L 3 GLN cc_start: 0.8068 (mp10) cc_final: 0.7711 (mm110) REVERT: L 18 ARG cc_start: 0.8423 (ttm170) cc_final: 0.8191 (ptm160) REVERT: L 27 GLN cc_start: 0.7423 (mm110) cc_final: 0.6892 (mm-40) REVERT: L 55 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8414 (tm-30) REVERT: L 71 PHE cc_start: 0.8322 (m-80) cc_final: 0.8115 (m-80) REVERT: L 75 ILE cc_start: 0.8768 (mp) cc_final: 0.8448 (tp) REVERT: L 90 GLN cc_start: 0.8837 (pp30) cc_final: 0.8425 (pp30) outliers start: 19 outliers final: 13 residues processed: 156 average time/residue: 0.9077 time to fit residues: 146.9685 Evaluate side-chains 168 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.1980 chunk 31 optimal weight: 0.0670 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.0670 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 overall best weight: 0.1654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3432 Z= 0.199 Angle : 0.779 12.808 4673 Z= 0.370 Chirality : 0.049 0.172 515 Planarity : 0.005 0.047 598 Dihedral : 5.422 23.268 465 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.36 % Allowed : 33.51 % Favored : 61.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.40), residues: 422 helix: -2.85 (1.12), residues: 19 sheet: -0.85 (0.45), residues: 132 loop : -0.82 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 38 HIS 0.003 0.001 HIS A 519 PHE 0.024 0.002 PHE H 27 TYR 0.013 0.001 TYR L 36 ARG 0.012 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8316 (t) REVERT: A 392 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8726 (m-80) REVERT: A 409 GLN cc_start: 0.8756 (mt0) cc_final: 0.8473 (tt0) REVERT: A 421 TYR cc_start: 0.8521 (m-10) cc_final: 0.8145 (m-80) REVERT: A 442 ASP cc_start: 0.8304 (m-30) cc_final: 0.7937 (m-30) REVERT: A 474 GLN cc_start: 0.8092 (tt0) cc_final: 0.7835 (tp-100) REVERT: H 106 ASP cc_start: 0.7950 (m-30) cc_final: 0.7674 (m-30) REVERT: L 2 MET cc_start: 0.8606 (tpt) cc_final: 0.8343 (tpt) REVERT: L 3 GLN cc_start: 0.8077 (mp10) cc_final: 0.7620 (mm110) REVERT: L 27 GLN cc_start: 0.7510 (mm110) cc_final: 0.6913 (mm-40) REVERT: L 55 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: L 61 ARG cc_start: 0.8500 (ptt-90) cc_final: 0.8256 (ptp-170) REVERT: L 90 GLN cc_start: 0.8850 (pp30) cc_final: 0.8341 (pp30) outliers start: 20 outliers final: 10 residues processed: 154 average time/residue: 0.8328 time to fit residues: 133.2912 Evaluate side-chains 148 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 24 optimal weight: 0.4980 chunk 39 optimal weight: 0.0980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 3432 Z= 0.299 Angle : 0.835 12.160 4673 Z= 0.401 Chirality : 0.050 0.184 515 Planarity : 0.006 0.051 598 Dihedral : 5.691 24.131 465 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.75 % Allowed : 35.92 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.53 (0.41), residues: 422 helix: -2.59 (1.21), residues: 19 sheet: -0.95 (0.47), residues: 128 loop : -0.91 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 38 HIS 0.000 0.000 HIS H 99 PHE 0.021 0.002 PHE H 24 TYR 0.023 0.002 TYR A 489 ARG 0.011 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 333 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8318 (t) REVERT: A 392 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: A 421 TYR cc_start: 0.8516 (m-10) cc_final: 0.8148 (m-80) REVERT: A 442 ASP cc_start: 0.8339 (m-30) cc_final: 0.7955 (m-30) REVERT: H 106 ASP cc_start: 0.7979 (m-30) cc_final: 0.7713 (m-30) REVERT: L 3 GLN cc_start: 0.8126 (mp10) cc_final: 0.7720 (mm110) REVERT: L 27 GLN cc_start: 0.7514 (mm110) cc_final: 0.7066 (mm-40) REVERT: L 37 GLN cc_start: 0.8644 (tt0) cc_final: 0.8433 (tt0) REVERT: L 55 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8521 (tm-30) REVERT: L 81 GLU cc_start: 0.8564 (pm20) cc_final: 0.7850 (pp20) REVERT: L 90 GLN cc_start: 0.8947 (pp30) cc_final: 0.8530 (pp30) outliers start: 14 outliers final: 8 residues processed: 155 average time/residue: 0.8751 time to fit residues: 140.6053 Evaluate side-chains 157 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 97 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 35 optimal weight: 0.1980 chunk 10 optimal weight: 0.3980 chunk 30 optimal weight: 0.0970 chunk 4 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 13 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3432 Z= 0.251 Angle : 0.893 14.509 4673 Z= 0.419 Chirality : 0.051 0.279 515 Planarity : 0.006 0.059 598 Dihedral : 5.572 23.857 465 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.95 % Allowed : 38.07 % Favored : 58.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.41), residues: 422 helix: -2.26 (1.70), residues: 12 sheet: -0.78 (0.47), residues: 127 loop : -0.93 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 38 HIS 0.002 0.001 HIS A 519 PHE 0.024 0.002 PHE H 27 TYR 0.029 0.002 TYR A 453 ARG 0.014 0.001 ARG L 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8297 (t) REVERT: A 355 ARG cc_start: 0.8557 (tpp-160) cc_final: 0.8166 (tpp-160) REVERT: A 392 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: A 421 TYR cc_start: 0.8490 (m-10) cc_final: 0.8192 (m-80) REVERT: A 442 ASP cc_start: 0.8288 (m-30) cc_final: 0.7929 (m-30) REVERT: A 474 GLN cc_start: 0.8033 (tt0) cc_final: 0.7778 (tp-100) REVERT: H 106 ASP cc_start: 0.7955 (m-30) cc_final: 0.7679 (m-30) REVERT: L 3 GLN cc_start: 0.8032 (mp10) cc_final: 0.7524 (mm110) REVERT: L 55 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: L 61 ARG cc_start: 0.8508 (ptt-90) cc_final: 0.7825 (ptt-90) REVERT: L 71 PHE cc_start: 0.8276 (m-80) cc_final: 0.8064 (m-80) REVERT: L 81 GLU cc_start: 0.8531 (pm20) cc_final: 0.8089 (pm20) REVERT: L 90 GLN cc_start: 0.8927 (pp30) cc_final: 0.8566 (pp30) outliers start: 11 outliers final: 7 residues processed: 146 average time/residue: 0.8314 time to fit residues: 125.9621 Evaluate side-chains 142 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 38 optimal weight: 0.0370 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.0010 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 overall best weight: 0.2664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 79 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 = 0.3560 r_free = 0.3560 target = 0.089716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078197 restraints weight = 7355.667| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.95 r_work: 0.3242 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3432 Z= 0.268 Angle : 0.890 13.530 4673 Z= 0.421 Chirality : 0.050 0.249 515 Planarity : 0.006 0.058 598 Dihedral : 5.490 23.192 465 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.75 % Allowed : 37.27 % Favored : 58.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.41), residues: 422 helix: -2.19 (1.72), residues: 12 sheet: -0.84 (0.47), residues: 127 loop : -0.98 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 38 HIS 0.001 0.001 HIS A 519 PHE 0.023 0.002 PHE H 27 TYR 0.029 0.002 TYR A 489 ARG 0.013 0.001 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2920.83 seconds wall clock time: 54 minutes 5.91 seconds (3245.91 seconds total)