Starting phenix.real_space_refine on Tue Feb 13 05:43:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/02_2024/7t01_25574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/02_2024/7t01_25574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/02_2024/7t01_25574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/02_2024/7t01_25574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t01_25574/02_2024/7t01_25574.pdb" } 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 Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 2.32, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 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: 1.20 Conformation dependent library (CDL) restraints added in 613.4 milliseconds 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: 0.94 Time building geometry restraints manager: 1.33 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: 100.05 - 106.85: 120 106.85 - 113.65: 1789 113.65 - 120.45: 1284 120.45 - 127.25: 1439 127.25 - 134.05: 41 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 2.440 nonbonded pdb=" O ALA L 25 " pdb=" OG1 THR L 69 " model vdw 2.379 2.440 nonbonded pdb=" ND2 ASN A 394 " pdb=" OE2 GLU A 516 " model vdw 2.419 2.520 nonbonded pdb=" OG SER A 438 " pdb=" OD2 ASP A 442 " model vdw 2.485 2.440 nonbonded pdb=" NH1 ARG H 60 " pdb=" OG1 THR L 94 " model vdw 2.508 2.520 ... (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 ========== 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: 6.020 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: 25.830 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.200 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 57.140 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.360 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: 0.8226 time to fit residues: 144.4451 Evaluate side-chains 149 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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: 0.0980 chunk 17 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 L 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3432 Z= 0.275 Angle : 0.751 9.601 4673 Z= 0.373 Chirality : 0.049 0.182 515 Planarity : 0.005 0.032 598 Dihedral : 6.513 23.453 465 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.29 % Allowed : 19.03 % Favored : 76.68 % 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: -0.81 (0.38), residues: 422 helix: -1.83 (1.38), residues: 18 sheet: -0.08 (0.45), residues: 125 loop : -0.65 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 436 HIS 0.004 0.001 HIS H 99 PHE 0.020 0.002 PHE L 83 TYR 0.013 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 172 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 VAL cc_start: 0.8582 (t) cc_final: 0.8318 (p) REVERT: A 425 LEU cc_start: 0.8889 (mt) cc_final: 0.8623 (mt) REVERT: A 454 ARG cc_start: 0.9123 (ttm-80) cc_final: 0.8806 (ttm110) REVERT: A 456 PHE cc_start: 0.7842 (m-80) cc_final: 0.7588 (m-80) REVERT: A 528 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8444 (mttp) REVERT: H 24 PHE cc_start: 0.8809 (p90) cc_final: 0.8597 (p90) REVERT: H 27 PHE cc_start: 0.8764 (p90) cc_final: 0.8456 (p90) REVERT: H 61 TYR cc_start: 0.8938 (m-80) cc_final: 0.8712 (m-80) REVERT: L 3 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7293 (mm-40) REVERT: L 18 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7986 (ttm170) REVERT: L 55 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8486 (tm-30) outliers start: 16 outliers final: 7 residues processed: 158 average time/residue: 0.7410 time to fit residues: 121.9440 Evaluate side-chains 160 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain L residue 3 GLN 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 56 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 30 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.8211 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3432 Z= 0.312 Angle : 0.740 10.795 4673 Z= 0.366 Chirality : 0.049 0.187 515 Planarity : 0.005 0.039 598 Dihedral : 6.182 23.146 465 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.63 % Allowed : 24.93 % Favored : 69.44 % 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: -1.00 (0.38), residues: 422 helix: -1.99 (1.36), residues: 18 sheet: -0.33 (0.46), residues: 120 loop : -0.71 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 55 HIS 0.003 0.001 HIS H 99 PHE 0.019 0.002 PHE H 96 TYR 0.011 0.002 TYR H 54 ARG 0.004 0.001 ARG L 61 *********************** 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 171 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 392 PHE cc_start: 0.9097 (m-80) cc_final: 0.8874 (m-80) REVERT: A 421 TYR cc_start: 0.8468 (m-10) cc_final: 0.8238 (m-10) REVERT: A 425 LEU cc_start: 0.8902 (mt) cc_final: 0.8677 (mt) REVERT: A 454 ARG cc_start: 0.9197 (ttm-80) cc_final: 0.8641 (ttm110) REVERT: A 456 PHE cc_start: 0.7899 (m-80) cc_final: 0.7663 (m-80) REVERT: A 528 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8495 (mttp) REVERT: H 24 PHE cc_start: 0.8764 (p90) cc_final: 0.8544 (p90) REVERT: H 61 TYR cc_start: 0.8942 (m-80) cc_final: 0.8638 (m-80) REVERT: L 55 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8508 (tm-30) outliers start: 21 outliers final: 11 residues processed: 156 average time/residue: 0.8417 time to fit residues: 136.1085 Evaluate side-chains 150 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 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 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 56 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8262 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3432 Z= 0.464 Angle : 0.800 10.871 4673 Z= 0.396 Chirality : 0.051 0.198 515 Planarity : 0.005 0.046 598 Dihedral : 6.306 25.995 465 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 7.51 % Allowed : 26.54 % Favored : 65.95 % 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: -1.04 (0.40), residues: 422 helix: -1.89 (1.89), residues: 12 sheet: -0.24 (0.47), residues: 121 loop : -0.85 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 55 HIS 0.005 0.001 HIS H 99 PHE 0.037 0.002 PHE H 27 TYR 0.013 0.002 TYR L 87 ARG 0.006 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 177 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.9130 (m-80) cc_final: 0.8837 (m-80) REVERT: A 425 LEU cc_start: 0.8920 (mt) cc_final: 0.8696 (mt) REVERT: A 456 PHE cc_start: 0.7976 (m-80) cc_final: 0.7697 (m-80) REVERT: H 61 TYR cc_start: 0.9024 (m-80) cc_final: 0.8788 (m-80) REVERT: H 77 LYS cc_start: 0.8614 (mtmm) cc_final: 0.8373 (mtmm) REVERT: H 84 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8401 (tm) REVERT: H 106 ASP cc_start: 0.7959 (m-30) cc_final: 0.7656 (m-30) REVERT: L 3 GLN cc_start: 0.8498 (mm-40) cc_final: 0.7979 (mm110) REVERT: L 55 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8721 (tm-30) REVERT: L 75 ILE cc_start: 0.8770 (mp) cc_final: 0.8490 (tp) outliers start: 28 outliers final: 14 residues processed: 157 average time/residue: 0.8217 time to fit residues: 133.7217 Evaluate side-chains 159 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 LYS 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 84 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 VAL 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 56 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.0370 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3432 Z= 0.298 Angle : 0.753 10.320 4673 Z= 0.370 Chirality : 0.049 0.187 515 Planarity : 0.005 0.044 598 Dihedral : 5.918 26.050 465 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 7.24 % Allowed : 28.69 % Favored : 64.08 % 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: -1.16 (0.40), residues: 422 helix: -1.74 (1.96), residues: 12 sheet: -0.68 (0.46), residues: 127 loop : -0.75 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 38 HIS 0.003 0.001 HIS H 99 PHE 0.034 0.002 PHE H 27 TYR 0.009 0.001 TYR L 36 ARG 0.007 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 179 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8711 (mm) cc_final: 0.8439 (mp) REVERT: A 392 PHE cc_start: 0.9120 (m-80) cc_final: 0.8850 (m-80) REVERT: A 409 GLN cc_start: 0.8945 (mt0) cc_final: 0.8683 (tt0) REVERT: A 425 LEU cc_start: 0.8901 (mt) cc_final: 0.8675 (mt) REVERT: A 456 PHE cc_start: 0.7874 (m-80) cc_final: 0.7632 (m-80) REVERT: H 55 TRP cc_start: 0.8718 (p90) cc_final: 0.8424 (p90) REVERT: H 61 TYR cc_start: 0.8973 (m-80) cc_final: 0.8741 (m-80) REVERT: H 106 ASP cc_start: 0.7921 (m-30) cc_final: 0.7599 (m-30) REVERT: L 18 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8200 (ptm160) REVERT: L 55 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8631 (tm-30) outliers start: 27 outliers final: 16 residues processed: 160 average time/residue: 0.7967 time to fit residues: 132.2792 Evaluate side-chains 170 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 LEU 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 34 ASN 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 60 SER Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.1980 chunk 40 optimal weight: 0.1980 chunk 33 optimal weight: 0.2980 chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.0020 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 0.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3432 Z= 0.218 Angle : 0.747 10.450 4673 Z= 0.361 Chirality : 0.048 0.172 515 Planarity : 0.005 0.047 598 Dihedral : 5.579 25.428 465 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 6.70 % Allowed : 31.64 % 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: -1.16 (0.40), residues: 422 helix: -1.92 (1.88), residues: 12 sheet: -0.75 (0.46), residues: 127 loop : -0.70 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 38 HIS 0.001 0.000 HIS H 99 PHE 0.029 0.002 PHE H 27 TYR 0.018 0.001 TYR A 380 ARG 0.009 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 186 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8333 (t) REVERT: A 390 LEU cc_start: 0.8695 (mm) cc_final: 0.8440 (mp) REVERT: A 392 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8746 (m-80) REVERT: A 409 GLN cc_start: 0.8929 (mt0) cc_final: 0.8568 (tt0) REVERT: A 425 LEU cc_start: 0.8873 (mt) cc_final: 0.8666 (mt) REVERT: A 454 ARG cc_start: 0.9229 (ttm-80) cc_final: 0.8782 (ttm110) REVERT: A 456 PHE cc_start: 0.7855 (m-80) cc_final: 0.7609 (m-80) REVERT: H 61 TYR cc_start: 0.8953 (m-80) cc_final: 0.8729 (m-80) REVERT: H 106 ASP cc_start: 0.7886 (m-30) cc_final: 0.7570 (m-30) REVERT: L 18 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8120 (ptm160) REVERT: L 55 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8508 (tm-30) REVERT: L 61 ARG cc_start: 0.8378 (ptt-90) cc_final: 0.8164 (ptp-170) outliers start: 25 outliers final: 16 residues processed: 169 average time/residue: 0.7421 time to fit residues: 130.6000 Evaluate side-chains 172 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP 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 56 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 74 THR 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: 0.9980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 16 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.8219 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3432 Z= 0.319 Angle : 0.805 12.673 4673 Z= 0.387 Chirality : 0.050 0.181 515 Planarity : 0.005 0.048 598 Dihedral : 5.679 25.796 465 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 7.77 % Allowed : 33.24 % 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: -1.20 (0.41), residues: 422 helix: -1.84 (1.92), residues: 12 sheet: -0.85 (0.46), residues: 125 loop : -0.70 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 38 HIS 0.000 0.000 HIS H 99 PHE 0.025 0.002 PHE H 24 TYR 0.031 0.002 TYR A 453 ARG 0.008 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 174 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8360 (t) REVERT: A 392 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8789 (m-80) REVERT: A 409 GLN cc_start: 0.8932 (mt0) cc_final: 0.8537 (tt0) REVERT: A 425 LEU cc_start: 0.8878 (mt) cc_final: 0.8677 (mt) REVERT: A 456 PHE cc_start: 0.7893 (m-80) cc_final: 0.7633 (m-80) REVERT: H 61 TYR cc_start: 0.8983 (m-80) cc_final: 0.8779 (m-80) REVERT: H 106 ASP cc_start: 0.7923 (m-30) cc_final: 0.7655 (m-30) REVERT: L 18 ARG cc_start: 0.8362 (ttm170) cc_final: 0.8112 (ptm160) REVERT: L 55 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8588 (tm-30) outliers start: 29 outliers final: 15 residues processed: 157 average time/residue: 0.8036 time to fit residues: 131.0085 Evaluate side-chains 166 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR 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 H residue 75 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 56 SER 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: 0.5980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3432 Z= 0.359 Angle : 0.821 12.206 4673 Z= 0.397 Chirality : 0.050 0.188 515 Planarity : 0.006 0.047 598 Dihedral : 5.829 26.453 465 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 7.51 % Allowed : 33.51 % 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: -1.26 (0.41), residues: 422 helix: -1.60 (2.01), residues: 12 sheet: -0.88 (0.46), residues: 125 loop : -0.77 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP H 38 HIS 0.000 0.000 HIS L 92 PHE 0.025 0.002 PHE H 24 TYR 0.028 0.002 TYR A 453 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 179 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8380 (t) REVERT: A 384 PRO cc_start: 0.8939 (Cg_endo) cc_final: 0.8716 (Cg_exo) REVERT: A 390 LEU cc_start: 0.8720 (mm) cc_final: 0.8466 (mp) REVERT: A 409 GLN cc_start: 0.8873 (mt0) cc_final: 0.8673 (tt0) REVERT: A 425 LEU cc_start: 0.8925 (mt) cc_final: 0.8708 (mt) REVERT: A 456 PHE cc_start: 0.7905 (m-80) cc_final: 0.7691 (m-80) REVERT: H 61 TYR cc_start: 0.8976 (m-80) cc_final: 0.8741 (m-80) REVERT: H 106 ASP cc_start: 0.7905 (m-30) cc_final: 0.7678 (m-30) REVERT: L 18 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8135 (ptm160) REVERT: L 55 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8591 (tm-30) outliers start: 28 outliers final: 18 residues processed: 160 average time/residue: 0.7635 time to fit residues: 126.9871 Evaluate side-chains 166 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 458 LYS 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 H residue 75 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 56 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 18 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.0020 chunk 3 optimal weight: 0.1980 chunk 25 optimal weight: 0.4980 overall best weight: 0.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 : 0.003 0.037 3432 Z= 0.224 Angle : 0.829 13.366 4673 Z= 0.392 Chirality : 0.049 0.175 515 Planarity : 0.005 0.057 598 Dihedral : 5.549 25.386 465 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.56 % Allowed : 37.80 % Favored : 57.64 % 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: -1.31 (0.41), residues: 422 helix: -2.11 (1.80), residues: 12 sheet: -0.88 (0.46), residues: 126 loop : -0.79 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 38 HIS 0.001 0.000 HIS H 99 PHE 0.027 0.002 PHE H 27 TYR 0.026 0.002 TYR A 453 ARG 0.004 0.000 ARG H 68 *********************** 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 168 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8367 (t) REVERT: A 409 GLN cc_start: 0.8921 (mt0) cc_final: 0.8554 (tt0) REVERT: A 425 LEU cc_start: 0.8875 (mt) cc_final: 0.8674 (mt) REVERT: A 442 ASP cc_start: 0.8096 (m-30) cc_final: 0.7780 (m-30) REVERT: H 61 TYR cc_start: 0.8941 (m-80) cc_final: 0.8725 (m-80) REVERT: H 106 ASP cc_start: 0.7862 (m-30) cc_final: 0.7623 (m-30) REVERT: L 3 GLN cc_start: 0.8661 (tp40) cc_final: 0.8110 (mm110) REVERT: L 18 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8109 (ptm160) REVERT: L 55 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8432 (tm-30) outliers start: 17 outliers final: 12 residues processed: 158 average time/residue: 0.7617 time to fit residues: 125.0362 Evaluate side-chains 164 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 33 optimal weight: 0.0370 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.3256 ------------------------------------------------------------------------------- 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: 0.8198 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3432 Z= 0.271 Angle : 0.848 12.437 4673 Z= 0.401 Chirality : 0.050 0.180 515 Planarity : 0.006 0.048 598 Dihedral : 5.524 25.340 465 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.02 % Allowed : 38.61 % Favored : 57.37 % 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: -1.35 (0.41), residues: 422 helix: -2.13 (1.78), residues: 12 sheet: -0.89 (0.46), residues: 126 loop : -0.82 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 38 HIS 0.001 0.000 HIS A 519 PHE 0.025 0.002 PHE H 27 TYR 0.026 0.002 TYR A 453 ARG 0.013 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 167 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 333 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8370 (t) REVERT: A 409 GLN cc_start: 0.8816 (mt0) cc_final: 0.8571 (tt0) REVERT: A 442 ASP cc_start: 0.8114 (m-30) cc_final: 0.7796 (m-30) REVERT: H 106 ASP cc_start: 0.7878 (m-30) cc_final: 0.7618 (m-30) REVERT: L 55 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8474 (tm-30) REVERT: L 61 ARG cc_start: 0.8139 (ptt-90) cc_final: 0.7741 (ptt-90) REVERT: L 71 PHE cc_start: 0.8431 (m-80) cc_final: 0.8146 (m-80) outliers start: 15 outliers final: 10 residues processed: 158 average time/residue: 0.7876 time to fit residues: 129.3928 Evaluate side-chains 159 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 458 LYS 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 H residue 75 THR Chi-restraints excluded: chain H residue 81 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 25 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.088795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.077318 restraints weight = 7368.275| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.87 r_work: 0.3220 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3432 Z= 0.302 Angle : 0.859 12.745 4673 Z= 0.406 Chirality : 0.055 0.526 515 Planarity : 0.006 0.053 598 Dihedral : 5.671 25.073 465 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.75 % Allowed : 39.14 % Favored : 57.10 % 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: -1.38 (0.42), residues: 422 helix: -2.07 (1.80), residues: 12 sheet: -0.90 (0.47), residues: 126 loop : -0.86 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 38 HIS 0.001 0.000 HIS A 519 PHE 0.025 0.002 PHE H 27 TYR 0.025 0.002 TYR A 453 ARG 0.011 0.001 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2791.49 seconds wall clock time: 49 minutes 59.23 seconds (2999.23 seconds total)