Starting phenix.real_space_refine on Tue Feb 13 05:14:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp2_32667/02_2024/7wp2_32667.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp2_32667/02_2024/7wp2_32667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp2_32667/02_2024/7wp2_32667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp2_32667/02_2024/7wp2_32667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp2_32667/02_2024/7wp2_32667.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp2_32667/02_2024/7wp2_32667.pdb" } resolution = 3.52 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= 0.011 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 14 5.16 5 C 2090 2.51 5 N 554 2.21 5 O 641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 34": "OD1" <-> "OD2" Residue "L GLU 85": "OE1" <-> "OE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F ASP 427": "OD1" <-> "OD2" Residue "F GLU 516": "OE1" <-> "OE2" 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: 3299 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 796 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "F" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1458 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.31, per 1000 atoms: 0.70 Number of scatterers: 3299 At special positions: 0 Unit cell: (76.244, 79.356, 80.912, 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 14 16.00 O 641 8.00 N 554 7.00 C 2090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 608.6 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 9 sheets defined 2.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.905A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.037A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.623A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'L' and resid 22 through 23 removed outlier: 3.520A pdb=" N SER L 69 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.564A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR L 89 " --> pdb=" O TYR L 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.785A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.880A pdb=" N ASN F 354 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER F 399 " --> pdb=" O ASN F 354 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS F 356 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS F 432 " --> pdb=" O LEU F 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 452 through 454 69 hydrogen bonds defined for protein. 159 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: 0.88 Time building geometry restraints manager: 1.39 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: 843 1.46 - 1.57: 1473 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3383 Sorted by residual: bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.87e+00 bond pdb=" C LYS F 462 " pdb=" N PRO F 463 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.12e-02 7.97e+03 3.02e+00 bond pdb=" CB CYS L 90 " pdb=" SG CYS L 90 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" C ASN L 55 " pdb=" N ARG L 56 " ideal model delta sigma weight residual 1.332 1.271 0.060 3.60e-02 7.72e+02 2.81e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 3378 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.33: 85 106.33 - 113.25: 1722 113.25 - 120.17: 1183 120.17 - 127.09: 1567 127.09 - 134.01: 37 Bond angle restraints: 4594 Sorted by residual: angle pdb=" C GLY L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" CA LEU F 387 " pdb=" CB LEU F 387 " pdb=" CG LEU F 387 " ideal model delta sigma weight residual 116.30 128.99 -12.69 3.50e+00 8.16e-02 1.31e+01 angle pdb=" C TYR F 369 " pdb=" N ASN F 370 " pdb=" CA ASN F 370 " ideal model delta sigma weight residual 122.07 127.10 -5.03 1.43e+00 4.89e-01 1.24e+01 angle pdb=" C ASP F 364 " pdb=" N TYR F 365 " pdb=" CA TYR F 365 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.58e+00 angle pdb=" C SER H 52 " pdb=" N PHE H 53 " pdb=" CA PHE H 53 " ideal model delta sigma weight residual 120.44 124.43 -3.99 1.30e+00 5.92e-01 9.40e+00 ... (remaining 4589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 1779 17.78 - 35.55: 173 35.55 - 53.33: 25 53.33 - 71.11: 5 71.11 - 88.88: 3 Dihedral angle restraints: 1985 sinusoidal: 780 harmonic: 1205 Sorted by residual: dihedral pdb=" CA ASP H 113 " pdb=" C ASP H 113 " pdb=" N TYR H 114 " pdb=" CA TYR H 114 " ideal model delta harmonic sigma weight residual -180.00 -150.46 -29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PHE F 338 " pdb=" C PHE F 338 " pdb=" N GLY F 339 " pdb=" CA GLY F 339 " ideal model delta harmonic sigma weight residual 180.00 155.35 24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA ILE F 472 " pdb=" C ILE F 472 " pdb=" N TYR F 473 " pdb=" CA TYR F 473 " ideal model delta harmonic sigma weight residual 180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 1982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 306 0.047 - 0.094: 137 0.094 - 0.141: 34 0.141 - 0.188: 7 0.188 - 0.235: 5 Chirality restraints: 489 Sorted by residual: chirality pdb=" CB ILE H 70 " pdb=" CA ILE H 70 " pdb=" CG1 ILE H 70 " pdb=" CG2 ILE H 70 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB THR H 91 " pdb=" CA THR H 91 " pdb=" OG1 THR H 91 " pdb=" CG2 THR H 91 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL H 100 " pdb=" CA VAL H 100 " pdb=" CG1 VAL H 100 " pdb=" CG2 VAL H 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 486 not shown) Planarity restraints: 595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 498 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO F 499 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 499 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 499 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 13 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO L 14 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO L 14 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 14 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 462 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO F 463 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO F 463 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 463 " -0.027 5.00e-02 4.00e+02 ... (remaining 592 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 909 2.79 - 3.32: 2630 3.32 - 3.85: 5262 3.85 - 4.37: 5959 4.37 - 4.90: 10778 Nonbonded interactions: 25538 Sorted by model distance: nonbonded pdb=" OH TYR L 93 " pdb=" OD1 ASP H 113 " model vdw 2.267 2.440 nonbonded pdb=" OG1 THR F 415 " pdb=" OD1 ASP F 420 " model vdw 2.270 2.440 nonbonded pdb=" OH TYR L 38 " pdb=" OE1 GLN L 91 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR L 51 " pdb=" O THR F 415 " model vdw 2.280 2.440 nonbonded pdb=" NE2 HIS L 36 " pdb=" O ASN H 115 " model vdw 2.288 2.520 ... (remaining 25533 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 38.080 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.720 Find NCS groups from input model: 0.080 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 : 0.007 0.060 3383 Z= 0.446 Angle : 0.907 12.687 4594 Z= 0.500 Chirality : 0.056 0.235 489 Planarity : 0.007 0.070 594 Dihedral : 13.822 88.882 1225 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.28 % Allowed : 9.66 % Favored : 90.06 % 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: -4.60 (0.34), residues: 416 helix: -5.07 (0.26), residues: 20 sheet: -2.60 (0.38), residues: 162 loop : -3.28 (0.31), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 353 HIS 0.004 0.002 HIS F 449 PHE 0.018 0.002 PHE F 490 TYR 0.028 0.003 TYR H 103 ARG 0.005 0.000 ARG F 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.378 Fit side-chains REVERT: L 93 TYR cc_start: 0.8650 (t80) cc_final: 0.8437 (t80) REVERT: H 19 ARG cc_start: 0.7666 (ttm170) cc_final: 0.6860 (ttp80) REVERT: H 29 PHE cc_start: 0.9274 (t80) cc_final: 0.9067 (t80) outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.1951 time to fit residues: 17.7065 Evaluate side-chains 61 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.0570 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 39 GLN H 84 ASN F 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3383 Z= 0.235 Angle : 0.588 7.764 4594 Z= 0.305 Chirality : 0.043 0.138 489 Planarity : 0.005 0.047 594 Dihedral : 6.923 55.675 516 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 1.99 % Allowed : 15.91 % Favored : 82.10 % 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: -4.00 (0.35), residues: 416 helix: -4.78 (0.46), residues: 20 sheet: -1.93 (0.41), residues: 151 loop : -3.06 (0.32), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 353 HIS 0.002 0.001 HIS F 449 PHE 0.013 0.001 PHE F 338 TYR 0.010 0.002 TYR F 369 ARG 0.005 0.000 ARG L 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.371 Fit side-chains REVERT: H 19 ARG cc_start: 0.7684 (ttm170) cc_final: 0.7103 (ttp80) REVERT: H 74 ASN cc_start: 0.8624 (m-40) cc_final: 0.8366 (m-40) REVERT: F 417 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7474 (ttmm) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.1820 time to fit residues: 13.5341 Evaluate side-chains 59 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.0980 chunk 33 optimal weight: 0.5980 chunk 36 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 13 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3383 Z= 0.222 Angle : 0.571 7.966 4594 Z= 0.292 Chirality : 0.042 0.138 489 Planarity : 0.004 0.036 594 Dihedral : 6.471 52.788 516 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.55 % Allowed : 15.34 % Favored : 80.11 % 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: -3.68 (0.36), residues: 416 helix: -4.68 (0.54), residues: 20 sheet: -1.72 (0.42), residues: 146 loop : -2.81 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 353 HIS 0.002 0.001 HIS F 449 PHE 0.012 0.001 PHE F 338 TYR 0.020 0.001 TYR L 93 ARG 0.006 0.000 ARG F 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.375 Fit side-chains REVERT: H 19 ARG cc_start: 0.7599 (ttm170) cc_final: 0.7000 (ttp80) REVERT: H 94 TYR cc_start: 0.8223 (m-80) cc_final: 0.7498 (m-80) REVERT: F 338 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6577 (p90) outliers start: 16 outliers final: 10 residues processed: 71 average time/residue: 0.1451 time to fit residues: 12.8389 Evaluate side-chains 64 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 0.0030 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 overall best weight: 0.2826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3383 Z= 0.168 Angle : 0.524 6.948 4594 Z= 0.267 Chirality : 0.042 0.133 489 Planarity : 0.003 0.032 594 Dihedral : 5.916 46.961 516 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.55 % Allowed : 17.05 % Favored : 78.41 % 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: -3.44 (0.37), residues: 416 helix: -4.65 (0.56), residues: 20 sheet: -1.53 (0.42), residues: 148 loop : -2.66 (0.33), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 353 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.001 PHE H 53 TYR 0.023 0.001 TYR L 93 ARG 0.005 0.000 ARG F 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.361 Fit side-chains REVERT: H 19 ARG cc_start: 0.7539 (ttm170) cc_final: 0.6737 (ttp80) REVERT: H 83 MET cc_start: 0.8039 (mtt) cc_final: 0.7815 (mtt) REVERT: H 94 TYR cc_start: 0.8148 (m-80) cc_final: 0.7572 (m-80) outliers start: 16 outliers final: 12 residues processed: 72 average time/residue: 0.1596 time to fit residues: 14.0812 Evaluate side-chains 65 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.0030 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 0.0270 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.3848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3383 Z= 0.208 Angle : 0.556 7.559 4594 Z= 0.283 Chirality : 0.042 0.137 489 Planarity : 0.003 0.032 594 Dihedral : 5.674 40.261 516 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.26 % Allowed : 19.32 % Favored : 76.42 % 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: -3.25 (0.37), residues: 416 helix: -4.69 (0.53), residues: 20 sheet: -1.32 (0.42), residues: 153 loop : -2.58 (0.34), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 353 HIS 0.002 0.001 HIS H 35 PHE 0.016 0.001 PHE H 53 TYR 0.020 0.001 TYR L 93 ARG 0.004 0.000 ARG F 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.364 Fit side-chains REVERT: H 19 ARG cc_start: 0.7591 (ttm170) cc_final: 0.7125 (ttp-170) REVERT: H 83 MET cc_start: 0.7972 (mtt) cc_final: 0.7720 (mtt) REVERT: H 94 TYR cc_start: 0.8240 (m-80) cc_final: 0.7523 (m-80) REVERT: F 338 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6646 (p90) outliers start: 15 outliers final: 11 residues processed: 68 average time/residue: 0.1618 time to fit residues: 13.4109 Evaluate side-chains 64 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 3383 Z= 0.380 Angle : 0.656 8.896 4594 Z= 0.332 Chirality : 0.045 0.149 489 Planarity : 0.004 0.033 594 Dihedral : 6.172 41.189 516 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 4.26 % Allowed : 19.60 % Favored : 76.14 % 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: -3.34 (0.37), residues: 416 helix: -4.80 (0.43), residues: 20 sheet: -1.46 (0.42), residues: 153 loop : -2.58 (0.34), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 353 HIS 0.004 0.002 HIS F 449 PHE 0.020 0.002 PHE F 338 TYR 0.020 0.002 TYR L 93 ARG 0.005 0.001 ARG F 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.354 Fit side-chains REVERT: H 19 ARG cc_start: 0.7650 (ttm170) cc_final: 0.6759 (ttp80) REVERT: H 94 TYR cc_start: 0.8386 (m-80) cc_final: 0.7485 (m-80) REVERT: F 338 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7046 (p90) outliers start: 15 outliers final: 12 residues processed: 67 average time/residue: 0.1405 time to fit residues: 11.8913 Evaluate side-chains 67 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 39 optimal weight: 0.0020 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3383 Z= 0.237 Angle : 0.584 7.586 4594 Z= 0.297 Chirality : 0.043 0.175 489 Planarity : 0.004 0.043 594 Dihedral : 5.782 39.912 516 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.55 % Allowed : 21.02 % Favored : 74.43 % 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: -3.24 (0.37), residues: 416 helix: -4.80 (0.40), residues: 20 sheet: -1.45 (0.43), residues: 146 loop : -2.44 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 353 HIS 0.003 0.001 HIS F 449 PHE 0.015 0.001 PHE H 53 TYR 0.018 0.001 TYR L 93 ARG 0.003 0.000 ARG F 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.391 Fit side-chains REVERT: H 19 ARG cc_start: 0.7610 (ttm170) cc_final: 0.6925 (ttp-170) REVERT: H 20 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7978 (mm) REVERT: H 94 TYR cc_start: 0.8267 (m-80) cc_final: 0.7440 (m-80) REVERT: F 338 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.6854 (p90) outliers start: 16 outliers final: 13 residues processed: 64 average time/residue: 0.1473 time to fit residues: 11.9022 Evaluate side-chains 66 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 16 optimal weight: 0.3980 chunk 28 optimal weight: 0.0040 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN F 448 ASN F 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3383 Z= 0.179 Angle : 0.544 6.997 4594 Z= 0.276 Chirality : 0.042 0.174 489 Planarity : 0.003 0.033 594 Dihedral : 5.197 35.436 516 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.98 % Allowed : 21.88 % Favored : 74.15 % 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: -3.03 (0.38), residues: 416 helix: -4.66 (0.47), residues: 20 sheet: -1.33 (0.44), residues: 144 loop : -2.27 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 353 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.001 PHE H 53 TYR 0.015 0.001 TYR L 93 ARG 0.003 0.000 ARG F 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.412 Fit side-chains REVERT: H 13 GLN cc_start: 0.6214 (OUTLIER) cc_final: 0.5546 (tt0) REVERT: H 19 ARG cc_start: 0.7557 (ttm170) cc_final: 0.7092 (ttp-170) REVERT: H 20 LEU cc_start: 0.8353 (mm) cc_final: 0.8129 (mt) REVERT: H 94 TYR cc_start: 0.8215 (m-80) cc_final: 0.7439 (m-80) REVERT: F 338 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.6684 (p90) outliers start: 14 outliers final: 11 residues processed: 65 average time/residue: 0.1610 time to fit residues: 12.7996 Evaluate side-chains 63 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.0970 chunk 33 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.0070 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 37 optimal weight: 3.9990 overall best weight: 0.2532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 448 ASN F 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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 : 0.003 0.030 3383 Z= 0.167 Angle : 0.546 6.947 4594 Z= 0.276 Chirality : 0.042 0.174 489 Planarity : 0.004 0.031 594 Dihedral : 5.027 35.154 516 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.98 % Allowed : 22.16 % Favored : 73.86 % 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: -2.86 (0.38), residues: 416 helix: -4.55 (0.52), residues: 20 sheet: -1.22 (0.44), residues: 146 loop : -2.15 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 353 HIS 0.002 0.001 HIS H 35 PHE 0.027 0.001 PHE H 29 TYR 0.014 0.001 TYR L 93 ARG 0.007 0.000 ARG F 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.375 Fit side-chains REVERT: H 19 ARG cc_start: 0.7577 (ttm170) cc_final: 0.7014 (ttp-170) REVERT: H 94 TYR cc_start: 0.8215 (m-80) cc_final: 0.7425 (m-80) REVERT: F 338 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6540 (p90) outliers start: 14 outliers final: 13 residues processed: 64 average time/residue: 0.1452 time to fit residues: 11.6227 Evaluate side-chains 65 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 448 ASN Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0670 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.0370 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3383 Z= 0.221 Angle : 0.561 7.012 4594 Z= 0.285 Chirality : 0.043 0.183 489 Planarity : 0.004 0.032 594 Dihedral : 5.072 35.676 516 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.83 % Allowed : 21.31 % Favored : 73.86 % 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: -2.83 (0.39), residues: 416 helix: -4.53 (0.52), residues: 20 sheet: -1.21 (0.44), residues: 146 loop : -2.12 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 353 HIS 0.004 0.002 HIS F 449 PHE 0.016 0.001 PHE H 53 TYR 0.017 0.001 TYR F 369 ARG 0.007 0.000 ARG F 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 0.438 Fit side-chains REVERT: H 19 ARG cc_start: 0.7551 (ttm170) cc_final: 0.7073 (ttp-170) REVERT: H 20 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8052 (mt) REVERT: H 94 TYR cc_start: 0.8171 (m-80) cc_final: 0.7365 (m-80) REVERT: F 338 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.6689 (p90) outliers start: 17 outliers final: 14 residues processed: 64 average time/residue: 0.1604 time to fit residues: 12.7577 Evaluate side-chains 67 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 448 ASN Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 37 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.0170 chunk 26 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 overall best weight: 0.2818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133407 restraints weight = 4624.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136591 restraints weight = 2531.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138707 restraints weight = 1689.021| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3383 Z= 0.178 Angle : 0.552 6.921 4594 Z= 0.279 Chirality : 0.042 0.183 489 Planarity : 0.004 0.031 594 Dihedral : 4.980 35.440 516 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.26 % Allowed : 22.16 % Favored : 73.58 % 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: -2.74 (0.39), residues: 416 helix: -4.49 (0.55), residues: 20 sheet: -1.15 (0.44), residues: 146 loop : -2.06 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 353 HIS 0.007 0.002 HIS F 449 PHE 0.016 0.001 PHE H 53 TYR 0.017 0.001 TYR F 369 ARG 0.007 0.000 ARG F 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1664.07 seconds wall clock time: 30 minutes 42.19 seconds (1842.19 seconds total)