Starting phenix.real_space_refine on Sun Mar 10 16:56:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wee_32448/03_2024/7wee_32448.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wee_32448/03_2024/7wee_32448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wee_32448/03_2024/7wee_32448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wee_32448/03_2024/7wee_32448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wee_32448/03_2024/7wee_32448.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wee_32448/03_2024/7wee_32448.pdb" } resolution = 4.0 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= 0.003 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 2139 2.51 5 N 560 2.21 5 O 637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 364": "OD1" <-> "OD2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 389": "OD1" <-> "OD2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "E PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3350 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Time building chain proxies: 2.55, per 1000 atoms: 0.76 Number of scatterers: 3350 At special positions: 0 Unit cell: (87.74, 66.34, 100.58, 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 637 8.00 N 560 7.00 C 2139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " 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: 1.28 Conformation dependent library (CDL) restraints added in 644.3 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 8.2% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.842A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.911A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.727A pdb=" N THR H 92 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.321A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.321A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS E 432 " --> pdb=" O LEU E 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.984A pdb=" N ALA H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG H 60 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.354A pdb=" N VAL L 11 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN L 40 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU L 49 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 97 hydrogen bonds defined for protein. 228 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: 0.80 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1057 1.34 - 1.46: 864 1.46 - 1.58: 1503 1.58 - 1.69: 1 1.69 - 1.81: 16 Bond restraints: 3441 Sorted by residual: bond pdb=" CG PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 1.503 1.344 0.159 3.40e-02 8.65e+02 2.18e+01 bond pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 1.492 1.672 -0.180 5.00e-02 4.00e+02 1.30e+01 bond pdb=" N PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.63e+00 bond pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 1.469 1.448 0.021 1.28e-02 6.10e+03 2.71e+00 bond pdb=" CA ASN H 86 " pdb=" CB ASN H 86 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.61e-02 3.86e+03 8.50e-01 ... (remaining 3436 not shown) Histogram of bond angle deviations from ideal: 91.07 - 100.53: 4 100.53 - 109.99: 562 109.99 - 119.45: 2255 119.45 - 128.91: 1846 128.91 - 138.37: 23 Bond angle restraints: 4690 Sorted by residual: angle pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 112.00 95.88 16.12 1.40e+00 5.10e-01 1.33e+02 angle pdb=" N PRO H 9 " pdb=" CD PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 103.20 91.07 12.13 1.50e+00 4.44e-01 6.54e+01 angle pdb=" N ILE E 418 " pdb=" CA ILE E 418 " pdb=" C ILE E 418 " ideal model delta sigma weight residual 113.53 108.95 4.58 9.80e-01 1.04e+00 2.19e+01 angle pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 104.50 96.01 8.49 1.90e+00 2.77e-01 2.00e+01 angle pdb=" N PRO H 9 " pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " ideal model delta sigma weight residual 103.25 99.58 3.67 1.05e+00 9.07e-01 1.22e+01 ... (remaining 4685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.10: 1760 14.10 - 28.20: 193 28.20 - 42.29: 61 42.29 - 56.39: 12 56.39 - 70.49: 1 Dihedral angle restraints: 2027 sinusoidal: 782 harmonic: 1245 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 22.51 70.49 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 130.56 -37.56 1 1.00e+01 1.00e-02 1.99e+01 dihedral pdb=" CA LEU E 517 " pdb=" C LEU E 517 " pdb=" N LEU E 518 " pdb=" CA LEU E 518 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 2024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 358 0.039 - 0.079: 114 0.079 - 0.118: 37 0.118 - 0.157: 6 0.157 - 0.197: 2 Chirality restraints: 517 Sorted by residual: chirality pdb=" CB THR E 333 " pdb=" CA THR E 333 " pdb=" OG1 THR E 333 " pdb=" CG2 THR E 333 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.68e-01 chirality pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" C PRO H 9 " pdb=" CB PRO H 9 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA ASN H 86 " pdb=" N ASN H 86 " pdb=" C ASN H 86 " pdb=" CB ASN H 86 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 514 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 8 " 0.056 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO H 9 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO H 9 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 9 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 88 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO H 89 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 89 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 89 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 490 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO E 491 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 491 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 491 " 0.019 5.00e-02 4.00e+02 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 50 2.67 - 3.23: 3069 3.23 - 3.79: 4699 3.79 - 4.34: 6398 4.34 - 4.90: 10716 Nonbonded interactions: 24932 Sorted by model distance: nonbonded pdb=" OG1 THR L 95 " pdb=" O SER L 98 " model vdw 2.116 2.440 nonbonded pdb=" OG1 THR H 104 " pdb=" OD1 ASP H 107 " model vdw 2.212 2.440 nonbonded pdb=" OG SER E 349 " pdb=" O LEU E 452 " model vdw 2.266 2.440 nonbonded pdb=" OG SER L 70 " pdb=" OG1 THR L 73 " model vdw 2.276 2.440 nonbonded pdb=" OG SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.285 2.440 ... (remaining 24927 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 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: 1.900 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: 9.750 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.150 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.005 0.180 3441 Z= 0.345 Angle : 0.720 16.124 4690 Z= 0.408 Chirality : 0.044 0.197 517 Planarity : 0.005 0.076 600 Dihedral : 12.682 54.785 1217 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.60 (0.40), residues: 423 helix: -3.73 (0.83), residues: 21 sheet: -0.23 (0.42), residues: 141 loop : -1.33 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.005 0.001 HIS L 41 PHE 0.011 0.001 PHE L 65 TYR 0.011 0.001 TYR E 501 ARG 0.005 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7649 (p0) cc_final: 0.6915 (p0) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1162 time to fit residues: 9.9057 Evaluate side-chains 52 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 10.0000 chunk 31 optimal weight: 0.0040 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.1980 overall best weight: 1.6398 ------------------------------------------------------------------------------- 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: 0.7919 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 3441 Z= 0.273 Angle : 0.614 6.758 4690 Z= 0.321 Chirality : 0.045 0.144 517 Planarity : 0.005 0.053 600 Dihedral : 4.869 24.817 470 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.35 % Allowed : 10.51 % Favored : 88.14 % 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: -1.51 (0.41), residues: 423 helix: -3.42 (0.84), residues: 26 sheet: -0.25 (0.40), residues: 154 loop : -1.21 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 436 HIS 0.002 0.001 HIS E 505 PHE 0.011 0.001 PHE E 374 TYR 0.009 0.001 TYR H 96 ARG 0.003 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7817 (p0) cc_final: 0.7148 (p0) REVERT: E 474 GLN cc_start: 0.7241 (pp30) cc_final: 0.6776 (pp30) REVERT: L 108 LYS cc_start: 0.7871 (tppt) cc_final: 0.7518 (tptt) outliers start: 5 outliers final: 5 residues processed: 56 average time/residue: 0.1042 time to fit residues: 7.9422 Evaluate side-chains 55 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 3441 Z= 0.391 Angle : 0.689 7.476 4690 Z= 0.366 Chirality : 0.047 0.149 517 Planarity : 0.005 0.063 600 Dihedral : 5.644 27.716 470 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 3.23 % Allowed : 15.90 % Favored : 80.86 % 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: -1.75 (0.41), residues: 423 helix: -3.48 (0.86), residues: 26 sheet: -0.22 (0.40), residues: 150 loop : -1.53 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 55 HIS 0.002 0.001 HIS L 100 PHE 0.016 0.002 PHE E 429 TYR 0.016 0.002 TYR L 52 ARG 0.004 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.431 Fit side-chains REVERT: E 389 ASP cc_start: 0.8101 (p0) cc_final: 0.7512 (p0) REVERT: E 474 GLN cc_start: 0.7324 (pp30) cc_final: 0.6806 (pp30) REVERT: L 108 LYS cc_start: 0.8097 (tppt) cc_final: 0.7816 (tptp) outliers start: 12 outliers final: 8 residues processed: 62 average time/residue: 0.1164 time to fit residues: 9.6032 Evaluate side-chains 62 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.0770 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 0.0670 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- 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: 0.7927 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3441 Z= 0.168 Angle : 0.587 7.855 4690 Z= 0.300 Chirality : 0.043 0.151 517 Planarity : 0.005 0.062 600 Dihedral : 4.934 25.587 470 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.77 % Allowed : 17.79 % Favored : 78.44 % 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: -1.62 (0.41), residues: 423 helix: -3.56 (0.80), residues: 27 sheet: -0.21 (0.39), residues: 153 loop : -1.36 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.001 0.000 HIS E 519 PHE 0.013 0.001 PHE H 106 TYR 0.013 0.001 TYR E 380 ARG 0.001 0.000 ARG L 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.8026 (p0) cc_final: 0.7409 (p0) REVERT: E 474 GLN cc_start: 0.7184 (pp30) cc_final: 0.6708 (pp30) REVERT: H 45 LYS cc_start: 0.8393 (ptmm) cc_final: 0.7892 (ptmm) REVERT: L 108 LYS cc_start: 0.8048 (tppt) cc_final: 0.7824 (tptp) outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.1085 time to fit residues: 10.0905 Evaluate side-chains 66 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3441 Z= 0.385 Angle : 0.685 6.230 4690 Z= 0.362 Chirality : 0.046 0.150 517 Planarity : 0.005 0.053 600 Dihedral : 5.715 27.647 470 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 5.12 % Allowed : 22.10 % Favored : 72.78 % 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: -1.76 (0.40), residues: 423 helix: -3.55 (0.84), residues: 26 sheet: -0.13 (0.41), residues: 143 loop : -1.58 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 109 HIS 0.002 0.001 HIS L 100 PHE 0.017 0.002 PHE E 515 TYR 0.017 0.002 TYR L 52 ARG 0.004 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.8108 (p0) cc_final: 0.7498 (p0) REVERT: E 474 GLN cc_start: 0.7305 (pp30) cc_final: 0.6782 (pp30) REVERT: L 103 PHE cc_start: 0.4718 (OUTLIER) cc_final: 0.4026 (m-10) REVERT: L 108 LYS cc_start: 0.8106 (tppt) cc_final: 0.7904 (tptp) outliers start: 19 outliers final: 16 residues processed: 64 average time/residue: 0.1007 time to fit residues: 8.7607 Evaluate side-chains 65 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3441 Z= 0.195 Angle : 0.603 9.648 4690 Z= 0.304 Chirality : 0.044 0.142 517 Planarity : 0.004 0.053 600 Dihedral : 5.155 25.548 470 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.31 % Allowed : 23.99 % Favored : 71.70 % 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: -1.56 (0.40), residues: 423 helix: -3.54 (0.80), residues: 26 sheet: 0.01 (0.41), residues: 143 loop : -1.42 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 109 HIS 0.001 0.000 HIS L 100 PHE 0.011 0.001 PHE H 24 TYR 0.011 0.001 TYR L 52 ARG 0.001 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.8063 (p0) cc_final: 0.7492 (p0) REVERT: E 474 GLN cc_start: 0.7176 (pp30) cc_final: 0.6795 (pp30) REVERT: H 45 LYS cc_start: 0.8385 (ptmm) cc_final: 0.7908 (ptmm) REVERT: L 54 VAL cc_start: 0.5945 (OUTLIER) cc_final: 0.5679 (m) REVERT: L 103 PHE cc_start: 0.4415 (OUTLIER) cc_final: 0.3573 (m-10) outliers start: 16 outliers final: 12 residues processed: 66 average time/residue: 0.1095 time to fit residues: 9.5993 Evaluate side-chains 66 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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: 0.7972 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3441 Z= 0.209 Angle : 0.611 8.876 4690 Z= 0.310 Chirality : 0.044 0.168 517 Planarity : 0.004 0.052 600 Dihedral : 5.070 24.375 470 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.58 % Allowed : 23.72 % Favored : 71.70 % 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: -1.52 (0.41), residues: 423 helix: -3.51 (0.81), residues: 26 sheet: -0.01 (0.42), residues: 146 loop : -1.37 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.001 0.000 HIS E 505 PHE 0.010 0.001 PHE H 24 TYR 0.020 0.001 TYR E 501 ARG 0.002 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.8059 (p0) cc_final: 0.7471 (p0) REVERT: E 474 GLN cc_start: 0.7150 (pp30) cc_final: 0.6748 (pp30) REVERT: H 45 LYS cc_start: 0.8395 (ptmm) cc_final: 0.7997 (ptmm) REVERT: L 54 VAL cc_start: 0.5838 (OUTLIER) cc_final: 0.5570 (m) REVERT: L 103 PHE cc_start: 0.4395 (OUTLIER) cc_final: 0.3449 (m-10) outliers start: 17 outliers final: 13 residues processed: 63 average time/residue: 0.1137 time to fit residues: 9.5355 Evaluate side-chains 66 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.0770 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 overall best weight: 3.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 3441 Z= 0.444 Angle : 0.750 9.437 4690 Z= 0.388 Chirality : 0.049 0.188 517 Planarity : 0.005 0.056 600 Dihedral : 5.909 26.681 470 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer: Outliers : 5.12 % Allowed : 23.72 % Favored : 71.16 % 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: -1.74 (0.40), residues: 423 helix: -3.81 (0.87), residues: 20 sheet: -0.05 (0.42), residues: 143 loop : -1.65 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 109 HIS 0.002 0.001 HIS E 505 PHE 0.019 0.002 PHE E 515 TYR 0.021 0.002 TYR E 501 ARG 0.004 0.001 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.416 Fit side-chains REVERT: E 389 ASP cc_start: 0.8197 (p0) cc_final: 0.7582 (p0) REVERT: E 474 GLN cc_start: 0.7196 (pp30) cc_final: 0.6728 (pp30) REVERT: H 45 LYS cc_start: 0.8467 (ptmm) cc_final: 0.8075 (ptmm) REVERT: L 103 PHE cc_start: 0.4726 (OUTLIER) cc_final: 0.3631 (m-10) outliers start: 19 outliers final: 16 residues processed: 60 average time/residue: 0.1264 time to fit residues: 10.0307 Evaluate side-chains 61 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 44 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 42 HIS Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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: 0.8013 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3441 Z= 0.251 Angle : 0.660 8.594 4690 Z= 0.335 Chirality : 0.046 0.167 517 Planarity : 0.005 0.055 600 Dihedral : 5.488 25.770 470 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.85 % Allowed : 24.26 % Favored : 70.89 % 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: -1.69 (0.40), residues: 423 helix: -3.80 (0.85), residues: 20 sheet: 0.03 (0.43), residues: 143 loop : -1.64 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 109 HIS 0.001 0.001 HIS L 100 PHE 0.014 0.002 PHE H 106 TYR 0.019 0.001 TYR E 501 ARG 0.002 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 0.430 Fit side-chains REVERT: E 389 ASP cc_start: 0.8100 (p0) cc_final: 0.7504 (p0) REVERT: E 474 GLN cc_start: 0.7126 (pp30) cc_final: 0.6647 (pp30) REVERT: H 45 LYS cc_start: 0.8457 (ptmm) cc_final: 0.8051 (ptmm) REVERT: L 103 PHE cc_start: 0.4475 (OUTLIER) cc_final: 0.3417 (m-10) outliers start: 18 outliers final: 14 residues processed: 65 average time/residue: 0.1019 time to fit residues: 8.9728 Evaluate side-chains 62 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.0570 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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: 0.7926 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3441 Z= 0.158 Angle : 0.609 7.525 4690 Z= 0.308 Chirality : 0.045 0.166 517 Planarity : 0.004 0.052 600 Dihedral : 4.916 22.977 470 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.04 % Allowed : 24.53 % Favored : 71.43 % 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: -1.53 (0.41), residues: 423 helix: -3.52 (0.80), residues: 26 sheet: 0.06 (0.42), residues: 148 loop : -1.44 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 109 HIS 0.001 0.000 HIS E 519 PHE 0.013 0.001 PHE H 24 TYR 0.017 0.001 TYR E 501 ARG 0.001 0.000 ARG L 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.396 Fit side-chains REVERT: E 389 ASP cc_start: 0.7990 (p0) cc_final: 0.7412 (p0) REVERT: E 425 LEU cc_start: 0.9159 (mp) cc_final: 0.8922 (mp) REVERT: E 474 GLN cc_start: 0.7086 (pp30) cc_final: 0.6669 (pp30) REVERT: H 45 LYS cc_start: 0.8327 (ptmm) cc_final: 0.8004 (ptmm) REVERT: H 117 VAL cc_start: 0.5800 (t) cc_final: 0.5579 (m) REVERT: L 54 VAL cc_start: 0.5820 (OUTLIER) cc_final: 0.5545 (m) REVERT: L 103 PHE cc_start: 0.4280 (OUTLIER) cc_final: 0.3175 (m-10) outliers start: 15 outliers final: 11 residues processed: 64 average time/residue: 0.1015 time to fit residues: 8.8363 Evaluate side-chains 71 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.0070 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 40 optimal weight: 4.9990 overall best weight: 1.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.126826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3322 r_free = 0.3322 target = 0.096474 restraints weight = 6861.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.090411 restraints weight = 9343.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.091291 restraints weight = 7168.852| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3441 Z= 0.238 Angle : 0.652 8.051 4690 Z= 0.327 Chirality : 0.046 0.170 517 Planarity : 0.005 0.054 600 Dihedral : 5.122 23.793 470 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.77 % Allowed : 25.88 % Favored : 70.35 % 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: -1.48 (0.41), residues: 423 helix: -3.54 (0.80), residues: 26 sheet: 0.21 (0.44), residues: 145 loop : -1.47 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 HIS 0.001 0.000 HIS E 505 PHE 0.022 0.002 PHE H 106 TYR 0.018 0.001 TYR E 501 ARG 0.002 0.000 ARG E 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1161.37 seconds wall clock time: 21 minutes 37.34 seconds (1297.34 seconds total)