Starting phenix.real_space_refine on Sun Mar 10 16:30:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcf_14629/03_2024/7zcf_14629.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcf_14629/03_2024/7zcf_14629.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/7zcf_14629/03_2024/7zcf_14629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcf_14629/03_2024/7zcf_14629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcf_14629/03_2024/7zcf_14629.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcf_14629/03_2024/7zcf_14629.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= -0.004 sd= 0.044 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 2107 2.51 5 N 556 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E GLU 215": "OE1" <-> "OE2" 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: 3312 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1595 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "E" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1703 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.32, per 1000 atoms: 0.70 Number of scatterers: 3312 At special positions: 0 Unit cell: (65.786, 91.567, 90.678, 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 635 8.00 N 556 7.00 C 2107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 222 " 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 NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 630.7 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 6 sheets defined 8.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.854A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.228A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.676A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.585A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.877A pdb=" N SER C 443 " --> pdb=" O ASN C 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 217 removed outlier: 3.954A pdb=" N PHE E 217 " --> pdb=" O PRO E 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.651A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.640A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 18 through 20 removed outlier: 3.639A pdb=" N LEU E 80 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR E 68 " --> pdb=" O GLN E 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.179A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR E 33 " --> pdb=" O ASP E 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 137 through 139 Processing sheet with id=AA6, first strand: chain 'E' and resid 187 through 188 removed outlier: 3.778A pdb=" N SER E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TRP E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR E 183 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU E 167 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR E 231 " --> pdb=" O GLN E 224 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 132 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: 0.71 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: 1.23 - 1.35: 1057 1.35 - 1.46: 899 1.46 - 1.58: 1423 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3395 Sorted by residual: bond pdb=" C PRO E 174 " pdb=" O PRO E 174 " ideal model delta sigma weight residual 1.235 1.268 -0.033 1.30e-02 5.92e+03 6.36e+00 bond pdb=" C PRO E 174 " pdb=" N GLY E 175 " ideal model delta sigma weight residual 1.333 1.368 -0.036 1.57e-02 4.06e+03 5.19e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C SER E 228 " pdb=" N PRO E 229 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.64e+00 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.13e+00 ... (remaining 3390 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.90: 98 106.90 - 113.67: 1758 113.67 - 120.43: 1272 120.43 - 127.20: 1455 127.20 - 133.97: 31 Bond angle restraints: 4614 Sorted by residual: angle pdb=" N SER E 140 " pdb=" CA SER E 140 " pdb=" C SER E 140 " ideal model delta sigma weight residual 109.81 116.47 -6.66 2.21e+00 2.05e-01 9.08e+00 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 118.46 -6.12 2.04e+00 2.40e-01 8.99e+00 angle pdb=" N GLN E 110 " pdb=" CA GLN E 110 " pdb=" C GLN E 110 " ideal model delta sigma weight residual 114.04 110.83 3.21 1.24e+00 6.50e-01 6.71e+00 angle pdb=" O PRO E 174 " pdb=" C PRO E 174 " pdb=" N GLY E 175 " ideal model delta sigma weight residual 122.64 126.13 -3.49 1.35e+00 5.49e-01 6.68e+00 angle pdb=" N PRO C 337 " pdb=" CA PRO C 337 " pdb=" C PRO C 337 " ideal model delta sigma weight residual 114.68 112.10 2.58 1.04e+00 9.25e-01 6.13e+00 ... (remaining 4609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1812 17.95 - 35.91: 160 35.91 - 53.86: 35 53.86 - 71.82: 4 71.82 - 89.77: 4 Dihedral angle restraints: 2015 sinusoidal: 790 harmonic: 1225 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 47.90 45.10 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 137.62 -44.62 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CA SER E 140 " pdb=" C SER E 140 " pdb=" N PRO E 141 " pdb=" CA PRO E 141 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 2012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 398 0.049 - 0.097: 80 0.097 - 0.146: 19 0.146 - 0.194: 2 0.194 - 0.243: 1 Chirality restraints: 500 Sorted by residual: chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE C 472 " pdb=" N ILE C 472 " pdb=" C ILE C 472 " pdb=" CB ILE C 472 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CB VAL E 116 " pdb=" CA VAL E 116 " pdb=" CG1 VAL E 116 " pdb=" CG2 VAL E 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 497 not shown) Planarity restraints: 598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO C 337 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 506 " -0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO C 507 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 507 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 507 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 411 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO C 412 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 412 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 412 " 0.018 5.00e-02 4.00e+02 ... (remaining 595 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 42 2.65 - 3.21: 2931 3.21 - 3.78: 4503 3.78 - 4.34: 6072 4.34 - 4.90: 10024 Nonbonded interactions: 23572 Sorted by model distance: nonbonded pdb=" OD1 ASN C 354 " pdb=" OG SER C 399 " model vdw 2.089 2.440 nonbonded pdb=" O LEU C 455 " pdb=" OH TYR E 33 " model vdw 2.219 2.440 nonbonded pdb=" OD1 ASN C 331 " pdb=" N ILE C 332 " model vdw 2.228 2.520 nonbonded pdb=" OH TYR C 421 " pdb=" O PRO E 53 " model vdw 2.256 2.440 nonbonded pdb=" N GLN E 3 " pdb=" OG SER E 25 " model vdw 2.311 2.520 ... (remaining 23567 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=0.50 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: 2.720 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: 12.920 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.860 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 : 0.003 0.036 3395 Z= 0.177 Angle : 0.658 6.658 4614 Z= 0.371 Chirality : 0.045 0.243 500 Planarity : 0.005 0.054 597 Dihedral : 14.299 89.770 1223 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 0.56 % Allowed : 0.28 % Favored : 99.16 % 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: -2.45 (0.40), residues: 420 helix: -4.94 (0.47), residues: 8 sheet: -0.46 (0.55), residues: 104 loop : -2.12 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 353 HIS 0.001 0.001 HIS C 519 PHE 0.015 0.001 PHE C 338 TYR 0.012 0.001 TYR C 473 ARG 0.002 0.000 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.387 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 71 average time/residue: 0.1599 time to fit residues: 13.8588 Evaluate side-chains 58 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 139 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3395 Z= 0.208 Angle : 0.640 6.987 4614 Z= 0.332 Chirality : 0.045 0.167 500 Planarity : 0.005 0.034 597 Dihedral : 6.276 50.822 496 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.62 % Favored : 82.38 % Rotamer: Outliers : 1.96 % Allowed : 12.85 % Favored : 85.20 % 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: -2.57 (0.41), residues: 420 helix: -4.90 (0.48), residues: 8 sheet: -1.04 (0.52), residues: 112 loop : -2.02 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS C 519 PHE 0.014 0.002 PHE C 374 TYR 0.026 0.002 TYR E 183 ARG 0.003 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: C 331 ASN cc_start: 0.6597 (OUTLIER) cc_final: 0.6376 (p0) REVERT: E 224 GLN cc_start: 0.8555 (pp30) cc_final: 0.8291 (pp30) outliers start: 7 outliers final: 4 residues processed: 79 average time/residue: 0.1312 time to fit residues: 13.1186 Evaluate side-chains 73 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3395 Z= 0.325 Angle : 0.743 7.621 4614 Z= 0.394 Chirality : 0.048 0.177 500 Planarity : 0.005 0.035 597 Dihedral : 6.973 52.006 493 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.24 % Favored : 79.76 % Rotamer: Outliers : 5.87 % Allowed : 16.48 % Favored : 77.65 % 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: -2.79 (0.41), residues: 420 helix: -4.91 (0.49), residues: 8 sheet: -1.41 (0.47), residues: 129 loop : -2.08 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 353 HIS 0.003 0.002 HIS C 519 PHE 0.017 0.002 PHE C 342 TYR 0.024 0.002 TYR E 183 ARG 0.004 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: C 353 TRP cc_start: 0.8564 (p-90) cc_final: 0.8141 (p-90) REVERT: E 224 GLN cc_start: 0.8751 (pp30) cc_final: 0.8364 (pp30) outliers start: 21 outliers final: 14 residues processed: 71 average time/residue: 0.1432 time to fit residues: 12.7369 Evaluate side-chains 72 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 230 TYR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.0470 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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: 0.7643 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3395 Z= 0.244 Angle : 0.688 6.940 4614 Z= 0.364 Chirality : 0.046 0.187 500 Planarity : 0.005 0.033 597 Dihedral : 6.734 50.528 493 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.62 % Favored : 82.38 % Rotamer: Outliers : 3.91 % Allowed : 19.55 % Favored : 76.54 % 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: -2.84 (0.41), residues: 420 helix: -4.71 (0.65), residues: 8 sheet: -1.56 (0.48), residues: 123 loop : -2.05 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.001 0.001 HIS C 519 PHE 0.012 0.001 PHE C 342 TYR 0.023 0.002 TYR E 183 ARG 0.002 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: C 353 TRP cc_start: 0.8472 (p-90) cc_final: 0.8192 (p-90) REVERT: E 139 GLN cc_start: 0.6898 (pm20) cc_final: 0.6331 (pm20) REVERT: E 224 GLN cc_start: 0.8614 (pp30) cc_final: 0.8287 (pp30) outliers start: 14 outliers final: 12 residues processed: 67 average time/residue: 0.1456 time to fit residues: 12.2032 Evaluate side-chains 70 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 199 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.0000 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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: 0.7641 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3395 Z= 0.217 Angle : 0.665 6.984 4614 Z= 0.348 Chirality : 0.045 0.178 500 Planarity : 0.005 0.032 597 Dihedral : 6.508 50.495 493 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.29 % Favored : 80.71 % Rotamer: Outliers : 5.31 % Allowed : 20.11 % Favored : 74.58 % 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: -2.84 (0.41), residues: 420 helix: -4.74 (0.62), residues: 8 sheet: -1.54 (0.48), residues: 123 loop : -2.07 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.001 0.000 HIS C 519 PHE 0.009 0.001 PHE C 342 TYR 0.021 0.001 TYR E 183 ARG 0.002 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: C 353 TRP cc_start: 0.8580 (p-90) cc_final: 0.8139 (p-90) REVERT: E 139 GLN cc_start: 0.6837 (pm20) cc_final: 0.6379 (pm20) REVERT: E 224 GLN cc_start: 0.8594 (pp30) cc_final: 0.8306 (pp30) outliers start: 19 outliers final: 16 residues processed: 69 average time/residue: 0.1380 time to fit residues: 12.0128 Evaluate side-chains 72 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.0470 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 overall best weight: 0.2676 ------------------------------------------------------------------------------- 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: 0.7571 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3395 Z= 0.170 Angle : 0.636 6.888 4614 Z= 0.329 Chirality : 0.044 0.174 500 Planarity : 0.004 0.033 597 Dihedral : 6.161 50.776 493 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 4.47 % Allowed : 21.51 % Favored : 74.02 % 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: -2.77 (0.41), residues: 420 helix: -4.78 (0.59), residues: 8 sheet: -1.39 (0.50), residues: 117 loop : -2.07 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.009 0.001 PHE E 232 TYR 0.019 0.001 TYR E 183 ARG 0.001 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: C 353 TRP cc_start: 0.8547 (p-90) cc_final: 0.8137 (p-90) REVERT: C 398 ASP cc_start: 0.7946 (m-30) cc_final: 0.7744 (m-30) REVERT: E 139 GLN cc_start: 0.6585 (pm20) cc_final: 0.6130 (pm20) REVERT: E 215 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7390 (tm-30) REVERT: E 224 GLN cc_start: 0.8553 (pp30) cc_final: 0.8265 (pp30) outliers start: 16 outliers final: 14 residues processed: 69 average time/residue: 0.1426 time to fit residues: 12.2080 Evaluate side-chains 73 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.0970 chunk 34 optimal weight: 0.0070 chunk 40 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 overall best weight: 0.2374 ------------------------------------------------------------------------------- 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: 0.7549 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3395 Z= 0.163 Angle : 0.625 6.963 4614 Z= 0.321 Chirality : 0.044 0.171 500 Planarity : 0.004 0.033 597 Dihedral : 6.021 51.176 493 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.62 % Favored : 82.38 % Rotamer: Outliers : 5.03 % Allowed : 21.79 % Favored : 73.18 % 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: -2.78 (0.41), residues: 420 helix: -4.77 (0.60), residues: 8 sheet: -1.44 (0.48), residues: 123 loop : -2.05 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.001 0.000 HIS C 519 PHE 0.008 0.001 PHE E 232 TYR 0.020 0.001 TYR E 183 ARG 0.002 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: E 139 GLN cc_start: 0.6596 (pm20) cc_final: 0.6140 (pm20) REVERT: E 215 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7353 (tm-30) REVERT: E 224 GLN cc_start: 0.8542 (pp30) cc_final: 0.8269 (pp30) outliers start: 18 outliers final: 16 residues processed: 70 average time/residue: 0.1386 time to fit residues: 12.3017 Evaluate side-chains 72 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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: 0.7669 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3395 Z= 0.255 Angle : 0.673 6.921 4614 Z= 0.351 Chirality : 0.045 0.172 500 Planarity : 0.005 0.033 597 Dihedral : 6.497 51.380 493 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.52 % Favored : 80.48 % Rotamer: Outliers : 6.42 % Allowed : 19.55 % Favored : 74.02 % 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 (0.41), residues: 420 helix: -4.64 (0.73), residues: 8 sheet: -1.50 (0.49), residues: 123 loop : -2.12 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.001 0.001 HIS C 519 PHE 0.016 0.002 PHE C 456 TYR 0.018 0.001 TYR E 183 ARG 0.003 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 56 time to evaluate : 0.389 Fit side-chains REVERT: E 139 GLN cc_start: 0.6703 (pm20) cc_final: 0.6235 (pm20) REVERT: E 215 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7343 (tm-30) REVERT: E 224 GLN cc_start: 0.8607 (pp30) cc_final: 0.8251 (pp30) outliers start: 23 outliers final: 21 residues processed: 66 average time/residue: 0.1595 time to fit residues: 13.0278 Evaluate side-chains 77 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 56 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.0170 chunk 39 optimal weight: 0.1980 chunk 18 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3395 Z= 0.180 Angle : 0.634 7.427 4614 Z= 0.327 Chirality : 0.044 0.171 500 Planarity : 0.004 0.034 597 Dihedral : 6.121 50.833 493 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 4.47 % Allowed : 21.79 % Favored : 73.74 % 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: -2.79 (0.42), residues: 420 helix: -4.51 (0.84), residues: 8 sheet: -1.50 (0.49), residues: 123 loop : -2.04 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.001 0.000 HIS C 519 PHE 0.013 0.001 PHE C 456 TYR 0.017 0.001 TYR C 473 ARG 0.002 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.346 Fit side-chains REVERT: E 139 GLN cc_start: 0.6481 (pm20) cc_final: 0.6006 (pm20) REVERT: E 215 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7350 (tm-30) REVERT: E 224 GLN cc_start: 0.8556 (pp30) cc_final: 0.8241 (pp30) outliers start: 16 outliers final: 14 residues processed: 67 average time/residue: 0.1343 time to fit residues: 11.3422 Evaluate side-chains 69 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.0010 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3395 Z= 0.206 Angle : 0.651 7.929 4614 Z= 0.337 Chirality : 0.044 0.172 500 Planarity : 0.004 0.034 597 Dihedral : 6.224 51.728 493 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.33 % Favored : 81.67 % Rotamer: Outliers : 4.47 % Allowed : 21.23 % Favored : 74.30 % 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: -2.79 (0.42), residues: 420 helix: -4.47 (0.88), residues: 8 sheet: -1.51 (0.50), residues: 121 loop : -2.05 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.001 0.001 HIS C 519 PHE 0.013 0.001 PHE C 456 TYR 0.017 0.001 TYR E 183 ARG 0.003 0.000 ARG E 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.347 Fit side-chains REVERT: E 139 GLN cc_start: 0.6577 (pm20) cc_final: 0.6099 (pm20) REVERT: E 215 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7336 (tm-30) REVERT: E 224 GLN cc_start: 0.8577 (pp30) cc_final: 0.8244 (pp30) outliers start: 16 outliers final: 16 residues processed: 65 average time/residue: 0.1381 time to fit residues: 11.3845 Evaluate side-chains 72 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.0050 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.159888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.142000 restraints weight = 5770.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144833 restraints weight = 3658.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146824 restraints weight = 2623.523| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3395 Z= 0.209 Angle : 0.650 8.154 4614 Z= 0.337 Chirality : 0.044 0.172 500 Planarity : 0.005 0.034 597 Dihedral : 6.251 51.686 493 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.14 % Favored : 82.86 % Rotamer: Outliers : 5.31 % Allowed : 20.11 % Favored : 74.58 % 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: -2.80 (0.42), residues: 420 helix: -4.64 (0.73), residues: 8 sheet: -1.45 (0.49), residues: 124 loop : -2.08 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.001 0.001 HIS C 519 PHE 0.012 0.001 PHE C 456 TYR 0.016 0.001 TYR C 473 ARG 0.003 0.000 ARG E 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1362.48 seconds wall clock time: 25 minutes 4.11 seconds (1504.11 seconds total)