Starting phenix.real_space_refine on Tue Feb 13 04:43:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp0_32665/02_2024/7wp0_32665.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp0_32665/02_2024/7wp0_32665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp0_32665/02_2024/7wp0_32665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp0_32665/02_2024/7wp0_32665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp0_32665/02_2024/7wp0_32665.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp0_32665/02_2024/7wp0_32665.pdb" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 2007 2.51 5 N 537 2.21 5 O 617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 94": "OD1" <-> "OD2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F ASP 442": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3174 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 811 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "F" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1346 Unusual residues: {'NAG': 1} Classifications: {'peptide': 165, 'undetermined': 1} Link IDs: {'PTRANS': 8, 'TRANS': 156, None: 1} Not linked: pdbres="LEU F 518 " pdbres="NAG F 601 " Chain breaks: 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: 2.53, per 1000 atoms: 0.80 Number of scatterers: 3174 At special positions: 0 Unit cell: (83.246, 63.018, 79.356, 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 13 16.00 O 617 8.00 N 537 7.00 C 2007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.02 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 F 601 " - " ASN F 343 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 580.3 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 4.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.760A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'F' and resid 349 through 353 removed outlier: 4.174A pdb=" N TRP F 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 410 removed outlier: 4.492A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.568A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.568A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR L 88 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.746A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.936A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 374 through 379 removed outlier: 6.669A pdb=" N ALA F 435 " --> pdb=" O SER F 375 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE F 377 " --> pdb=" O VAL F 433 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL F 433 " --> pdb=" O PHE F 377 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS F 379 " --> pdb=" O GLY F 431 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY F 431 " --> pdb=" O CYS F 379 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP F 436 " --> pdb=" O ARG F 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 453 through 454 73 hydrogen bonds defined for protein. 165 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: 0.72 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 973 1.33 - 1.45: 693 1.45 - 1.57: 1569 1.57 - 1.69: 0 1.69 - 1.81: 17 Bond restraints: 3252 Sorted by residual: bond pdb=" C GLY H 99 " pdb=" N VAL H 100 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.57e-02 4.06e+03 8.43e+00 bond pdb=" C1 NAG F 601 " pdb=" O5 NAG F 601 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" CA ASP L 62 " pdb=" C ASP L 62 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.56e-02 4.11e+03 3.03e+00 bond pdb=" C CYS F 336 " pdb=" N PRO F 337 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.64e+00 bond pdb=" CA CYS F 336 " pdb=" C CYS F 336 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.37e+00 ... (remaining 3247 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.85: 65 105.85 - 112.90: 1602 112.90 - 119.95: 1130 119.95 - 127.00: 1578 127.00 - 134.04: 39 Bond angle restraints: 4414 Sorted by residual: angle pdb=" C GLY L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.54 132.69 -11.15 1.91e+00 2.74e-01 3.41e+01 angle pdb=" N TYR H 103 " pdb=" CA TYR H 103 " pdb=" C TYR H 103 " ideal model delta sigma weight residual 110.44 105.25 5.19 1.20e+00 6.94e-01 1.87e+01 angle pdb=" C SER F 359 " pdb=" N ASN F 360 " pdb=" CA ASN F 360 " ideal model delta sigma weight residual 122.08 128.22 -6.14 1.47e+00 4.63e-01 1.75e+01 angle pdb=" CA ASP L 62 " pdb=" C ASP L 62 " pdb=" O ASP L 62 " ideal model delta sigma weight residual 119.43 123.76 -4.33 1.21e+00 6.83e-01 1.28e+01 angle pdb=" CA ASN F 360 " pdb=" CB ASN F 360 " pdb=" CG ASN F 360 " ideal model delta sigma weight residual 112.60 116.10 -3.50 1.00e+00 1.00e+00 1.23e+01 ... (remaining 4409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 1677 16.84 - 33.68: 187 33.68 - 50.52: 33 50.52 - 67.36: 6 67.36 - 84.20: 3 Dihedral angle restraints: 1906 sinusoidal: 743 harmonic: 1163 Sorted by residual: dihedral pdb=" CA ARG H 16 " pdb=" C ARG H 16 " pdb=" N SER H 17 " pdb=" CA SER H 17 " ideal model delta harmonic sigma weight residual -180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ASN F 460 " pdb=" C ASN F 460 " pdb=" N LEU F 461 " pdb=" CA LEU F 461 " ideal model delta harmonic sigma weight residual -180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA CYS F 336 " pdb=" C CYS F 336 " pdb=" N PRO F 337 " pdb=" CA PRO F 337 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 1903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 297 0.048 - 0.096: 121 0.096 - 0.144: 38 0.144 - 0.192: 10 0.192 - 0.240: 2 Chirality restraints: 468 Sorted by residual: chirality pdb=" CB THR H 28 " pdb=" CA THR H 28 " pdb=" OG1 THR H 28 " pdb=" CG2 THR H 28 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ASN F 360 " pdb=" N ASN F 360 " pdb=" C ASN F 360 " pdb=" CB ASN F 360 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA PRO F 337 " pdb=" N PRO F 337 " pdb=" C PRO F 337 " pdb=" CB PRO F 337 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.93e-01 ... (remaining 465 not shown) Planarity restraints: 574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 462 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO F 463 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO F 463 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 463 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 411 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO F 412 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 412 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 412 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 6 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO L 7 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 7 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 7 " 0.027 5.00e-02 4.00e+02 ... (remaining 571 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 968 2.80 - 3.33: 2577 3.33 - 3.85: 4987 3.85 - 4.38: 5544 4.38 - 4.90: 9966 Nonbonded interactions: 24042 Sorted by model distance: nonbonded pdb=" OH TYR L 51 " pdb=" O THR F 415 " model vdw 2.281 2.440 nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 72 " model vdw 2.345 2.520 nonbonded pdb=" O THR F 430 " pdb=" OG1 THR F 430 " model vdw 2.350 2.440 nonbonded pdb=" O PRO L 7 " pdb=" OG1 THR L 106 " model vdw 2.362 2.440 nonbonded pdb=" NH1 ARG F 457 " pdb=" O SER F 459 " model vdw 2.377 2.520 ... (remaining 24037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 39.410 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.020 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 3252 Z= 0.438 Angle : 0.944 11.148 4414 Z= 0.547 Chirality : 0.060 0.240 468 Planarity : 0.007 0.067 573 Dihedral : 14.465 84.198 1167 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.59 % Allowed : 11.14 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.33), residues: 399 helix: -5.05 (0.23), residues: 21 sheet: -2.27 (0.39), residues: 149 loop : -3.48 (0.30), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 436 HIS 0.002 0.001 HIS L 36 PHE 0.014 0.003 PHE F 377 TYR 0.023 0.002 TYR F 453 ARG 0.004 0.000 ARG F 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.388 Fit side-chains REVERT: L 40 GLN cc_start: 0.8384 (tt0) cc_final: 0.8114 (tt0) REVERT: H 89 GLU cc_start: 0.7737 (pt0) cc_final: 0.7511 (pt0) outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 0.1640 time to fit residues: 15.8772 Evaluate side-chains 69 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 16 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3252 Z= 0.224 Angle : 0.618 6.674 4414 Z= 0.329 Chirality : 0.045 0.152 468 Planarity : 0.005 0.046 573 Dihedral : 6.064 45.576 478 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 2.05 % Allowed : 21.11 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.36), residues: 399 helix: -4.93 (0.28), residues: 21 sheet: -1.68 (0.41), residues: 141 loop : -3.06 (0.33), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 436 HIS 0.002 0.001 HIS L 36 PHE 0.011 0.001 PHE F 338 TYR 0.017 0.002 TYR H 59 ARG 0.004 0.000 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.376 Fit side-chains REVERT: L 68 LYS cc_start: 0.8536 (ttpp) cc_final: 0.8220 (tttm) REVERT: H 78 THR cc_start: 0.8879 (m) cc_final: 0.8588 (p) outliers start: 7 outliers final: 5 residues processed: 82 average time/residue: 0.1949 time to fit residues: 18.7142 Evaluate side-chains 75 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.0570 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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: 0.7875 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3252 Z= 0.233 Angle : 0.631 8.107 4414 Z= 0.324 Chirality : 0.047 0.217 468 Planarity : 0.005 0.041 573 Dihedral : 5.847 45.475 478 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.11 % Allowed : 25.22 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.38), residues: 399 helix: -4.92 (0.32), residues: 27 sheet: -1.34 (0.44), residues: 131 loop : -2.58 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 436 HIS 0.001 0.001 HIS H 35 PHE 0.015 0.002 PHE H 29 TYR 0.017 0.001 TYR F 369 ARG 0.005 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.375 Fit side-chains REVERT: H 18 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7711 (tt) REVERT: H 78 THR cc_start: 0.8849 (m) cc_final: 0.8512 (p) REVERT: F 452 ARG cc_start: 0.8833 (mtp85) cc_final: 0.8449 (mtm-85) outliers start: 14 outliers final: 8 residues processed: 77 average time/residue: 0.1657 time to fit residues: 15.3288 Evaluate side-chains 74 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3252 Z= 0.242 Angle : 0.634 9.490 4414 Z= 0.325 Chirality : 0.045 0.183 468 Planarity : 0.004 0.041 573 Dihedral : 5.724 44.392 478 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 5.87 % Allowed : 23.75 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.38), residues: 399 helix: -4.84 (0.38), residues: 27 sheet: -1.17 (0.44), residues: 133 loop : -2.36 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 436 HIS 0.001 0.001 HIS L 36 PHE 0.011 0.001 PHE H 68 TYR 0.016 0.001 TYR F 369 ARG 0.003 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 0.369 Fit side-chains REVERT: H 53 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7532 (t80) REVERT: H 78 THR cc_start: 0.8783 (m) cc_final: 0.8337 (p) REVERT: F 452 ARG cc_start: 0.8874 (mtp85) cc_final: 0.8519 (mtm-85) outliers start: 20 outliers final: 15 residues processed: 76 average time/residue: 0.1666 time to fit residues: 15.3125 Evaluate side-chains 79 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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: 0.7896 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3252 Z= 0.292 Angle : 0.656 9.510 4414 Z= 0.337 Chirality : 0.046 0.160 468 Planarity : 0.004 0.039 573 Dihedral : 5.933 46.670 478 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 5.57 % Allowed : 24.93 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.39), residues: 399 helix: -4.79 (0.43), residues: 27 sheet: -1.19 (0.46), residues: 124 loop : -2.20 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 436 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.002 PHE F 338 TYR 0.015 0.002 TYR F 380 ARG 0.003 0.000 ARG F 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 0.375 Fit side-chains REVERT: F 452 ARG cc_start: 0.8835 (mtp85) cc_final: 0.8468 (mtm-85) REVERT: F 511 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8698 (m) outliers start: 19 outliers final: 16 residues processed: 73 average time/residue: 0.1632 time to fit residues: 14.4499 Evaluate side-chains 79 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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: 0.7895 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3252 Z= 0.285 Angle : 0.634 6.574 4414 Z= 0.332 Chirality : 0.046 0.164 468 Planarity : 0.004 0.040 573 Dihedral : 5.940 47.665 478 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 5.57 % Allowed : 25.81 % Favored : 68.62 % 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: -2.92 (0.39), residues: 399 helix: -4.62 (0.57), residues: 20 sheet: -1.22 (0.47), residues: 124 loop : -2.18 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.002 PHE F 338 TYR 0.015 0.002 TYR F 380 ARG 0.003 0.000 ARG F 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.354 Fit side-chains REVERT: F 452 ARG cc_start: 0.8778 (mtp85) cc_final: 0.8439 (mtm-85) REVERT: F 511 VAL cc_start: 0.8988 (OUTLIER) cc_final: 0.8680 (m) outliers start: 19 outliers final: 16 residues processed: 77 average time/residue: 0.1656 time to fit residues: 15.3844 Evaluate side-chains 82 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 442 ASP Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 38 optimal weight: 0.0970 chunk 24 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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: 0.7852 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3252 Z= 0.211 Angle : 0.607 7.131 4414 Z= 0.316 Chirality : 0.045 0.181 468 Planarity : 0.004 0.039 573 Dihedral : 5.549 45.348 478 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 5.87 % Allowed : 25.51 % Favored : 68.62 % 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 (0.39), residues: 399 helix: -4.79 (0.43), residues: 27 sheet: -1.20 (0.47), residues: 119 loop : -1.89 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.001 0.001 HIS H 35 PHE 0.008 0.001 PHE H 68 TYR 0.015 0.001 TYR F 369 ARG 0.002 0.000 ARG F 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.346 Fit side-chains REVERT: F 452 ARG cc_start: 0.8704 (mtp85) cc_final: 0.8341 (mtm-85) outliers start: 20 outliers final: 16 residues processed: 78 average time/residue: 0.1661 time to fit residues: 15.6103 Evaluate side-chains 80 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 33 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3252 Z= 0.167 Angle : 0.584 7.606 4414 Z= 0.302 Chirality : 0.044 0.151 468 Planarity : 0.004 0.039 573 Dihedral : 5.143 40.326 478 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.11 % Allowed : 28.15 % Favored : 67.74 % 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: -2.50 (0.40), residues: 399 helix: -4.64 (0.52), residues: 21 sheet: -0.73 (0.46), residues: 135 loop : -2.00 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.001 0.000 HIS H 35 PHE 0.007 0.001 PHE H 68 TYR 0.016 0.001 TYR F 369 ARG 0.002 0.000 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: F 452 ARG cc_start: 0.8614 (mtp85) cc_final: 0.8320 (mtm110) outliers start: 14 outliers final: 12 residues processed: 75 average time/residue: 0.1556 time to fit residues: 14.2066 Evaluate side-chains 77 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3252 Z= 0.209 Angle : 0.604 7.405 4414 Z= 0.313 Chirality : 0.044 0.155 468 Planarity : 0.004 0.037 573 Dihedral : 5.220 41.339 478 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.11 % Allowed : 27.27 % Favored : 68.62 % 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: -2.46 (0.40), residues: 399 helix: -4.64 (0.52), residues: 21 sheet: -0.66 (0.45), residues: 135 loop : -2.00 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.001 0.001 HIS L 36 PHE 0.008 0.001 PHE H 68 TYR 0.014 0.001 TYR F 369 ARG 0.002 0.000 ARG F 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: F 406 GLU cc_start: 0.7931 (tt0) cc_final: 0.7686 (tt0) REVERT: F 408 ARG cc_start: 0.7888 (mpt-90) cc_final: 0.7457 (mpt-90) REVERT: F 452 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8333 (mtm110) REVERT: F 511 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8629 (m) outliers start: 14 outliers final: 13 residues processed: 75 average time/residue: 0.1602 time to fit residues: 14.4001 Evaluate side-chains 78 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 0.0040 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3252 Z= 0.203 Angle : 0.606 7.821 4414 Z= 0.313 Chirality : 0.044 0.175 468 Planarity : 0.004 0.039 573 Dihedral : 5.204 41.304 478 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.81 % Allowed : 28.15 % Favored : 68.04 % 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: -2.35 (0.40), residues: 399 helix: -4.60 (0.60), residues: 20 sheet: -0.53 (0.46), residues: 134 loop : -1.98 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.001 0.001 HIS L 36 PHE 0.009 0.001 PHE H 68 TYR 0.014 0.001 TYR F 369 ARG 0.002 0.000 ARG F 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: F 406 GLU cc_start: 0.7959 (tt0) cc_final: 0.7623 (tt0) REVERT: F 417 LYS cc_start: 0.8570 (ttpt) cc_final: 0.8349 (ttmt) REVERT: F 452 ARG cc_start: 0.8607 (mtp85) cc_final: 0.8314 (mtm110) REVERT: F 511 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8624 (m) outliers start: 13 outliers final: 12 residues processed: 73 average time/residue: 0.1580 time to fit residues: 14.1157 Evaluate side-chains 76 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.157535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137716 restraints weight = 4643.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141384 restraints weight = 2884.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143952 restraints weight = 2059.175| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3252 Z= 0.201 Angle : 0.606 7.876 4414 Z= 0.311 Chirality : 0.044 0.170 468 Planarity : 0.004 0.037 573 Dihedral : 5.175 41.335 478 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.69 % Allowed : 27.27 % Favored : 68.04 % 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: -2.27 (0.40), residues: 399 helix: -4.27 (0.82), residues: 14 sheet: -0.43 (0.48), residues: 123 loop : -2.00 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.001 0.001 HIS L 36 PHE 0.009 0.001 PHE H 68 TYR 0.014 0.001 TYR F 369 ARG 0.002 0.000 ARG F 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1620.20 seconds wall clock time: 29 minutes 46.90 seconds (1786.90 seconds total)