Starting phenix.real_space_refine on Tue Feb 13 05:32:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjn_40095/02_2024/8gjn_40095.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjn_40095/02_2024/8gjn_40095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjn_40095/02_2024/8gjn_40095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjn_40095/02_2024/8gjn_40095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjn_40095/02_2024/8gjn_40095.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjn_40095/02_2024/8gjn_40095.pdb" } resolution = 3.6 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 15 5.16 5 C 2102 2.51 5 N 550 2.21 5 O 652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3319 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1566 Unusual residues: {'NAG': 1} Classifications: {'peptide': 196, 'undetermined': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184, None: 1} Not linked: pdbres="LYS C 528 " pdbres="NAG C 601 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.54, per 1000 atoms: 0.77 Number of scatterers: 3319 At special positions: 0 Unit cell: (86.625, 54.45, 107.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 652 8.00 N 550 7.00 C 2102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 115 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 108 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 657.6 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 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: 9 helices and 8 sheets defined 13.1% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.719A pdb=" N TYR A 51 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 4.450A pdb=" N GLY A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.106A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.074A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.661A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.213A pdb=" N GLU A 29 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET A 53 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY A 69 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP A 55 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 42 Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 26 removed outlier: 4.157A pdb=" N VAL B 39 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.388A pdb=" N TRP B 55 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 33 Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 108 hydrogen bonds defined for protein. 249 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: 0.85 Time building geometry restraints manager: 1.36 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: 801 1.33 - 1.46: 791 1.46 - 1.58: 1791 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3401 Sorted by residual: bond pdb=" N ILE C 472 " pdb=" CA ILE C 472 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" N CYS A 115 " pdb=" CA CYS A 115 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" N VAL A 37 " pdb=" CA VAL A 37 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ARG C 457 " pdb=" CA ARG C 457 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.18e-02 7.18e+03 9.94e+00 bond pdb=" N VAL C 524 " pdb=" CA VAL C 524 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 9.93e+00 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.83: 84 105.83 - 113.07: 1591 113.07 - 120.32: 1636 120.32 - 127.57: 1279 127.57 - 134.81: 25 Bond angle restraints: 4615 Sorted by residual: angle pdb=" N PHE C 490 " pdb=" CA PHE C 490 " pdb=" C PHE C 490 " ideal model delta sigma weight residual 109.24 100.49 8.75 1.39e+00 5.18e-01 3.96e+01 angle pdb=" N CYS C 488 " pdb=" CA CYS C 488 " pdb=" C CYS C 488 " ideal model delta sigma weight residual 109.54 101.74 7.80 1.37e+00 5.33e-01 3.25e+01 angle pdb=" N TYR C 489 " pdb=" CA TYR C 489 " pdb=" C TYR C 489 " ideal model delta sigma weight residual 110.43 116.65 -6.22 1.31e+00 5.83e-01 2.25e+01 angle pdb=" C GLY A 27 " pdb=" N PRO A 28 " pdb=" CA PRO A 28 " ideal model delta sigma weight residual 119.90 124.65 -4.75 1.02e+00 9.61e-01 2.16e+01 angle pdb=" C LYS B 80 " pdb=" CA LYS B 80 " pdb=" CB LYS B 80 " ideal model delta sigma weight residual 116.54 111.44 5.10 1.15e+00 7.56e-01 1.97e+01 ... (remaining 4610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 1851 17.49 - 34.98: 134 34.98 - 52.47: 21 52.47 - 69.95: 21 69.95 - 87.44: 2 Dihedral angle restraints: 2029 sinusoidal: 809 harmonic: 1220 Sorted by residual: dihedral pdb=" CA ASP B 61 " pdb=" C ASP B 61 " pdb=" N GLY B 62 " pdb=" CA GLY B 62 " ideal model delta harmonic sigma weight residual 180.00 150.37 29.63 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER B 97 " pdb=" C SER B 97 " pdb=" N PRO B 98 " pdb=" CA PRO B 98 " ideal model delta harmonic sigma weight residual 180.00 153.41 26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA ALA A 111 " pdb=" C ALA A 111 " pdb=" N VAL A 112 " pdb=" CA VAL A 112 " ideal model delta harmonic sigma weight residual 180.00 153.44 26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 2026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 226 0.060 - 0.120: 168 0.120 - 0.180: 80 0.180 - 0.240: 17 0.240 - 0.300: 5 Chirality restraints: 496 Sorted by residual: chirality pdb=" CA PHE C 464 " pdb=" N PHE C 464 " pdb=" C PHE C 464 " pdb=" CB PHE C 464 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA PRO A 33 " pdb=" N PRO A 33 " pdb=" C PRO A 33 " pdb=" CB PRO A 33 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA LEU C 461 " pdb=" N LEU C 461 " pdb=" C LEU C 461 " pdb=" CB LEU C 461 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 493 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 601 " -0.104 2.00e-02 2.50e+03 8.66e-02 9.37e+01 pdb=" C7 NAG C 601 " 0.024 2.00e-02 2.50e+03 pdb=" C8 NAG C 601 " -0.076 2.00e-02 2.50e+03 pdb=" N2 NAG C 601 " 0.142 2.00e-02 2.50e+03 pdb=" O7 NAG C 601 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 380 " -0.094 2.00e-02 2.50e+03 5.01e-02 5.01e+01 pdb=" CG TYR C 380 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 380 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR C 380 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR C 380 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR C 380 " 0.029 2.00e-02 2.50e+03 pdb=" CZ TYR C 380 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 380 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 69 " -0.071 2.00e-02 2.50e+03 4.07e-02 3.31e+01 pdb=" CG TYR B 69 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR B 69 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR B 69 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 69 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR B 69 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR B 69 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 69 " -0.063 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 1409 2.92 - 3.42: 3062 3.42 - 3.91: 5638 3.91 - 4.41: 6166 4.41 - 4.90: 10475 Nonbonded interactions: 26750 Sorted by model distance: nonbonded pdb=" O TYR B 111 " pdb=" OG1 THR C 478 " model vdw 2.431 2.440 nonbonded pdb=" OG1 THR C 333 " pdb=" N ASN C 334 " model vdw 2.451 2.520 nonbonded pdb=" O GLN A 24 " pdb=" N LYS A 42 " model vdw 2.470 2.520 nonbonded pdb=" OH TYR C 453 " pdb=" OE1 GLN C 493 " model vdw 2.482 2.440 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.506 2.440 ... (remaining 26745 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 21.130 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.290 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.013 0.046 3401 Z= 0.832 Angle : 1.648 8.747 4615 Z= 1.119 Chirality : 0.093 0.300 496 Planarity : 0.013 0.098 595 Dihedral : 14.166 87.440 1237 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 1.10 % Allowed : 7.40 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.73 (0.37), residues: 415 helix: -3.89 (0.58), residues: 26 sheet: -1.56 (0.46), residues: 116 loop : -1.77 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.009 TRP C 353 HIS 0.001 0.000 HIS C 519 PHE 0.062 0.008 PHE C 464 TYR 0.094 0.014 TYR C 380 ARG 0.009 0.001 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.7469 (tttt) cc_final: 0.7225 (tttt) REVERT: C 367 VAL cc_start: 0.8406 (t) cc_final: 0.8095 (p) outliers start: 4 outliers final: 0 residues processed: 70 average time/residue: 0.1519 time to fit residues: 13.2136 Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 12 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 62 GLN A 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3401 Z= 0.271 Angle : 0.622 8.502 4615 Z= 0.326 Chirality : 0.044 0.198 496 Planarity : 0.004 0.033 595 Dihedral : 5.644 37.376 488 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.19 % Allowed : 12.60 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.38), residues: 415 helix: -3.66 (0.68), residues: 27 sheet: -1.29 (0.43), residues: 138 loop : -1.01 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 353 HIS 0.001 0.000 HIS A 60 PHE 0.014 0.002 PHE C 497 TYR 0.016 0.002 TYR C 380 ARG 0.003 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 41 LEU cc_start: 0.6445 (mt) cc_final: 0.6242 (mt) REVERT: B 83 SER cc_start: 0.7403 (p) cc_final: 0.7129 (p) REVERT: C 367 VAL cc_start: 0.8410 (t) cc_final: 0.8166 (p) REVERT: C 423 TYR cc_start: 0.8379 (t80) cc_final: 0.8131 (t80) REVERT: C 438 SER cc_start: 0.8620 (m) cc_final: 0.8037 (p) outliers start: 8 outliers final: 4 residues processed: 92 average time/residue: 0.1142 time to fit residues: 13.6838 Evaluate side-chains 86 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 32 optimal weight: 0.0470 chunk 12 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.0030 overall best weight: 0.1246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN C 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 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 : 0.002 0.021 3401 Z= 0.131 Angle : 0.513 6.865 4615 Z= 0.266 Chirality : 0.042 0.203 496 Planarity : 0.004 0.036 595 Dihedral : 4.531 32.593 488 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.19 % Allowed : 18.08 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.40), residues: 415 helix: -2.93 (0.76), residues: 33 sheet: -0.90 (0.42), residues: 147 loop : -0.70 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS A 60 PHE 0.009 0.001 PHE C 497 TYR 0.013 0.001 TYR C 380 ARG 0.002 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 SER cc_start: 0.7394 (p) cc_final: 0.7132 (p) REVERT: C 423 TYR cc_start: 0.8317 (t80) cc_final: 0.8075 (t80) REVERT: C 438 SER cc_start: 0.8447 (m) cc_final: 0.7937 (p) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 0.1059 time to fit residues: 10.5708 Evaluate side-chains 77 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.0060 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 3401 Z= 0.350 Angle : 0.618 9.213 4615 Z= 0.321 Chirality : 0.045 0.220 496 Planarity : 0.004 0.042 595 Dihedral : 5.569 37.725 488 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.01 % Allowed : 16.99 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.39), residues: 415 helix: -2.90 (0.79), residues: 34 sheet: -0.81 (0.42), residues: 144 loop : -0.95 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 55 HIS 0.001 0.000 HIS A 60 PHE 0.013 0.002 PHE A 54 TYR 0.026 0.002 TYR B 111 ARG 0.002 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 HIS cc_start: 0.8530 (OUTLIER) cc_final: 0.8117 (p-80) REVERT: B 83 SER cc_start: 0.8363 (p) cc_final: 0.8050 (p) REVERT: C 353 TRP cc_start: 0.8798 (p-90) cc_final: 0.8254 (p-90) REVERT: C 380 TYR cc_start: 0.7510 (m-80) cc_final: 0.7218 (m-80) REVERT: C 478 THR cc_start: 0.8179 (m) cc_final: 0.7928 (p) outliers start: 11 outliers final: 9 residues processed: 73 average time/residue: 0.1190 time to fit residues: 11.2608 Evaluate side-chains 72 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.0050 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 34 optimal weight: 0.0570 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 overall best weight: 0.1690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3401 Z= 0.138 Angle : 0.518 6.998 4615 Z= 0.260 Chirality : 0.041 0.216 496 Planarity : 0.004 0.038 595 Dihedral : 4.633 33.106 488 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.47 % Allowed : 18.90 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.40), residues: 415 helix: -2.97 (0.74), residues: 34 sheet: -0.80 (0.42), residues: 146 loop : -0.66 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS A 60 PHE 0.007 0.001 PHE C 497 TYR 0.008 0.001 TYR B 106 ARG 0.002 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 353 TRP cc_start: 0.8820 (p-90) cc_final: 0.8241 (p-90) REVERT: C 380 TYR cc_start: 0.7398 (m-80) cc_final: 0.7035 (m-80) REVERT: C 423 TYR cc_start: 0.8483 (t80) cc_final: 0.8020 (t80) REVERT: C 478 THR cc_start: 0.8151 (m) cc_final: 0.7872 (p) outliers start: 9 outliers final: 5 residues processed: 73 average time/residue: 0.1043 time to fit residues: 10.0986 Evaluate side-chains 72 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.6917 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 3401 Z= 0.294 Angle : 0.568 6.869 4615 Z= 0.290 Chirality : 0.043 0.224 496 Planarity : 0.004 0.043 595 Dihedral : 5.207 34.117 488 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.66 % Allowed : 18.63 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.40), residues: 415 helix: -2.98 (0.76), residues: 34 sheet: -0.83 (0.42), residues: 147 loop : -0.83 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 55 HIS 0.001 0.000 HIS A 60 PHE 0.011 0.001 PHE C 400 TYR 0.019 0.002 TYR B 111 ARG 0.002 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.8138 (p-80) REVERT: C 353 TRP cc_start: 0.8823 (p-90) cc_final: 0.8151 (p-90) REVERT: C 380 TYR cc_start: 0.7486 (m-80) cc_final: 0.7187 (m-80) REVERT: C 387 LEU cc_start: 0.7763 (mm) cc_final: 0.7513 (mt) REVERT: C 478 THR cc_start: 0.8095 (m) cc_final: 0.7862 (p) outliers start: 17 outliers final: 13 residues processed: 80 average time/residue: 0.1189 time to fit residues: 12.2534 Evaluate side-chains 78 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.0040 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3401 Z= 0.234 Angle : 0.558 7.256 4615 Z= 0.283 Chirality : 0.043 0.237 496 Planarity : 0.004 0.041 595 Dihedral : 5.112 34.302 488 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.66 % Allowed : 19.18 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.40), residues: 415 helix: -3.17 (0.71), residues: 34 sheet: -0.80 (0.41), residues: 149 loop : -0.83 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.000 0.000 HIS A 60 PHE 0.009 0.001 PHE C 400 TYR 0.012 0.001 TYR B 111 ARG 0.001 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 353 TRP cc_start: 0.8818 (p-90) cc_final: 0.8193 (p-90) REVERT: C 380 TYR cc_start: 0.7468 (m-80) cc_final: 0.7152 (m-80) REVERT: C 387 LEU cc_start: 0.7746 (mm) cc_final: 0.7495 (mt) REVERT: C 438 SER cc_start: 0.8572 (m) cc_final: 0.7795 (p) REVERT: C 478 THR cc_start: 0.8108 (m) cc_final: 0.7835 (p) outliers start: 17 outliers final: 13 residues processed: 88 average time/residue: 0.1288 time to fit residues: 14.5287 Evaluate side-chains 88 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 36 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3401 Z= 0.301 Angle : 0.603 7.718 4615 Z= 0.310 Chirality : 0.044 0.245 496 Planarity : 0.004 0.042 595 Dihedral : 5.360 34.784 488 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.75 % Allowed : 18.63 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.40), residues: 415 helix: -3.20 (0.73), residues: 34 sheet: -0.70 (0.42), residues: 142 loop : -0.95 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 55 HIS 0.001 0.000 HIS A 60 PHE 0.008 0.001 PHE C 497 TYR 0.018 0.002 TYR B 111 ARG 0.006 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 60 HIS cc_start: 0.8394 (OUTLIER) cc_final: 0.8168 (p-80) REVERT: A 109 ASP cc_start: 0.5529 (OUTLIER) cc_final: 0.4907 (p0) REVERT: C 380 TYR cc_start: 0.7488 (m-80) cc_final: 0.7195 (m-80) REVERT: C 387 LEU cc_start: 0.7807 (mm) cc_final: 0.7499 (mt) REVERT: C 423 TYR cc_start: 0.8563 (t80) cc_final: 0.7925 (t80) REVERT: C 438 SER cc_start: 0.8577 (m) cc_final: 0.7789 (p) REVERT: C 478 THR cc_start: 0.8061 (m) cc_final: 0.7821 (p) REVERT: C 506 GLN cc_start: 0.7967 (mt0) cc_final: 0.7527 (mt0) outliers start: 21 outliers final: 15 residues processed: 91 average time/residue: 0.1256 time to fit residues: 14.5512 Evaluate side-chains 91 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0050 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.0170 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 overall best weight: 0.0832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3401 Z= 0.147 Angle : 0.597 7.925 4615 Z= 0.300 Chirality : 0.043 0.239 496 Planarity : 0.004 0.036 595 Dihedral : 4.842 29.537 488 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.34 % Favored : 95.42 % Rotamer: Outliers : 2.47 % Allowed : 21.92 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.39), residues: 415 helix: -3.35 (0.64), residues: 34 sheet: -0.65 (0.40), residues: 142 loop : -0.67 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 55 HIS 0.001 0.000 HIS A 60 PHE 0.013 0.001 PHE A 99 TYR 0.007 0.001 TYR B 106 ARG 0.009 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: C 380 TYR cc_start: 0.7390 (m-80) cc_final: 0.7054 (m-80) REVERT: C 387 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7368 (mt) REVERT: C 393 THR cc_start: 0.8611 (m) cc_final: 0.8354 (t) REVERT: C 423 TYR cc_start: 0.8357 (t80) cc_final: 0.7894 (t80) REVERT: C 438 SER cc_start: 0.8173 (m) cc_final: 0.7847 (p) REVERT: C 478 THR cc_start: 0.8020 (m) cc_final: 0.7714 (p) outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 0.1147 time to fit residues: 11.5789 Evaluate side-chains 75 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C 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: 0.7980 chunk 29 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.0980 chunk 1 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3401 Z= 0.268 Angle : 0.695 13.162 4615 Z= 0.345 Chirality : 0.048 0.372 496 Planarity : 0.004 0.034 595 Dihedral : 5.193 35.369 488 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.06 % Favored : 94.70 % Rotamer: Outliers : 3.29 % Allowed : 21.37 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.40), residues: 415 helix: -3.27 (0.67), residues: 34 sheet: -0.82 (0.40), residues: 149 loop : -0.75 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP A 55 HIS 0.001 0.000 HIS A 60 PHE 0.012 0.001 PHE A 54 TYR 0.015 0.002 TYR B 111 ARG 0.003 0.000 ARG C 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 109 ASP cc_start: 0.5496 (OUTLIER) cc_final: 0.5111 (p0) REVERT: A 128 TRP cc_start: 0.7880 (m100) cc_final: 0.7671 (m100) REVERT: B 65 LYS cc_start: 0.7394 (tptt) cc_final: 0.7108 (tptt) REVERT: C 380 TYR cc_start: 0.7488 (m-80) cc_final: 0.7137 (m-80) REVERT: C 387 LEU cc_start: 0.7794 (mm) cc_final: 0.7478 (mt) REVERT: C 423 TYR cc_start: 0.8431 (t80) cc_final: 0.7966 (t80) REVERT: C 438 SER cc_start: 0.8406 (m) cc_final: 0.7863 (p) REVERT: C 478 THR cc_start: 0.7999 (m) cc_final: 0.7690 (p) REVERT: C 506 GLN cc_start: 0.7849 (mt0) cc_final: 0.7046 (mt0) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.1373 time to fit residues: 13.7978 Evaluate side-chains 78 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C 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: 0.2980 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.0040 chunk 39 optimal weight: 0.6980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.161084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.134971 restraints weight = 5711.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.139001 restraints weight = 3012.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.141568 restraints weight = 1878.167| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3401 Z= 0.242 Angle : 0.721 14.056 4615 Z= 0.351 Chirality : 0.046 0.247 496 Planarity : 0.004 0.037 595 Dihedral : 5.125 34.460 488 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.10 % Favored : 95.66 % Rotamer: Outliers : 3.84 % Allowed : 22.19 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.40), residues: 415 helix: -3.28 (0.67), residues: 34 sheet: -0.79 (0.41), residues: 149 loop : -0.76 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.004 TRP A 55 HIS 0.000 0.000 HIS A 60 PHE 0.011 0.001 PHE A 54 TYR 0.010 0.001 TYR B 111 ARG 0.001 0.000 ARG A 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1499.73 seconds wall clock time: 27 minutes 52.23 seconds (1672.23 seconds total)