Starting phenix.real_space_refine on Thu Jul 18 19:48:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/07_2024/7wlc_32581.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/07_2024/7wlc_32581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/07_2024/7wlc_32581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/07_2024/7wlc_32581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/07_2024/7wlc_32581.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/07_2024/7wlc_32581.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2094 2.51 5 N 563 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3307 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 187} Chain: "H" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 892 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.35, per 1000 atoms: 0.71 Number of scatterers: 3307 At special positions: 0 Unit cell: (53.04, 80.08, 95.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 636 8.00 N 563 7.00 C 2094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 604.8 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 8.8% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.781A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 386 through 389 removed outlier: 3.657A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 386 through 389' Processing helix chain 'E' and resid 405 through 411 removed outlier: 4.535A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA E 411 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.569A pdb=" N ASN E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.730A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.730A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 391 through 392 removed outlier: 3.634A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 453 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.789A pdb=" N GLU H 10 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA H 118 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.625A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA9, first strand: chain 'L' and resid 18 through 23 100 hydrogen bonds defined for protein. 237 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: 0.77 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1071 1.34 - 1.47: 889 1.47 - 1.59: 1416 1.59 - 1.71: 0 1.71 - 1.84: 16 Bond restraints: 3392 Sorted by residual: bond pdb=" CB LYS H 13 " pdb=" CG LYS H 13 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB ASN E 448 " pdb=" CG ASN E 448 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" N GLY H 112 " pdb=" CA GLY H 112 " ideal model delta sigma weight residual 1.444 1.454 -0.010 9.60e-03 1.09e+04 9.95e-01 bond pdb=" C ASN E 331 " pdb=" N ILE E 332 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.40e-02 5.10e+03 9.85e-01 bond pdb=" CG LYS H 13 " pdb=" CD LYS H 13 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.82e-01 ... (remaining 3387 not shown) Histogram of bond angle deviations from ideal: 102.09 - 108.48: 187 108.48 - 114.87: 1827 114.87 - 121.26: 1591 121.26 - 127.65: 979 127.65 - 134.04: 30 Bond angle restraints: 4614 Sorted by residual: angle pdb=" C ASN E 331 " pdb=" N ILE E 332 " pdb=" CA ILE E 332 " ideal model delta sigma weight residual 121.70 128.16 -6.46 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA MET H 81 " pdb=" CB MET H 81 " pdb=" CG MET H 81 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CB LYS H 13 " pdb=" CG LYS H 13 " pdb=" CD LYS H 13 " ideal model delta sigma weight residual 111.30 119.20 -7.90 2.30e+00 1.89e-01 1.18e+01 angle pdb=" CB MET H 81 " pdb=" CG MET H 81 " pdb=" SD MET H 81 " ideal model delta sigma weight residual 112.70 103.11 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CA TRP H 111 " pdb=" CB TRP H 111 " pdb=" CG TRP H 111 " ideal model delta sigma weight residual 113.60 119.66 -6.06 1.90e+00 2.77e-01 1.02e+01 ... (remaining 4609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 1779 15.37 - 30.74: 175 30.74 - 46.11: 29 46.11 - 61.48: 13 61.48 - 76.85: 8 Dihedral angle restraints: 2004 sinusoidal: 768 harmonic: 1236 Sorted by residual: dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 28.64 64.36 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS E 336 " pdb=" SG CYS E 336 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual 93.00 34.26 58.74 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CA MET H 81 " pdb=" C MET H 81 " pdb=" N GLU H 82 " pdb=" CA GLU H 82 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 2001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 244 0.028 - 0.056: 160 0.056 - 0.084: 57 0.084 - 0.111: 25 0.111 - 0.139: 11 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA ILE H 70 " pdb=" N ILE H 70 " pdb=" C ILE H 70 " pdb=" CB ILE H 70 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO E 373 " pdb=" N PRO E 373 " pdb=" C PRO E 373 " pdb=" CB PRO E 373 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE L 76 " pdb=" N ILE L 76 " pdb=" C ILE L 76 " pdb=" CB ILE L 76 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 494 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 59 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO L 60 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 111 " -0.015 2.00e-02 2.50e+03 9.52e-03 2.27e+00 pdb=" CG TRP H 111 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP H 111 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP H 111 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 111 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 111 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 111 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 111 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 111 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 111 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS E 336 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO E 337 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 337 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 337 " 0.019 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 234 2.74 - 3.28: 3348 3.28 - 3.82: 5244 3.82 - 4.36: 5995 4.36 - 4.90: 10460 Nonbonded interactions: 25281 Sorted by model distance: nonbonded pdb=" O ASN E 448 " pdb=" OG SER E 494 " model vdw 2.198 2.440 nonbonded pdb=" NZ LYS H 23 " pdb=" O THR H 76 " model vdw 2.242 2.520 nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 115 " model vdw 2.263 2.440 nonbonded pdb=" O TYR H 108 " pdb=" OH TYR L 37 " model vdw 2.264 2.440 nonbonded pdb=" O ARG H 67 " pdb=" OG SER H 84 " model vdw 2.271 2.440 ... (remaining 25276 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: 0.020 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.390 Find NCS groups from input model: 0.050 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3392 Z= 0.193 Angle : 0.701 9.586 4614 Z= 0.378 Chirality : 0.044 0.139 497 Planarity : 0.005 0.039 601 Dihedral : 13.708 76.851 1202 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.35 (0.42), residues: 424 helix: -3.38 (0.98), residues: 18 sheet: 0.25 (0.50), residues: 131 loop : -1.37 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 111 HIS 0.001 0.000 HIS H 110 PHE 0.021 0.002 PHE E 497 TYR 0.018 0.001 TYR E 351 ARG 0.006 0.000 ARG E 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 392 PHE cc_start: 0.8997 (m-80) cc_final: 0.8779 (m-80) REVERT: E 467 ASP cc_start: 0.7961 (t70) cc_final: 0.7735 (t0) REVERT: H 29 PHE cc_start: 0.7613 (t80) cc_final: 0.7264 (t80) REVERT: H 67 ARG cc_start: 0.8905 (ptp-170) cc_final: 0.8544 (ttp-110) REVERT: L 39 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7662 (tp-100) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1647 time to fit residues: 19.1832 Evaluate side-chains 80 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 50.0000 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 chunk 24 optimal weight: 50.0000 chunk 38 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3392 Z= 0.183 Angle : 0.681 10.150 4614 Z= 0.347 Chirality : 0.046 0.152 497 Planarity : 0.005 0.039 601 Dihedral : 5.375 19.361 471 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.67 % Allowed : 14.48 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.28 (0.41), residues: 424 helix: -3.47 (1.27), residues: 12 sheet: 0.30 (0.49), residues: 131 loop : -1.38 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 111 HIS 0.002 0.001 HIS H 110 PHE 0.025 0.002 PHE E 429 TYR 0.014 0.002 TYR E 449 ARG 0.005 0.000 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7725 (t80) cc_final: 0.7277 (t80) REVERT: H 67 ARG cc_start: 0.8809 (ptp-170) cc_final: 0.8521 (ttp-110) REVERT: L 36 TRP cc_start: 0.7347 (m100) cc_final: 0.6980 (m100) REVERT: L 39 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7625 (tp-100) outliers start: 6 outliers final: 4 residues processed: 83 average time/residue: 0.1853 time to fit residues: 18.4086 Evaluate side-chains 79 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 94 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.0170 chunk 25 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 50.0000 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 50.0000 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 30 optimal weight: 50.0000 chunk 28 optimal weight: 50.0000 chunk 19 optimal weight: 20.0000 overall best weight: 6.2028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3392 Z= 0.211 Angle : 0.673 10.164 4614 Z= 0.340 Chirality : 0.046 0.151 497 Planarity : 0.004 0.041 601 Dihedral : 5.383 19.384 471 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.51 % Allowed : 15.04 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.38 (0.41), residues: 424 helix: -3.95 (0.95), residues: 18 sheet: 0.34 (0.45), residues: 145 loop : -1.50 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.013 0.002 PHE H 64 TYR 0.013 0.001 TYR E 365 ARG 0.003 0.000 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7796 (t80) cc_final: 0.7387 (t80) REVERT: H 67 ARG cc_start: 0.8796 (ptp-170) cc_final: 0.8510 (ttp-110) REVERT: L 36 TRP cc_start: 0.7392 (m100) cc_final: 0.7125 (m100) REVERT: L 46 LYS cc_start: 0.9259 (tppp) cc_final: 0.8991 (tppp) outliers start: 9 outliers final: 8 residues processed: 82 average time/residue: 0.1887 time to fit residues: 18.4691 Evaluate side-chains 85 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 40.0000 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 50.0000 chunk 20 optimal weight: 30.0000 chunk 36 optimal weight: 0.0010 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 23 optimal weight: 50.0000 chunk 0 optimal weight: 30.0000 overall best weight: 9.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3392 Z= 0.270 Angle : 0.704 10.512 4614 Z= 0.363 Chirality : 0.046 0.138 497 Planarity : 0.005 0.042 601 Dihedral : 5.617 19.966 471 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.46 % Allowed : 17.27 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.40), residues: 424 helix: -3.37 (1.40), residues: 12 sheet: 0.23 (0.46), residues: 139 loop : -1.66 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.018 0.002 PHE E 338 TYR 0.011 0.002 TYR E 423 ARG 0.004 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 474 GLN cc_start: 0.2838 (pp30) cc_final: 0.2527 (pp30) REVERT: H 29 PHE cc_start: 0.7966 (t80) cc_final: 0.7512 (t80) REVERT: H 67 ARG cc_start: 0.8849 (ptp-170) cc_final: 0.8626 (ttp-110) REVERT: L 39 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7499 (tp-100) REVERT: L 46 LYS cc_start: 0.9353 (tppp) cc_final: 0.9147 (tppp) REVERT: L 93 ASP cc_start: 0.7709 (t0) cc_final: 0.7492 (t0) outliers start: 16 outliers final: 13 residues processed: 85 average time/residue: 0.2022 time to fit residues: 19.9680 Evaluate side-chains 92 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 40.0000 chunk 16 optimal weight: 30.0000 chunk 34 optimal weight: 0.0270 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 50.0000 overall best weight: 5.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 394 ASN ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3392 Z= 0.197 Angle : 0.676 10.509 4614 Z= 0.343 Chirality : 0.045 0.139 497 Planarity : 0.004 0.042 601 Dihedral : 5.396 19.899 471 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.18 % Allowed : 19.22 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.43 (0.41), residues: 424 helix: -3.34 (1.38), residues: 12 sheet: 0.16 (0.46), residues: 141 loop : -1.53 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 111 HIS 0.004 0.001 HIS H 110 PHE 0.012 0.002 PHE H 64 TYR 0.012 0.001 TYR L 86 ARG 0.006 0.000 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 392 PHE cc_start: 0.8963 (m-80) cc_final: 0.8739 (m-10) REVERT: E 474 GLN cc_start: 0.2882 (pp30) cc_final: 0.2470 (pp30) REVERT: H 29 PHE cc_start: 0.7871 (t80) cc_final: 0.7459 (t80) REVERT: H 67 ARG cc_start: 0.8836 (ptp-170) cc_final: 0.8601 (ttp-110) REVERT: L 39 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7395 (tp-100) outliers start: 15 outliers final: 14 residues processed: 83 average time/residue: 0.1855 time to fit residues: 18.1163 Evaluate side-chains 94 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 50.0000 chunk 33 optimal weight: 30.0000 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 50.0000 chunk 39 optimal weight: 50.0000 chunk 4 optimal weight: 7.9990 chunk 23 optimal weight: 50.0000 chunk 29 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3392 Z= 0.218 Angle : 0.685 10.576 4614 Z= 0.347 Chirality : 0.045 0.137 497 Planarity : 0.005 0.042 601 Dihedral : 5.439 20.361 471 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.90 % Allowed : 23.40 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: 424 helix: -3.44 (1.33), residues: 12 sheet: 0.06 (0.46), residues: 141 loop : -1.58 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 111 HIS 0.004 0.001 HIS H 110 PHE 0.013 0.002 PHE E 338 TYR 0.009 0.001 TYR L 86 ARG 0.007 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7839 (t80) cc_final: 0.7390 (t80) REVERT: H 48 MET cc_start: 0.8387 (mmp) cc_final: 0.7669 (mmm) REVERT: H 67 ARG cc_start: 0.8811 (ptp-170) cc_final: 0.8586 (ttp-110) outliers start: 14 outliers final: 13 residues processed: 81 average time/residue: 0.1908 time to fit residues: 17.9851 Evaluate side-chains 90 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 50.0000 chunk 34 optimal weight: 50.0000 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 40.0000 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 16 optimal weight: 40.0000 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 40.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3392 Z= 0.233 Angle : 0.674 8.381 4614 Z= 0.346 Chirality : 0.045 0.151 497 Planarity : 0.005 0.043 601 Dihedral : 5.447 19.357 471 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.18 % Allowed : 23.68 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: 424 helix: -3.43 (1.34), residues: 12 sheet: -0.05 (0.46), residues: 140 loop : -1.54 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 111 HIS 0.003 0.001 HIS H 110 PHE 0.014 0.002 PHE E 338 TYR 0.014 0.001 TYR E 351 ARG 0.006 0.000 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7851 (t80) cc_final: 0.7329 (t80) REVERT: H 48 MET cc_start: 0.8218 (mmp) cc_final: 0.7531 (mmm) REVERT: H 67 ARG cc_start: 0.8825 (ptp-170) cc_final: 0.8597 (ttp-110) outliers start: 15 outliers final: 14 residues processed: 83 average time/residue: 0.1882 time to fit residues: 18.2062 Evaluate side-chains 89 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 40.0000 chunk 38 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 50.0000 chunk 16 optimal weight: 40.0000 chunk 29 optimal weight: 30.0000 chunk 11 optimal weight: 0.0040 chunk 34 optimal weight: 5.9990 overall best weight: 5.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3392 Z= 0.199 Angle : 0.661 7.510 4614 Z= 0.338 Chirality : 0.045 0.140 497 Planarity : 0.004 0.043 601 Dihedral : 5.351 19.711 471 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.46 % Allowed : 23.96 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.55 (0.40), residues: 424 helix: -3.42 (1.33), residues: 12 sheet: -0.08 (0.46), residues: 140 loop : -1.51 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 111 HIS 0.004 0.001 HIS H 110 PHE 0.011 0.002 PHE E 338 TYR 0.010 0.001 TYR L 86 ARG 0.008 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7830 (t80) cc_final: 0.7217 (t80) REVERT: H 48 MET cc_start: 0.8117 (mmp) cc_final: 0.7700 (mmm) REVERT: H 67 ARG cc_start: 0.8797 (ptp-170) cc_final: 0.8534 (ttp-110) outliers start: 16 outliers final: 13 residues processed: 81 average time/residue: 0.1834 time to fit residues: 17.5473 Evaluate side-chains 88 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 33 optimal weight: 40.0000 chunk 3 optimal weight: 30.0000 chunk 25 optimal weight: 50.0000 overall best weight: 6.5188 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3392 Z= 0.215 Angle : 0.675 7.304 4614 Z= 0.347 Chirality : 0.046 0.151 497 Planarity : 0.005 0.043 601 Dihedral : 5.404 21.743 471 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.74 % Allowed : 23.96 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: 424 helix: -3.55 (1.27), residues: 12 sheet: -0.09 (0.46), residues: 140 loop : -1.52 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 111 HIS 0.004 0.001 HIS H 110 PHE 0.018 0.002 PHE E 374 TYR 0.021 0.002 TYR E 351 ARG 0.008 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7908 (t80) cc_final: 0.7319 (t80) REVERT: H 48 MET cc_start: 0.8119 (mmp) cc_final: 0.7528 (mmm) REVERT: H 67 ARG cc_start: 0.8798 (ptp-170) cc_final: 0.8421 (ptp90) outliers start: 17 outliers final: 15 residues processed: 82 average time/residue: 0.1931 time to fit residues: 18.5915 Evaluate side-chains 92 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 0.0050 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 50.0000 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 33 optimal weight: 30.0000 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3392 Z= 0.183 Angle : 0.668 7.080 4614 Z= 0.343 Chirality : 0.045 0.148 497 Planarity : 0.004 0.042 601 Dihedral : 5.258 22.933 471 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.90 % Allowed : 25.07 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.50 (0.41), residues: 424 helix: -3.64 (0.87), residues: 20 sheet: -0.08 (0.48), residues: 132 loop : -1.30 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 111 HIS 0.003 0.001 HIS H 110 PHE 0.021 0.002 PHE E 374 TYR 0.024 0.002 TYR E 351 ARG 0.008 0.001 ARG L 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7767 (t80) cc_final: 0.7044 (t80) REVERT: H 48 MET cc_start: 0.8122 (mmp) cc_final: 0.7599 (mmm) REVERT: H 67 ARG cc_start: 0.8785 (ptp-170) cc_final: 0.8499 (ttp-110) outliers start: 14 outliers final: 12 residues processed: 85 average time/residue: 0.1904 time to fit residues: 19.0662 Evaluate side-chains 90 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 28 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 40.0000 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.131361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.103409 restraints weight = 9218.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.106031 restraints weight = 5534.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.107863 restraints weight = 3970.496| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3392 Z= 0.256 Angle : 0.701 7.376 4614 Z= 0.366 Chirality : 0.046 0.146 497 Planarity : 0.004 0.044 601 Dihedral : 5.566 21.595 471 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 3.34 % Allowed : 26.18 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.65 (0.40), residues: 424 helix: -3.62 (0.97), residues: 18 sheet: -0.16 (0.46), residues: 140 loop : -1.49 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 111 HIS 0.003 0.001 HIS H 110 PHE 0.031 0.003 PHE E 497 TYR 0.019 0.002 TYR E 351 ARG 0.003 0.000 ARG L 17 =============================================================================== Job complete usr+sys time: 1012.73 seconds wall clock time: 21 minutes 5.24 seconds (1265.24 seconds total)