Starting phenix.real_space_refine on Tue Feb 13 04:35:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gsb_34228/02_2024/8gsb_34228.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gsb_34228/02_2024/8gsb_34228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gsb_34228/02_2024/8gsb_34228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gsb_34228/02_2024/8gsb_34228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gsb_34228/02_2024/8gsb_34228.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gsb_34228/02_2024/8gsb_34228.pdb" } resolution = 3.99 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= -0.002 sd= 0.038 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 16 5.16 5 C 2001 2.51 5 N 544 2.21 5 O 596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "K GLU 17": "OE1" <-> "OE2" 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: 3157 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1404 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain breaks: 1 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "K" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 2.18, per 1000 atoms: 0.69 Number of scatterers: 3157 At special positions: 0 Unit cell: (78.306, 60.624, 95.988, 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 16 16.00 O 596 8.00 N 544 7.00 C 2001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 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: 1.17 Conformation dependent library (CDL) restraints added in 503.9 milliseconds 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 4.2% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.238A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 379 removed outlier: 3.751A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 379 removed outlier: 3.751A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.632A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.743A pdb=" N THR H 120 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.743A pdb=" N THR H 120 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.527A pdb=" N THR K 66 " --> pdb=" O THR K 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AA9, first strand: chain 'K' and resid 54 through 55 removed outlier: 6.456A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 204 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: 0.70 Time building geometry restraints manager: 1.27 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: 1010 1.34 - 1.46: 819 1.46 - 1.58: 1389 1.58 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3237 Sorted by residual: bond pdb=" C PRO K 81 " pdb=" N GLU K 82 " ideal model delta sigma weight residual 1.334 1.280 0.054 1.38e-02 5.25e+03 1.54e+01 bond pdb=" C LEU K 74 " pdb=" N THR K 75 " ideal model delta sigma weight residual 1.331 1.388 -0.057 1.55e-02 4.16e+03 1.33e+01 bond pdb=" C GLN K 90 " pdb=" N GLN K 91 " ideal model delta sigma weight residual 1.330 1.378 -0.048 1.39e-02 5.18e+03 1.19e+01 bond pdb=" C ALA A 419 " pdb=" N ASP A 420 " ideal model delta sigma weight residual 1.333 1.290 0.043 1.51e-02 4.39e+03 8.15e+00 bond pdb=" C GLU H 46 " pdb=" N TRP H 47 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.31e-02 5.83e+03 7.24e+00 ... (remaining 3232 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.11: 95 107.11 - 113.89: 1695 113.89 - 120.68: 1321 120.68 - 127.47: 1246 127.47 - 134.26: 37 Bond angle restraints: 4394 Sorted by residual: angle pdb=" N GLN K 91 " pdb=" CA GLN K 91 " pdb=" C GLN K 91 " ideal model delta sigma weight residual 109.24 100.32 8.92 1.63e+00 3.76e-01 3.00e+01 angle pdb=" N VAL A 341 " pdb=" CA VAL A 341 " pdb=" C VAL A 341 " ideal model delta sigma weight residual 109.34 117.51 -8.17 2.08e+00 2.31e-01 1.54e+01 angle pdb=" N GLY A 476 " pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 113.18 104.87 8.31 2.37e+00 1.78e-01 1.23e+01 angle pdb=" N PHE A 400 " pdb=" CA PHE A 400 " pdb=" C PHE A 400 " ideal model delta sigma weight residual 108.99 114.35 -5.36 1.57e+00 4.06e-01 1.17e+01 angle pdb=" N GLN A 474 " pdb=" CA GLN A 474 " pdb=" C GLN A 474 " ideal model delta sigma weight residual 110.80 118.07 -7.27 2.13e+00 2.20e-01 1.16e+01 ... (remaining 4389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 1655 14.28 - 28.56: 186 28.56 - 42.85: 46 42.85 - 57.13: 16 57.13 - 71.41: 4 Dihedral angle restraints: 1907 sinusoidal: 752 harmonic: 1155 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 154.88 -61.88 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CA ALA A 475 " pdb=" C ALA A 475 " pdb=" N GLY A 476 " pdb=" CA GLY A 476 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CB CYS H 101 " pdb=" SG CYS H 101 " pdb=" SG CYS H 106 " pdb=" CB CYS H 106 " ideal model delta sinusoidal sigma weight residual 93.00 133.22 -40.22 1 1.00e+01 1.00e-02 2.27e+01 ... (remaining 1904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 385 0.052 - 0.104: 61 0.104 - 0.156: 20 0.156 - 0.207: 0 0.207 - 0.259: 1 Chirality restraints: 467 Sorted by residual: chirality pdb=" CA GLN A 474 " pdb=" N GLN A 474 " pdb=" C GLN A 474 " pdb=" CB GLN A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL A 511 " pdb=" N VAL A 511 " pdb=" C VAL A 511 " pdb=" CB VAL A 511 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL H 119 " pdb=" N VAL H 119 " pdb=" C VAL H 119 " pdb=" CB VAL H 119 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 464 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 44 " -0.181 9.50e-02 1.11e+02 8.12e-02 4.43e+00 pdb=" NE ARG H 44 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG H 44 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG H 44 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 44 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER K 7 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO K 8 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 8 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 8 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 492 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C LEU A 492 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU A 492 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 493 " 0.011 2.00e-02 2.50e+03 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1168 2.85 - 3.36: 2819 3.36 - 3.88: 4750 3.88 - 4.39: 5283 4.39 - 4.90: 9213 Nonbonded interactions: 23233 Sorted by model distance: nonbonded pdb=" O GLY H 26 " pdb=" OG1 THR H 30 " model vdw 2.338 2.440 nonbonded pdb=" O GLN A 474 " pdb=" O ASN A 487 " model vdw 2.372 3.040 nonbonded pdb=" O SER A 514 " pdb=" OG SER A 514 " model vdw 2.395 2.440 nonbonded pdb=" O ASP K 61 " pdb=" OD1 ASP K 61 " model vdw 2.406 3.040 nonbonded pdb=" O ASP A 339 " pdb=" OD1 ASP A 339 " model vdw 2.414 3.040 ... (remaining 23228 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.690 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.690 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.004 0.057 3237 Z= 0.253 Angle : 0.728 8.922 4394 Z= 0.429 Chirality : 0.045 0.259 467 Planarity : 0.005 0.081 569 Dihedral : 13.337 71.409 1158 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.42 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.84 (0.42), residues: 392 helix: -3.19 (1.17), residues: 8 sheet: -0.89 (0.49), residues: 119 loop : -1.36 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 97 HIS 0.001 0.001 HIS A 505 PHE 0.011 0.001 PHE A 486 TYR 0.027 0.002 TYR K 92 ARG 0.011 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.339 Fit side-chains REVERT: A 474 GLN cc_start: 0.7006 (tp-100) cc_final: 0.6603 (tp-100) REVERT: H 47 TRP cc_start: 0.8813 (t60) cc_final: 0.8193 (t60) REVERT: K 8 PRO cc_start: 0.8518 (Cg_exo) cc_final: 0.8288 (Cg_endo) REVERT: K 33 TYR cc_start: 0.7996 (m-10) cc_final: 0.7765 (m-10) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2345 time to fit residues: 20.5683 Evaluate side-chains 64 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3237 Z= 0.272 Angle : 0.632 8.984 4394 Z= 0.337 Chirality : 0.044 0.147 467 Planarity : 0.004 0.042 569 Dihedral : 5.171 24.611 447 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.04 % Allowed : 9.62 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.71 (0.42), residues: 392 helix: -4.14 (0.87), residues: 14 sheet: -0.74 (0.46), residues: 132 loop : -1.17 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 97 HIS 0.002 0.001 HIS H 100 PHE 0.013 0.002 PHE A 392 TYR 0.027 0.002 TYR K 92 ARG 0.005 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.336 Fit side-chains REVERT: H 47 TRP cc_start: 0.8757 (t60) cc_final: 0.8234 (t60) REVERT: H 57 ASN cc_start: 0.8345 (t0) cc_final: 0.7887 (t0) REVERT: H 69 THR cc_start: 0.8871 (m) cc_final: 0.8627 (p) REVERT: K 106 GLU cc_start: 0.6908 (pm20) cc_final: 0.6668 (pm20) outliers start: 7 outliers final: 3 residues processed: 75 average time/residue: 0.1986 time to fit residues: 17.4244 Evaluate side-chains 65 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain K residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8036 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3237 Z= 0.248 Angle : 0.601 8.298 4394 Z= 0.321 Chirality : 0.044 0.137 467 Planarity : 0.004 0.034 569 Dihedral : 5.055 25.735 447 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.21 % Allowed : 12.83 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.68 (0.41), residues: 392 helix: -4.22 (0.84), residues: 15 sheet: -0.71 (0.45), residues: 135 loop : -1.14 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 36 HIS 0.001 0.000 HIS H 100 PHE 0.010 0.001 PHE A 490 TYR 0.034 0.002 TYR K 92 ARG 0.005 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8325 (m-30) cc_final: 0.7970 (m-30) REVERT: H 47 TRP cc_start: 0.8753 (t60) cc_final: 0.8293 (t60) REVERT: H 57 ASN cc_start: 0.8306 (t0) cc_final: 0.7912 (t0) REVERT: H 69 THR cc_start: 0.8912 (m) cc_final: 0.8679 (p) REVERT: K 80 GLU cc_start: 0.8239 (mp0) cc_final: 0.7927 (mp0) outliers start: 11 outliers final: 8 residues processed: 73 average time/residue: 0.1996 time to fit residues: 16.9568 Evaluate side-chains 67 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.0070 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.0170 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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: 0.7936 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3237 Z= 0.153 Angle : 0.555 8.228 4394 Z= 0.291 Chirality : 0.042 0.132 467 Planarity : 0.004 0.034 569 Dihedral : 4.484 22.616 447 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.21 % Allowed : 14.29 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.40 (0.41), residues: 392 helix: -4.14 (0.93), residues: 15 sheet: -0.50 (0.45), residues: 129 loop : -0.94 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS A 505 PHE 0.009 0.001 PHE A 392 TYR 0.022 0.001 TYR K 92 ARG 0.006 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8269 (m-30) cc_final: 0.7946 (m-30) REVERT: H 47 TRP cc_start: 0.8603 (t60) cc_final: 0.8153 (t60) REVERT: H 57 ASN cc_start: 0.8062 (t0) cc_final: 0.7610 (t0) REVERT: H 74 MET cc_start: 0.7294 (mmm) cc_final: 0.6957 (mmm) REVERT: K 80 GLU cc_start: 0.8197 (mp0) cc_final: 0.7793 (mp0) outliers start: 11 outliers final: 7 residues processed: 80 average time/residue: 0.1858 time to fit residues: 17.4932 Evaluate side-chains 69 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8047 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3237 Z= 0.246 Angle : 0.592 8.236 4394 Z= 0.315 Chirality : 0.043 0.141 467 Planarity : 0.004 0.033 569 Dihedral : 4.806 22.679 447 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.79 % Allowed : 17.20 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.41), residues: 392 helix: -4.28 (0.78), residues: 15 sheet: -0.58 (0.45), residues: 134 loop : -1.09 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 36 HIS 0.001 0.000 HIS H 100 PHE 0.010 0.002 PHE A 400 TYR 0.022 0.002 TYR K 92 ARG 0.006 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8317 (m-30) cc_final: 0.7880 (m-30) REVERT: A 474 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7426 (tm-30) REVERT: H 47 TRP cc_start: 0.8859 (t60) cc_final: 0.8562 (t60) REVERT: H 57 ASN cc_start: 0.8274 (t0) cc_final: 0.7903 (t0) outliers start: 13 outliers final: 11 residues processed: 71 average time/residue: 0.1896 time to fit residues: 15.8903 Evaluate side-chains 69 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.0170 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3237 Z= 0.157 Angle : 0.568 7.987 4394 Z= 0.294 Chirality : 0.042 0.133 467 Planarity : 0.004 0.035 569 Dihedral : 4.492 22.667 447 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.92 % Allowed : 18.66 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.42), residues: 392 helix: -4.24 (0.82), residues: 15 sheet: -0.49 (0.46), residues: 134 loop : -1.01 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.000 HIS A 505 PHE 0.006 0.001 PHE A 486 TYR 0.016 0.001 TYR K 92 ARG 0.006 0.000 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8259 (m-30) cc_final: 0.7894 (m-30) REVERT: A 474 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7192 (tm-30) REVERT: H 47 TRP cc_start: 0.8766 (t60) cc_final: 0.8350 (t60) REVERT: H 57 ASN cc_start: 0.8108 (t0) cc_final: 0.7741 (t0) outliers start: 10 outliers final: 7 residues processed: 74 average time/residue: 0.1865 time to fit residues: 16.1438 Evaluate side-chains 74 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3237 Z= 0.176 Angle : 0.561 7.774 4394 Z= 0.293 Chirality : 0.042 0.131 467 Planarity : 0.004 0.033 569 Dihedral : 4.471 22.474 447 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.50 % Allowed : 18.08 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.43 (0.42), residues: 392 helix: -4.27 (0.78), residues: 15 sheet: -0.43 (0.46), residues: 134 loop : -1.02 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 36 HIS 0.000 0.000 HIS A 505 PHE 0.007 0.001 PHE A 392 TYR 0.020 0.001 TYR K 92 ARG 0.006 0.000 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8275 (m-30) cc_final: 0.7888 (m-30) REVERT: A 474 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7253 (tm-30) REVERT: H 47 TRP cc_start: 0.8828 (t60) cc_final: 0.8354 (t60) REVERT: H 57 ASN cc_start: 0.8123 (t0) cc_final: 0.7783 (t0) REVERT: K 39 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7988 (tt0) outliers start: 12 outliers final: 8 residues processed: 73 average time/residue: 0.2098 time to fit residues: 17.8981 Evaluate side-chains 74 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3237 Z= 0.296 Angle : 0.612 8.090 4394 Z= 0.325 Chirality : 0.044 0.144 467 Planarity : 0.004 0.033 569 Dihedral : 4.918 23.612 447 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.21 % Allowed : 18.66 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.46 (0.42), residues: 392 helix: -4.39 (0.69), residues: 15 sheet: -0.49 (0.48), residues: 129 loop : -1.00 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 36 HIS 0.001 0.001 HIS H 100 PHE 0.015 0.002 PHE A 400 TYR 0.021 0.002 TYR K 92 ARG 0.007 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 474 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7423 (tm-30) REVERT: H 57 ASN cc_start: 0.8328 (t0) cc_final: 0.8055 (t0) outliers start: 11 outliers final: 10 residues processed: 72 average time/residue: 0.2004 time to fit residues: 16.7777 Evaluate side-chains 73 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.0170 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3237 Z= 0.168 Angle : 0.598 9.393 4394 Z= 0.310 Chirality : 0.042 0.127 467 Planarity : 0.004 0.035 569 Dihedral : 4.626 23.216 447 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.92 % Allowed : 19.24 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.32 (0.43), residues: 392 helix: -3.85 (0.85), residues: 21 sheet: -0.24 (0.48), residues: 132 loop : -0.96 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.001 0.000 HIS A 505 PHE 0.008 0.001 PHE K 72 TYR 0.016 0.001 TYR K 92 ARG 0.007 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8322 (m-30) cc_final: 0.7995 (m-30) REVERT: A 474 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7349 (tm-30) REVERT: H 57 ASN cc_start: 0.8179 (t0) cc_final: 0.7880 (t0) outliers start: 10 outliers final: 9 residues processed: 73 average time/residue: 0.1995 time to fit residues: 16.9898 Evaluate side-chains 74 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3237 Z= 0.243 Angle : 0.626 9.124 4394 Z= 0.328 Chirality : 0.044 0.158 467 Planarity : 0.004 0.034 569 Dihedral : 4.807 23.779 447 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.50 % Allowed : 19.24 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.38 (0.43), residues: 392 helix: -3.89 (0.89), residues: 21 sheet: -0.36 (0.48), residues: 127 loop : -0.93 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 36 HIS 0.001 0.000 HIS H 100 PHE 0.011 0.002 PHE A 400 TYR 0.019 0.001 TYR K 92 ARG 0.007 0.001 ARG H 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8334 (m-30) cc_final: 0.7982 (m-30) REVERT: A 474 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7428 (tm-30) REVERT: H 57 ASN cc_start: 0.8261 (t0) cc_final: 0.8033 (t0) REVERT: K 39 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8033 (tt0) outliers start: 12 outliers final: 11 residues processed: 71 average time/residue: 0.1962 time to fit residues: 16.3262 Evaluate side-chains 76 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101565 restraints weight = 6630.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.101582 restraints weight = 5518.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.102260 restraints weight = 5164.202| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3237 Z= 0.207 Angle : 0.621 8.655 4394 Z= 0.324 Chirality : 0.043 0.158 467 Planarity : 0.004 0.035 569 Dihedral : 4.758 23.435 447 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.79 % Allowed : 18.37 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.32 (0.43), residues: 392 helix: -3.85 (0.90), residues: 21 sheet: -0.29 (0.49), residues: 127 loop : -0.91 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.000 0.000 HIS A 505 PHE 0.008 0.001 PHE A 400 TYR 0.017 0.001 TYR K 92 ARG 0.007 0.001 ARG H 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.15 seconds wall clock time: 23 minutes 27.96 seconds (1407.96 seconds total)