Starting phenix.real_space_refine on Tue Feb 13 05:41:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ix3_35788/02_2024/8ix3_35788.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ix3_35788/02_2024/8ix3_35788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ix3_35788/02_2024/8ix3_35788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ix3_35788/02_2024/8ix3_35788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ix3_35788/02_2024/8ix3_35788.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ix3_35788/02_2024/8ix3_35788.pdb" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 2130 2.51 5 N 562 2.21 5 O 633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 1": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 346": "NH1" <-> "NH2" Residue "G ARG 357": "NH1" <-> "NH2" Residue "G GLU 516": "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: 3339 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "G" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1547 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Time building chain proxies: 2.25, per 1000 atoms: 0.67 Number of scatterers: 3339 At special positions: 0 Unit cell: (61.462, 87.136, 87.914, 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 633 8.00 N 562 7.00 C 2130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.02 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " 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: 1.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 3.5% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.565A pdb=" N ASP H 90 " --> pdb=" O GLY H 87 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR H 91 " --> pdb=" O VAL H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'G' and resid 366 through 370 removed outlier: 3.840A pdb=" N TYR G 369 " --> pdb=" O SER G 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 410 removed outlier: 3.579A pdb=" N GLN G 409 " --> pdb=" O GLU G 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.650A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.639A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLN L 37 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.859A pdb=" N ASP H 73 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 59 through 60 removed outlier: 5.252A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET H 34 " --> pdb=" O THR H 51 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR H 114 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 59 through 60 removed outlier: 5.252A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET H 34 " --> pdb=" O THR H 51 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE H 119 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 376 through 379 Processing sheet with id=AA7, first strand: chain 'G' and resid 376 through 379 Processing sheet with id=AA8, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'G' and resid 473 through 474 96 hydrogen bonds defined for protein. 234 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: 0.79 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 927 1.33 - 1.45: 702 1.45 - 1.57: 1784 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3429 Sorted by residual: bond pdb=" C ALA G 520 " pdb=" N PRO G 521 " ideal model delta sigma weight residual 1.336 1.387 -0.051 1.20e-02 6.94e+03 1.79e+01 bond pdb=" C CYS G 336 " pdb=" N PRO G 337 " ideal model delta sigma weight residual 1.333 1.354 -0.020 1.01e-02 9.80e+03 4.09e+00 bond pdb=" C ALA H 40 " pdb=" N PRO H 41 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.28e-02 6.10e+03 2.80e+00 bond pdb=" C SER H 104 " pdb=" O SER H 104 " ideal model delta sigma weight residual 1.236 1.220 0.016 9.60e-03 1.09e+04 2.76e+00 bond pdb=" C SER H 100 " pdb=" O SER H 100 " ideal model delta sigma weight residual 1.235 1.211 0.024 1.43e-02 4.89e+03 2.75e+00 ... (remaining 3424 not shown) Histogram of bond angle deviations from ideal: 100.57 - 107.26: 114 107.26 - 113.95: 1786 113.95 - 120.64: 1384 120.64 - 127.33: 1347 127.33 - 134.01: 31 Bond angle restraints: 4662 Sorted by residual: angle pdb=" N SER H 104 " pdb=" CA SER H 104 " pdb=" C SER H 104 " ideal model delta sigma weight residual 108.24 120.53 -12.29 1.32e+00 5.74e-01 8.67e+01 angle pdb=" N ASP H 103 " pdb=" CA ASP H 103 " pdb=" C ASP H 103 " ideal model delta sigma weight residual 112.93 123.63 -10.70 1.33e+00 5.65e-01 6.47e+01 angle pdb=" N SER H 105 " pdb=" CA SER H 105 " pdb=" C SER H 105 " ideal model delta sigma weight residual 111.28 119.24 -7.96 1.09e+00 8.42e-01 5.33e+01 angle pdb=" N TYR H 102 " pdb=" CA TYR H 102 " pdb=" C TYR H 102 " ideal model delta sigma weight residual 111.28 118.65 -7.37 1.09e+00 8.42e-01 4.58e+01 angle pdb=" N GLY H 106 " pdb=" CA GLY H 106 " pdb=" C GLY H 106 " ideal model delta sigma weight residual 112.73 119.23 -6.50 1.20e+00 6.94e-01 2.94e+01 ... (remaining 4657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 1779 16.73 - 33.46: 175 33.46 - 50.19: 30 50.19 - 66.92: 10 66.92 - 83.65: 5 Dihedral angle restraints: 1999 sinusoidal: 771 harmonic: 1228 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 151.76 -58.76 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CA CYS G 361 " pdb=" C CYS G 361 " pdb=" N VAL G 362 " pdb=" CA VAL G 362 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PRO G 337 " pdb=" C PRO G 337 " pdb=" N PHE G 338 " pdb=" CA PHE G 338 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 1996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 429 0.085 - 0.171: 57 0.171 - 0.256: 5 0.256 - 0.341: 0 0.341 - 0.427: 2 Chirality restraints: 493 Sorted by residual: chirality pdb=" CA ASP H 103 " pdb=" N ASP H 103 " pdb=" C ASP H 103 " pdb=" CB ASP H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA TYR H 102 " pdb=" N TYR H 102 " pdb=" C TYR H 102 " pdb=" CB TYR H 102 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA SER H 100 " pdb=" N SER H 100 " pdb=" C SER H 100 " pdb=" CB SER H 100 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 490 not shown) Planarity restraints: 607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA G 411 " 0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO G 412 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 412 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 412 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO H 14 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 99 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.06e+00 pdb=" C ASP H 99 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP H 99 " -0.013 2.00e-02 2.50e+03 pdb=" N SER H 100 " -0.012 2.00e-02 2.50e+03 ... (remaining 604 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 822 2.79 - 3.32: 2663 3.32 - 3.84: 5249 3.84 - 4.37: 5705 4.37 - 4.90: 10347 Nonbonded interactions: 24786 Sorted by model distance: nonbonded pdb=" OD2 ASP G 398 " pdb=" OH TYR G 423 " model vdw 2.262 2.440 nonbonded pdb=" O ASN G 439 " pdb=" OG SER G 443 " model vdw 2.319 2.440 nonbonded pdb=" NH1 ARG G 457 " pdb=" OD2 ASP G 467 " model vdw 2.346 2.520 nonbonded pdb=" NH2 ARG G 454 " pdb=" O SER G 469 " model vdw 2.371 2.520 nonbonded pdb=" O SER L 7 " pdb=" OG1 THR L 22 " model vdw 2.380 2.440 ... (remaining 24781 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: 11.040 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: 38.150 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.460 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 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 : 0.005 0.051 3429 Z= 0.330 Angle : 0.922 12.290 4662 Z= 0.571 Chirality : 0.062 0.427 493 Planarity : 0.007 0.055 607 Dihedral : 14.179 83.646 1208 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.56 % Allowed : 6.94 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.32), residues: 420 helix: -5.14 (0.19), residues: 20 sheet: -2.03 (0.45), residues: 120 loop : -3.04 (0.27), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 436 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.002 PHE H 27 TYR 0.013 0.002 TYR G 453 ARG 0.003 0.000 ARG G 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 ASP cc_start: 0.7689 (m-30) cc_final: 0.6842 (m-30) REVERT: L 37 GLN cc_start: 0.7695 (tt0) cc_final: 0.6433 (tt0) REVERT: L 45 LYS cc_start: 0.7666 (mmtm) cc_final: 0.7450 (mmtm) REVERT: L 81 GLU cc_start: 0.8783 (pt0) cc_final: 0.8336 (tm-30) REVERT: H 18 LEU cc_start: 0.7235 (tt) cc_final: 0.7016 (tt) REVERT: H 47 TRP cc_start: 0.7622 (t60) cc_final: 0.7306 (t60) REVERT: H 83 MET cc_start: 0.7212 (ptp) cc_final: 0.6949 (ptp) REVERT: H 111 ASN cc_start: 0.8113 (p0) cc_final: 0.7850 (p0) REVERT: G 390 LEU cc_start: 0.8615 (mp) cc_final: 0.8167 (mp) REVERT: G 406 GLU cc_start: 0.8606 (pt0) cc_final: 0.8360 (pt0) REVERT: G 457 ARG cc_start: 0.7239 (ttt90) cc_final: 0.6900 (ttt90) REVERT: G 460 ASN cc_start: 0.8182 (m-40) cc_final: 0.7903 (m-40) REVERT: G 467 ASP cc_start: 0.7802 (t0) cc_final: 0.6906 (p0) REVERT: G 471 GLU cc_start: 0.7827 (tp30) cc_final: 0.7438 (mm-30) REVERT: G 474 GLN cc_start: 0.5260 (tp40) cc_final: 0.4755 (mm-40) REVERT: G 498 ARG cc_start: 0.7047 (mtt90) cc_final: 0.6781 (ttm-80) outliers start: 2 outliers final: 2 residues processed: 117 average time/residue: 0.1742 time to fit residues: 24.2869 Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 123 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN G 409 GLN ** G 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3429 Z= 0.366 Angle : 0.666 6.823 4662 Z= 0.356 Chirality : 0.046 0.171 493 Planarity : 0.005 0.037 607 Dihedral : 6.915 70.993 477 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.83 % Allowed : 15.28 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.35), residues: 420 helix: -4.65 (0.50), residues: 20 sheet: -1.61 (0.47), residues: 112 loop : -2.51 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 436 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.002 PHE H 27 TYR 0.027 0.002 TYR L 49 ARG 0.003 0.001 ARG G 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 ASP cc_start: 0.7623 (m-30) cc_final: 0.6789 (m-30) REVERT: L 36 TYR cc_start: 0.7822 (m-80) cc_final: 0.6580 (m-80) REVERT: L 45 LYS cc_start: 0.7626 (mmtm) cc_final: 0.7405 (mmtm) REVERT: L 81 GLU cc_start: 0.8760 (pt0) cc_final: 0.8278 (tm-30) REVERT: H 6 GLU cc_start: 0.8367 (pm20) cc_final: 0.8065 (pm20) REVERT: H 7 SER cc_start: 0.7464 (m) cc_final: 0.7237 (p) REVERT: H 47 TRP cc_start: 0.7604 (t60) cc_final: 0.7128 (t60) REVERT: H 104 SER cc_start: 0.5577 (OUTLIER) cc_final: 0.5318 (m) REVERT: H 111 ASN cc_start: 0.8529 (p0) cc_final: 0.8329 (p0) REVERT: G 390 LEU cc_start: 0.8348 (mp) cc_final: 0.7860 (mp) REVERT: G 406 GLU cc_start: 0.8597 (pt0) cc_final: 0.8104 (pt0) REVERT: G 457 ARG cc_start: 0.7149 (ttt90) cc_final: 0.6776 (ttt-90) REVERT: G 460 ASN cc_start: 0.8144 (m-40) cc_final: 0.7857 (m-40) REVERT: G 467 ASP cc_start: 0.8061 (t0) cc_final: 0.6726 (p0) REVERT: G 471 GLU cc_start: 0.7771 (tp30) cc_final: 0.7372 (mm-30) outliers start: 21 outliers final: 12 residues processed: 103 average time/residue: 0.1761 time to fit residues: 21.5793 Evaluate side-chains 98 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain G residue 394 ASN Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 422 ASN Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 518 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.0030 chunk 30 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 overall best weight: 0.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3429 Z= 0.193 Angle : 0.587 6.316 4662 Z= 0.308 Chirality : 0.044 0.147 493 Planarity : 0.004 0.033 607 Dihedral : 6.217 61.621 477 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.89 % Allowed : 19.17 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.37), residues: 420 helix: -4.50 (0.61), residues: 20 sheet: -1.28 (0.48), residues: 112 loop : -2.13 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.002 0.000 HIS H 35 PHE 0.007 0.001 PHE G 377 TYR 0.026 0.001 TYR L 49 ARG 0.003 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 ASP cc_start: 0.7556 (m-30) cc_final: 0.6722 (m-30) REVERT: L 22 THR cc_start: 0.7330 (p) cc_final: 0.6973 (t) REVERT: L 36 TYR cc_start: 0.7803 (m-80) cc_final: 0.6439 (m-80) REVERT: L 45 LYS cc_start: 0.7648 (mmtm) cc_final: 0.7437 (mmtm) REVERT: L 81 GLU cc_start: 0.8722 (pt0) cc_final: 0.8202 (tm-30) REVERT: H 7 SER cc_start: 0.7484 (m) cc_final: 0.7278 (p) REVERT: H 111 ASN cc_start: 0.8302 (p0) cc_final: 0.8085 (p0) REVERT: G 379 CYS cc_start: 0.6793 (m) cc_final: 0.6493 (m) REVERT: G 390 LEU cc_start: 0.8292 (mp) cc_final: 0.7826 (mp) REVERT: G 403 ARG cc_start: 0.6948 (mtt-85) cc_final: 0.5826 (mtm-85) REVERT: G 457 ARG cc_start: 0.7220 (ttt90) cc_final: 0.6881 (ttt180) REVERT: G 467 ASP cc_start: 0.8112 (t0) cc_final: 0.6729 (p0) REVERT: G 471 GLU cc_start: 0.7659 (tp30) cc_final: 0.7404 (mm-30) outliers start: 14 outliers final: 10 residues processed: 105 average time/residue: 0.1817 time to fit residues: 22.4810 Evaluate side-chains 99 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 518 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.0570 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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: 0.6559 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3429 Z= 0.240 Angle : 0.593 6.393 4662 Z= 0.308 Chirality : 0.044 0.147 493 Planarity : 0.004 0.031 607 Dihedral : 5.757 47.679 477 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.72 % Allowed : 19.72 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.38), residues: 420 helix: -4.65 (0.49), residues: 26 sheet: -1.01 (0.49), residues: 112 loop : -1.93 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE G 377 TYR 0.026 0.001 TYR L 49 ARG 0.003 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 ASP cc_start: 0.7505 (m-30) cc_final: 0.6682 (m-30) REVERT: L 22 THR cc_start: 0.7307 (p) cc_final: 0.6978 (t) REVERT: H 7 SER cc_start: 0.7468 (m) cc_final: 0.7261 (p) REVERT: H 47 TRP cc_start: 0.7945 (t60) cc_final: 0.7268 (t60) REVERT: G 379 CYS cc_start: 0.6848 (m) cc_final: 0.6557 (m) REVERT: G 390 LEU cc_start: 0.8270 (mp) cc_final: 0.7809 (mp) REVERT: G 406 GLU cc_start: 0.7853 (pt0) cc_final: 0.7271 (tt0) REVERT: G 457 ARG cc_start: 0.7171 (ttt90) cc_final: 0.6847 (ttt180) REVERT: G 467 ASP cc_start: 0.8128 (t0) cc_final: 0.6719 (p0) REVERT: G 471 GLU cc_start: 0.7644 (tp30) cc_final: 0.7288 (mm-30) outliers start: 17 outliers final: 13 residues processed: 99 average time/residue: 0.1699 time to fit residues: 20.0587 Evaluate side-chains 98 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 422 ASN Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 518 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3429 Z= 0.236 Angle : 0.605 9.696 4662 Z= 0.307 Chirality : 0.044 0.147 493 Planarity : 0.004 0.032 607 Dihedral : 5.549 38.921 477 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.17 % Allowed : 22.22 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.39), residues: 420 helix: -4.60 (0.53), residues: 26 sheet: -0.86 (0.50), residues: 112 loop : -1.81 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE H 68 TYR 0.029 0.001 TYR L 49 ARG 0.003 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 17 ASP cc_start: 0.7477 (m-30) cc_final: 0.6651 (m-30) REVERT: L 22 THR cc_start: 0.7297 (p) cc_final: 0.6966 (t) REVERT: L 30 ASP cc_start: 0.5846 (t0) cc_final: 0.5429 (t70) REVERT: H 7 SER cc_start: 0.7459 (m) cc_final: 0.7250 (p) REVERT: H 16 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7571 (mtt-85) REVERT: H 47 TRP cc_start: 0.7945 (t60) cc_final: 0.7314 (t60) REVERT: G 380 TYR cc_start: 0.7534 (m-10) cc_final: 0.7333 (m-10) REVERT: G 390 LEU cc_start: 0.8225 (mp) cc_final: 0.7763 (mp) REVERT: G 406 GLU cc_start: 0.7711 (pt0) cc_final: 0.7275 (tt0) REVERT: G 457 ARG cc_start: 0.7211 (ttt90) cc_final: 0.6758 (ttt180) REVERT: G 467 ASP cc_start: 0.8129 (t0) cc_final: 0.6772 (p0) REVERT: G 471 GLU cc_start: 0.7656 (tp30) cc_final: 0.7436 (mm-30) outliers start: 15 outliers final: 12 residues processed: 97 average time/residue: 0.1626 time to fit residues: 19.0313 Evaluate side-chains 94 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 443 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.0370 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.0770 chunk 22 optimal weight: 0.6980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3429 Z= 0.203 Angle : 0.590 8.509 4662 Z= 0.295 Chirality : 0.043 0.143 493 Planarity : 0.004 0.033 607 Dihedral : 5.275 32.248 477 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.56 % Allowed : 22.22 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.39), residues: 420 helix: -5.16 (0.20), residues: 20 sheet: -0.60 (0.51), residues: 112 loop : -1.59 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE G 377 TYR 0.025 0.001 TYR L 49 ARG 0.006 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 17 ASP cc_start: 0.7397 (m-30) cc_final: 0.6581 (m-30) REVERT: L 22 THR cc_start: 0.7289 (p) cc_final: 0.6978 (t) REVERT: H 7 SER cc_start: 0.7451 (m) cc_final: 0.7246 (p) REVERT: H 16 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7629 (mtt-85) REVERT: H 47 TRP cc_start: 0.7951 (t60) cc_final: 0.7430 (t60) REVERT: H 120 LEU cc_start: 0.8813 (pp) cc_final: 0.8494 (tt) REVERT: G 390 LEU cc_start: 0.8197 (mp) cc_final: 0.7756 (mp) REVERT: G 406 GLU cc_start: 0.7631 (pt0) cc_final: 0.7275 (tt0) REVERT: G 457 ARG cc_start: 0.7206 (ttt90) cc_final: 0.6765 (ttt180) REVERT: G 467 ASP cc_start: 0.8029 (t0) cc_final: 0.6703 (p0) REVERT: G 471 GLU cc_start: 0.7610 (tp30) cc_final: 0.7409 (mm-30) outliers start: 20 outliers final: 14 residues processed: 98 average time/residue: 0.1510 time to fit residues: 18.0593 Evaluate side-chains 94 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 518 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.0070 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3429 Z= 0.223 Angle : 0.608 8.914 4662 Z= 0.306 Chirality : 0.044 0.144 493 Planarity : 0.004 0.033 607 Dihedral : 5.266 29.797 477 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.28 % Allowed : 21.94 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.39), residues: 420 helix: -5.15 (0.20), residues: 20 sheet: -0.60 (0.51), residues: 112 loop : -1.58 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 436 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE G 377 TYR 0.026 0.001 TYR L 49 ARG 0.007 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 ASP cc_start: 0.7364 (m-30) cc_final: 0.6556 (m-30) REVERT: L 22 THR cc_start: 0.7291 (p) cc_final: 0.6978 (t) REVERT: L 30 ASP cc_start: 0.6062 (t0) cc_final: 0.5810 (t0) REVERT: H 7 SER cc_start: 0.7443 (m) cc_final: 0.7231 (p) REVERT: H 16 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7627 (mtt-85) REVERT: H 47 TRP cc_start: 0.8021 (t60) cc_final: 0.7466 (t60) REVERT: H 120 LEU cc_start: 0.8808 (pp) cc_final: 0.8488 (tt) REVERT: G 390 LEU cc_start: 0.8193 (mp) cc_final: 0.7744 (mp) REVERT: G 406 GLU cc_start: 0.7623 (pt0) cc_final: 0.7273 (tt0) REVERT: G 457 ARG cc_start: 0.7187 (ttt90) cc_final: 0.6758 (ttt180) REVERT: G 467 ASP cc_start: 0.8066 (t0) cc_final: 0.6645 (p0) REVERT: G 498 ARG cc_start: 0.7233 (mtt90) cc_final: 0.6959 (ttm-80) outliers start: 19 outliers final: 16 residues processed: 94 average time/residue: 0.1615 time to fit residues: 18.4891 Evaluate side-chains 97 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 518 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 0.0040 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3429 Z= 0.236 Angle : 0.611 9.283 4662 Z= 0.307 Chirality : 0.044 0.144 493 Planarity : 0.004 0.033 607 Dihedral : 5.257 27.259 477 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.83 % Allowed : 22.22 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.39), residues: 420 helix: -5.15 (0.20), residues: 20 sheet: -0.58 (0.50), residues: 112 loop : -1.55 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 436 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE G 377 TYR 0.024 0.001 TYR L 49 ARG 0.007 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 ASP cc_start: 0.7361 (m-30) cc_final: 0.6562 (m-30) REVERT: L 22 THR cc_start: 0.7286 (p) cc_final: 0.6976 (t) REVERT: L 30 ASP cc_start: 0.6188 (t0) cc_final: 0.5946 (t0) REVERT: H 7 SER cc_start: 0.7437 (m) cc_final: 0.7223 (p) REVERT: H 16 ARG cc_start: 0.8295 (mtp85) cc_final: 0.7587 (mtt-85) REVERT: H 47 TRP cc_start: 0.7988 (t60) cc_final: 0.7423 (t60) REVERT: H 120 LEU cc_start: 0.8751 (pp) cc_final: 0.8457 (tt) REVERT: G 390 LEU cc_start: 0.8215 (mp) cc_final: 0.7776 (mp) REVERT: G 406 GLU cc_start: 0.7639 (pt0) cc_final: 0.7279 (tt0) REVERT: G 457 ARG cc_start: 0.7124 (ttt90) cc_final: 0.6695 (ttt180) REVERT: G 467 ASP cc_start: 0.8119 (t0) cc_final: 0.6543 (p0) REVERT: G 471 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7579 (mm-30) REVERT: G 498 ARG cc_start: 0.7205 (mtt90) cc_final: 0.6934 (ttm-80) outliers start: 21 outliers final: 17 residues processed: 98 average time/residue: 0.1505 time to fit residues: 18.0208 Evaluate side-chains 101 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 518 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.0030 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 40 optimal weight: 0.0270 chunk 37 optimal weight: 0.8980 overall best weight: 0.2648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN H 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3429 Z= 0.166 Angle : 0.591 9.667 4662 Z= 0.291 Chirality : 0.043 0.148 493 Planarity : 0.004 0.033 607 Dihedral : 4.988 27.557 477 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.17 % Allowed : 23.61 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.39), residues: 420 helix: -5.16 (0.20), residues: 20 sheet: -0.52 (0.50), residues: 112 loop : -1.40 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 436 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE G 400 TYR 0.025 0.001 TYR L 49 ARG 0.007 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 ASP cc_start: 0.7353 (m-30) cc_final: 0.6540 (m-30) REVERT: L 22 THR cc_start: 0.7317 (p) cc_final: 0.7024 (t) REVERT: L 30 ASP cc_start: 0.6226 (t0) cc_final: 0.6001 (t0) REVERT: H 7 SER cc_start: 0.7434 (m) cc_final: 0.7186 (p) REVERT: H 16 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7684 (mtt-85) REVERT: H 47 TRP cc_start: 0.7977 (t60) cc_final: 0.7470 (t60) REVERT: H 70 ILE cc_start: 0.8035 (tt) cc_final: 0.7831 (tp) REVERT: H 120 LEU cc_start: 0.8790 (pp) cc_final: 0.8461 (tt) REVERT: G 390 LEU cc_start: 0.8109 (mp) cc_final: 0.7664 (mp) REVERT: G 406 GLU cc_start: 0.7527 (pt0) cc_final: 0.7248 (tt0) REVERT: G 467 ASP cc_start: 0.8021 (t0) cc_final: 0.6642 (p0) REVERT: G 498 ARG cc_start: 0.7213 (mtt90) cc_final: 0.6971 (ttm-80) outliers start: 15 outliers final: 14 residues processed: 104 average time/residue: 0.1542 time to fit residues: 19.5971 Evaluate side-chains 107 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 3429 Z= 0.309 Angle : 1.266 59.197 4662 Z= 0.735 Chirality : 0.047 0.382 493 Planarity : 0.004 0.065 607 Dihedral : 4.999 27.560 475 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.72 % Allowed : 23.61 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.39), residues: 420 helix: -5.16 (0.20), residues: 20 sheet: -0.52 (0.50), residues: 112 loop : -1.39 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE H 112 TYR 0.024 0.001 TYR L 49 ARG 0.005 0.001 ARG H 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 ASP cc_start: 0.7357 (m-30) cc_final: 0.6545 (m-30) REVERT: L 22 THR cc_start: 0.7325 (p) cc_final: 0.7030 (t) REVERT: L 30 ASP cc_start: 0.6224 (t0) cc_final: 0.6012 (t0) REVERT: H 7 SER cc_start: 0.7405 (m) cc_final: 0.7190 (p) REVERT: H 16 ARG cc_start: 0.8294 (mtp85) cc_final: 0.7680 (mtt-85) REVERT: H 47 TRP cc_start: 0.7992 (t60) cc_final: 0.7476 (t60) REVERT: H 70 ILE cc_start: 0.8075 (tt) cc_final: 0.7873 (tp) REVERT: H 111 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.7704 (p0) REVERT: H 120 LEU cc_start: 0.8792 (pp) cc_final: 0.8462 (tt) REVERT: G 390 LEU cc_start: 0.8119 (mp) cc_final: 0.7673 (mp) REVERT: G 406 GLU cc_start: 0.7535 (pt0) cc_final: 0.7247 (tt0) REVERT: G 467 ASP cc_start: 0.7969 (t0) cc_final: 0.6605 (p0) REVERT: G 498 ARG cc_start: 0.7215 (mtt90) cc_final: 0.6973 (ttm-80) outliers start: 17 outliers final: 15 residues processed: 102 average time/residue: 0.1537 time to fit residues: 19.3551 Evaluate side-chains 109 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 443 SER Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.0970 chunk 1 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 24 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 40 optimal weight: 0.1980 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117304 restraints weight = 5582.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120331 restraints weight = 3505.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.122246 restraints weight = 2511.956| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 3429 Z= 0.317 Angle : 1.208 47.092 4662 Z= 0.751 Chirality : 0.048 0.445 493 Planarity : 0.005 0.065 607 Dihedral : 4.999 27.560 475 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.44 % Allowed : 23.89 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.39), residues: 420 helix: -5.16 (0.20), residues: 20 sheet: -0.52 (0.50), residues: 112 loop : -1.39 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE H 112 TYR 0.024 0.001 TYR L 49 ARG 0.005 0.001 ARG H 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1707.30 seconds wall clock time: 31 minutes 14.96 seconds (1874.96 seconds total)