Starting phenix.real_space_refine on Mon Aug 5 10:40:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/08_2024/8tj3_41299.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/08_2024/8tj3_41299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/08_2024/8tj3_41299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/08_2024/8tj3_41299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/08_2024/8tj3_41299.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/08_2024/8tj3_41299.cif" } resolution = 3.2 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: 5 Type Number sf(0) Gaussians S 31 5.16 5 C 4204 2.51 5 N 1098 2.21 5 O 1142 1.98 5 H 6652 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 12": "OD1" <-> "OD2" Residue "B ASP 131": "OD1" <-> "OD2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C ARG 500": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 502": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 632": "OD1" <-> "OD2" Residue "C TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 852": "OD1" <-> "OD2" Residue "C ASP 894": "OD1" <-> "OD2" Residue "C PHE 911": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13127 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 5418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 5418 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 17, 'TRANS': 323} Chain breaks: 1 Chain: "C" Number of atoms: 7709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 7709 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 29, 'TRANS': 462} Chain breaks: 3 Time building chain proxies: 7.05, per 1000 atoms: 0.54 Number of scatterers: 13127 At special positions: 0 Unit cell: (80.51, 90.47, 132.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 O 1142 8.00 N 1098 7.00 C 4204 6.00 H 6652 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 10.38 Conformation dependent library (CDL) restraints added in 1.4 seconds 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 58.9% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 39 Processing helix chain 'B' and resid 42 through 64 Processing helix chain 'B' and resid 67 through 91 Proline residue: B 76 - end of helix Processing helix chain 'B' and resid 112 through 130 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 140 through 157 Proline residue: B 150 - end of helix Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.744A pdb=" N LEU B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY B 170 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 Proline residue: B 196 - end of helix Processing helix chain 'B' and resid 204 through 216 Processing helix chain 'B' and resid 223 through 237 removed outlier: 4.225A pdb=" N HIS B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 296 removed outlier: 7.869A pdb=" N LEU B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N VAL B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 327 removed outlier: 3.625A pdb=" N ALA B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 363 removed outlier: 4.021A pdb=" N LEU B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 421 Processing helix chain 'C' and resid 423 through 427 removed outlier: 3.687A pdb=" N TYR C 427 " --> pdb=" O PHE C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 472 removed outlier: 3.917A pdb=" N VAL C 472 " --> pdb=" O PRO C 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 469 through 472' Processing helix chain 'C' and resid 474 through 487 Processing helix chain 'C' and resid 489 through 503 Processing helix chain 'C' and resid 516 through 526 Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 572 through 577 Processing helix chain 'C' and resid 586 through 591 Processing helix chain 'C' and resid 591 through 597 Processing helix chain 'C' and resid 632 through 644 Processing helix chain 'C' and resid 671 through 676 Processing helix chain 'C' and resid 679 through 688 Processing helix chain 'C' and resid 705 through 708 Processing helix chain 'C' and resid 709 through 720 Processing helix chain 'C' and resid 780 through 789 Processing helix chain 'C' and resid 838 through 851 Processing helix chain 'C' and resid 887 through 901 Processing helix chain 'C' and resid 907 through 911 Processing helix chain 'C' and resid 970 through 972 No H-bonds generated for 'chain 'C' and resid 970 through 972' Processing helix chain 'C' and resid 976 through 990 removed outlier: 3.522A pdb=" N LEU C 980 " --> pdb=" O ALA C 976 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 438 through 441 removed outlier: 3.674A pdb=" N TYR C 601 " --> pdb=" O VAL C 619 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 617 " --> pdb=" O GLU C 603 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 509 through 512 removed outlier: 3.688A pdb=" N ILE C 509 " --> pdb=" O MET C 467 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET C 467 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 465 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 460 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 556 through 558 Processing sheet with id=AA4, first strand: chain 'C' and resid 606 through 607 removed outlier: 3.868A pdb=" N ARG C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 628 through 629 removed outlier: 6.715A pdb=" N TYR C 628 " --> pdb=" O MET C 862 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 662 through 665 365 hydrogen bonds defined for protein. 1062 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: 4.50 Time building geometry restraints manager: 10.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6650 1.03 - 1.23: 19 1.23 - 1.42: 2678 1.42 - 1.62: 3865 1.62 - 1.81: 60 Bond restraints: 13272 Sorted by residual: bond pdb=" N THR C 692 " pdb=" CA THR C 692 " ideal model delta sigma weight residual 1.458 1.484 -0.026 7.40e-03 1.83e+04 1.22e+01 bond pdb=" N ARG C 647 " pdb=" CA ARG C 647 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.22e-02 6.72e+03 1.16e+01 bond pdb=" C ARG C 397 " pdb=" O ARG C 397 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" N MET B 203 " pdb=" CA MET B 203 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.94e+00 bond pdb=" C THR B 140 " pdb=" O THR B 140 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.43e-02 4.89e+03 7.47e+00 ... (remaining 13267 not shown) Histogram of bond angle deviations from ideal: 95.67 - 103.35: 82 103.35 - 111.03: 14757 111.03 - 118.70: 3629 118.70 - 126.38: 5483 126.38 - 134.05: 143 Bond angle restraints: 24094 Sorted by residual: angle pdb=" CA ARG C 647 " pdb=" C ARG C 647 " pdb=" O ARG C 647 " ideal model delta sigma weight residual 121.16 114.97 6.19 1.12e+00 7.97e-01 3.06e+01 angle pdb=" CA VAL C 652 " pdb=" C VAL C 652 " pdb=" O VAL C 652 " ideal model delta sigma weight residual 121.59 116.60 4.99 1.03e+00 9.43e-01 2.34e+01 angle pdb=" CA ARG C 397 " pdb=" C ARG C 397 " pdb=" O ARG C 397 " ideal model delta sigma weight residual 120.55 115.44 5.11 1.06e+00 8.90e-01 2.33e+01 angle pdb=" CA VAL C 552 " pdb=" C VAL C 552 " pdb=" O VAL C 552 " ideal model delta sigma weight residual 121.18 115.93 5.25 1.16e+00 7.43e-01 2.05e+01 angle pdb=" CA SER C 646 " pdb=" C SER C 646 " pdb=" O SER C 646 " ideal model delta sigma weight residual 120.51 114.07 6.44 1.43e+00 4.89e-01 2.03e+01 ... (remaining 24089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5475 17.72 - 35.44: 479 35.44 - 53.15: 183 53.15 - 70.87: 58 70.87 - 88.59: 16 Dihedral angle restraints: 6211 sinusoidal: 3411 harmonic: 2800 Sorted by residual: dihedral pdb=" CD ARG C 500 " pdb=" NE ARG C 500 " pdb=" CZ ARG C 500 " pdb=" NH1 ARG C 500 " ideal model delta sinusoidal sigma weight residual 0.00 -77.72 77.72 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CD ARG C 502 " pdb=" NE ARG C 502 " pdb=" CZ ARG C 502 " pdb=" NH1 ARG C 502 " ideal model delta sinusoidal sigma weight residual 0.00 50.19 -50.19 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CA HIS B 204 " pdb=" C HIS B 204 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta harmonic sigma weight residual -180.00 -154.85 -25.15 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 6208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 748 0.041 - 0.082: 199 0.082 - 0.123: 85 0.123 - 0.164: 13 0.164 - 0.205: 2 Chirality restraints: 1047 Sorted by residual: chirality pdb=" CA VAL C 652 " pdb=" N VAL C 652 " pdb=" C VAL C 652 " pdb=" CB VAL C 652 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL C 552 " pdb=" N VAL C 552 " pdb=" C VAL C 552 " pdb=" CB VAL C 552 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA VAL C 650 " pdb=" N VAL C 650 " pdb=" C VAL C 650 " pdb=" CB VAL C 650 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 1044 not shown) Planarity restraints: 1917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 397 " 0.629 9.50e-02 1.11e+02 4.85e-01 4.35e+03 pdb=" NE ARG C 397 " 0.426 2.00e-02 2.50e+03 pdb=" CZ ARG C 397 " 0.117 2.00e-02 2.50e+03 pdb=" NH1 ARG C 397 " -0.056 2.00e-02 2.50e+03 pdb=" NH2 ARG C 397 " -0.058 2.00e-02 2.50e+03 pdb="HH11 ARG C 397 " -0.697 2.00e-02 2.50e+03 pdb="HH12 ARG C 397 " 0.469 2.00e-02 2.50e+03 pdb="HH21 ARG C 397 " -0.743 2.00e-02 2.50e+03 pdb="HH22 ARG C 397 " 0.513 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 500 " -1.064 9.50e-02 1.11e+02 5.08e-01 3.09e+03 pdb=" NE ARG C 500 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG C 500 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG C 500 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG C 500 " -0.045 2.00e-02 2.50e+03 pdb="HH11 ARG C 500 " -0.233 2.00e-02 2.50e+03 pdb="HH12 ARG C 500 " 0.330 2.00e-02 2.50e+03 pdb="HH21 ARG C 500 " -0.779 2.00e-02 2.50e+03 pdb="HH22 ARG C 500 " 0.639 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 435 " 0.132 9.50e-02 1.11e+02 3.72e-01 3.08e+03 pdb=" NE ARG C 435 " -0.113 2.00e-02 2.50e+03 pdb=" CZ ARG C 435 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG C 435 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG C 435 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG C 435 " 0.806 2.00e-02 2.50e+03 pdb="HH12 ARG C 435 " -0.720 2.00e-02 2.50e+03 pdb="HH21 ARG C 435 " 0.165 2.00e-02 2.50e+03 pdb="HH22 ARG C 435 " -0.148 2.00e-02 2.50e+03 ... (remaining 1914 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 2667 2.28 - 2.86: 31213 2.86 - 3.44: 36086 3.44 - 4.02: 48169 4.02 - 4.60: 72881 Nonbonded interactions: 191016 Sorted by model distance: nonbonded pdb=" H ARG C 451 " pdb=" O LEU C 631 " model vdw 1.701 2.450 nonbonded pdb=" H THR C 630 " pdb=" O LEU C 860 " model vdw 1.739 2.450 nonbonded pdb=" O ILE B 35 " pdb=" HG SER B 39 " model vdw 1.741 2.450 nonbonded pdb=" H ARG C 435 " pdb=" O VAL C 606 " model vdw 1.757 2.450 nonbonded pdb=" OG1 THR C 630 " pdb=" H VAL C 660 " model vdw 1.767 2.450 ... (remaining 191011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic 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: 4.610 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: 0.200 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 44.420 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 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 0.042 6620 Z= 0.269 Angle : 0.723 7.944 9006 Z= 0.461 Chirality : 0.045 0.205 1047 Planarity : 0.020 0.481 1136 Dihedral : 13.852 87.650 2410 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.43 % Favored : 92.45 % Rotamer: Outliers : 1.16 % Allowed : 1.16 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.31), residues: 821 helix: 1.43 (0.25), residues: 458 sheet: -2.33 (0.53), residues: 58 loop : -1.48 (0.39), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 889 HIS 0.006 0.001 HIS C 859 PHE 0.019 0.001 PHE B 315 TYR 0.015 0.001 TYR B 206 ARG 0.010 0.000 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 324 MET cc_start: 0.5273 (tpt) cc_final: 0.4984 (tpt) REVERT: C 573 LEU cc_start: 0.7735 (mm) cc_final: 0.7415 (pt) REVERT: C 609 ARG cc_start: 0.6500 (mpp-170) cc_final: 0.6289 (mmt90) REVERT: C 628 TYR cc_start: 0.4046 (m-80) cc_final: 0.3788 (m-80) REVERT: C 838 THR cc_start: 0.7376 (p) cc_final: 0.7123 (t) REVERT: C 839 PRO cc_start: 0.5568 (Cg_exo) cc_final: 0.4736 (Cg_endo) REVERT: C 871 VAL cc_start: 0.6665 (p) cc_final: 0.5814 (p) REVERT: C 896 MET cc_start: 0.3207 (mtp) cc_final: 0.2579 (tpt) outliers start: 8 outliers final: 2 residues processed: 207 average time/residue: 0.4343 time to fit residues: 116.7436 Evaluate side-chains 135 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 952 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6620 Z= 0.250 Angle : 0.648 8.103 9006 Z= 0.337 Chirality : 0.043 0.165 1047 Planarity : 0.006 0.123 1136 Dihedral : 5.469 66.307 910 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.45 % Allowed : 8.67 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.31), residues: 821 helix: 1.34 (0.25), residues: 459 sheet: -2.04 (0.62), residues: 54 loop : -1.24 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 181 HIS 0.007 0.001 HIS C 987 PHE 0.020 0.002 PHE B 315 TYR 0.014 0.002 TYR C 916 ARG 0.021 0.001 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 573 LEU cc_start: 0.7869 (mm) cc_final: 0.7489 (pt) REVERT: C 699 THR cc_start: 0.3713 (p) cc_final: 0.3439 (p) REVERT: C 700 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.6390 (mp10) REVERT: C 839 PRO cc_start: 0.5795 (Cg_exo) cc_final: 0.5203 (Cg_endo) REVERT: C 896 MET cc_start: 0.3473 (mtp) cc_final: 0.2930 (tpt) outliers start: 10 outliers final: 8 residues processed: 148 average time/residue: 0.3395 time to fit residues: 70.7925 Evaluate side-chains 140 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 580 HIS Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 864 THR Chi-restraints excluded: chain C residue 911 PHE Chi-restraints excluded: chain C residue 952 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 GLN ** C 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6620 Z= 0.271 Angle : 0.665 6.933 9006 Z= 0.345 Chirality : 0.042 0.155 1047 Planarity : 0.005 0.073 1136 Dihedral : 5.587 72.843 910 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.30 % Allowed : 11.99 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.31), residues: 821 helix: 1.42 (0.25), residues: 461 sheet: -2.27 (0.70), residues: 43 loop : -1.50 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 36 HIS 0.013 0.002 HIS C 987 PHE 0.018 0.002 PHE B 315 TYR 0.021 0.002 TYR C 703 ARG 0.006 0.001 ARG C 802 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 573 LEU cc_start: 0.8011 (mm) cc_final: 0.7661 (pt) REVERT: C 862 MET cc_start: 0.6488 (tpp) cc_final: 0.6136 (ttm) REVERT: C 896 MET cc_start: 0.3675 (mtp) cc_final: 0.2802 (tpt) outliers start: 9 outliers final: 6 residues processed: 139 average time/residue: 0.3279 time to fit residues: 64.1084 Evaluate side-chains 136 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 952 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 615 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6620 Z= 0.319 Angle : 0.688 6.710 9006 Z= 0.354 Chirality : 0.044 0.200 1047 Planarity : 0.005 0.046 1136 Dihedral : 4.769 45.604 907 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.59 % Allowed : 14.74 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.31), residues: 821 helix: 1.25 (0.24), residues: 460 sheet: -2.50 (0.57), residues: 59 loop : -1.66 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 245 HIS 0.007 0.001 HIS B 247 PHE 0.026 0.002 PHE B 172 TYR 0.014 0.002 TYR C 463 ARG 0.014 0.001 ARG C 609 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 306 MET cc_start: 0.8529 (tpt) cc_final: 0.8093 (tpt) REVERT: C 573 LEU cc_start: 0.8150 (mm) cc_final: 0.7800 (tp) REVERT: C 700 GLN cc_start: 0.7558 (mt0) cc_final: 0.7145 (mp10) REVERT: C 966 MET cc_start: 0.7179 (ptt) cc_final: 0.6905 (ptt) outliers start: 11 outliers final: 9 residues processed: 136 average time/residue: 0.3377 time to fit residues: 66.2106 Evaluate side-chains 128 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 911 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 0.0050 chunk 55 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 841 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6620 Z= 0.229 Angle : 0.596 6.106 9006 Z= 0.306 Chirality : 0.041 0.164 1047 Planarity : 0.004 0.036 1136 Dihedral : 4.372 21.062 906 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.01 % Allowed : 16.04 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.31), residues: 821 helix: 1.42 (0.24), residues: 461 sheet: -2.56 (0.55), residues: 60 loop : -1.55 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 873 HIS 0.004 0.001 HIS B 360 PHE 0.024 0.002 PHE B 172 TYR 0.012 0.001 TYR C 545 ARG 0.008 0.000 ARG C 609 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 573 LEU cc_start: 0.8191 (mm) cc_final: 0.7854 (tp) REVERT: C 700 GLN cc_start: 0.7445 (mt0) cc_final: 0.6970 (mp10) REVERT: C 989 MET cc_start: 0.4769 (tmm) cc_final: 0.3698 (ptp) outliers start: 7 outliers final: 7 residues processed: 131 average time/residue: 0.3031 time to fit residues: 57.6628 Evaluate side-chains 128 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 911 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.0270 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 841 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.7256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6620 Z= 0.243 Angle : 0.609 6.267 9006 Z= 0.315 Chirality : 0.041 0.155 1047 Planarity : 0.005 0.035 1136 Dihedral : 4.277 18.113 906 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.01 % Allowed : 16.47 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.31), residues: 821 helix: 1.46 (0.24), residues: 461 sheet: -2.30 (0.55), residues: 63 loop : -1.53 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 873 HIS 0.004 0.001 HIS B 247 PHE 0.042 0.002 PHE B 172 TYR 0.040 0.002 TYR C 910 ARG 0.004 0.000 ARG C 802 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 MET cc_start: 0.6696 (tmm) cc_final: 0.6488 (tmm) REVERT: B 306 MET cc_start: 0.8650 (tpt) cc_final: 0.8276 (tpt) REVERT: C 563 ASP cc_start: 0.8639 (m-30) cc_final: 0.8402 (m-30) REVERT: C 573 LEU cc_start: 0.8246 (mm) cc_final: 0.7883 (tp) REVERT: C 847 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.5661 (ttp) REVERT: C 951 MET cc_start: 0.6968 (tmm) cc_final: 0.6763 (tmm) outliers start: 7 outliers final: 5 residues processed: 129 average time/residue: 0.3226 time to fit residues: 59.9442 Evaluate side-chains 122 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 847 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 452 ASN C 841 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.8188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6620 Z= 0.305 Angle : 0.637 6.578 9006 Z= 0.337 Chirality : 0.041 0.136 1047 Planarity : 0.005 0.043 1136 Dihedral : 4.439 17.202 906 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.94 % Favored : 92.94 % Rotamer: Outliers : 1.30 % Allowed : 16.91 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.30), residues: 821 helix: 1.30 (0.24), residues: 455 sheet: -2.31 (0.53), residues: 65 loop : -1.65 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 873 HIS 0.006 0.001 HIS C 859 PHE 0.026 0.002 PHE C 496 TYR 0.040 0.002 TYR C 910 ARG 0.004 0.001 ARG C 697 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8207 (tpt) cc_final: 0.7591 (tpt) REVERT: C 563 ASP cc_start: 0.8681 (m-30) cc_final: 0.8441 (m-30) REVERT: C 573 LEU cc_start: 0.8385 (mm) cc_final: 0.8051 (tp) REVERT: C 847 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.5943 (ttp) outliers start: 9 outliers final: 8 residues processed: 126 average time/residue: 0.3237 time to fit residues: 57.5280 Evaluate side-chains 120 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 847 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 452 ASN ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.8493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6620 Z= 0.230 Angle : 0.606 6.146 9006 Z= 0.315 Chirality : 0.041 0.142 1047 Planarity : 0.005 0.042 1136 Dihedral : 4.320 17.354 906 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.30 % Allowed : 19.51 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.30), residues: 821 helix: 1.34 (0.24), residues: 461 sheet: -2.23 (0.55), residues: 62 loop : -1.55 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 74 HIS 0.005 0.001 HIS C 859 PHE 0.023 0.002 PHE B 315 TYR 0.016 0.001 TYR C 545 ARG 0.003 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 MET cc_start: 0.7658 (ttm) cc_final: 0.7365 (ttm) REVERT: B 203 MET cc_start: 0.6615 (tmm) cc_final: 0.6303 (tmm) REVERT: C 563 ASP cc_start: 0.8676 (m-30) cc_final: 0.8441 (m-30) REVERT: C 847 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.6044 (ttp) outliers start: 9 outliers final: 8 residues processed: 114 average time/residue: 0.2912 time to fit residues: 48.6367 Evaluate side-chains 110 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 871 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.0670 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 688 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.8844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6620 Z= 0.233 Angle : 0.601 5.930 9006 Z= 0.313 Chirality : 0.041 0.151 1047 Planarity : 0.005 0.042 1136 Dihedral : 4.295 16.451 906 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 1.59 % Allowed : 19.08 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.31), residues: 821 helix: 1.44 (0.24), residues: 461 sheet: -2.24 (0.54), residues: 65 loop : -1.52 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 873 HIS 0.005 0.001 HIS C 859 PHE 0.025 0.002 PHE B 172 TYR 0.016 0.001 TYR C 910 ARG 0.003 0.000 ARG C 505 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 MET cc_start: 0.7706 (ttm) cc_final: 0.7469 (ttm) REVERT: C 563 ASP cc_start: 0.8689 (m-30) cc_final: 0.8455 (m-30) REVERT: C 847 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.6178 (ttp) outliers start: 11 outliers final: 8 residues processed: 114 average time/residue: 0.3099 time to fit residues: 52.7535 Evaluate side-chains 108 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 871 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 6 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 580 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.9047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6620 Z= 0.230 Angle : 0.601 5.899 9006 Z= 0.311 Chirality : 0.041 0.138 1047 Planarity : 0.005 0.041 1136 Dihedral : 4.274 16.768 906 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.30 % Allowed : 19.65 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.31), residues: 821 helix: 1.45 (0.24), residues: 461 sheet: -2.23 (0.54), residues: 65 loop : -1.48 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 873 HIS 0.007 0.001 HIS C 859 PHE 0.021 0.002 PHE B 315 TYR 0.014 0.001 TYR C 910 ARG 0.002 0.000 ARG C 505 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 MET cc_start: 0.7682 (ttm) cc_final: 0.7461 (ttm) REVERT: B 63 MET cc_start: 0.8423 (mmt) cc_final: 0.8056 (mmt) REVERT: C 563 ASP cc_start: 0.8697 (m-30) cc_final: 0.8463 (m-30) REVERT: C 688 ASN cc_start: 0.8214 (t0) cc_final: 0.7918 (p0) REVERT: C 847 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.6256 (ttp) outliers start: 9 outliers final: 8 residues processed: 111 average time/residue: 0.3167 time to fit residues: 50.0614 Evaluate side-chains 111 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 871 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.113705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.090078 restraints weight = 50839.856| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.84 r_work: 0.3487 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.9319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6620 Z= 0.220 Angle : 0.609 7.664 9006 Z= 0.311 Chirality : 0.041 0.137 1047 Planarity : 0.005 0.045 1136 Dihedral : 4.272 18.094 906 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.43 % Favored : 92.45 % Rotamer: Outliers : 1.45 % Allowed : 20.23 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.31), residues: 821 helix: 1.47 (0.24), residues: 461 sheet: -2.35 (0.52), residues: 65 loop : -1.47 (0.40), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 873 HIS 0.006 0.001 HIS C 859 PHE 0.025 0.002 PHE C 523 TYR 0.013 0.001 TYR C 910 ARG 0.006 0.000 ARG C 982 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4135.58 seconds wall clock time: 72 minutes 26.14 seconds (4346.14 seconds total)