Starting phenix.real_space_refine on Fri Mar 15 23:26:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/03_2024/8tj3_41299.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/03_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_41299/03_2024/8tj3_41299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/03_2024/8tj3_41299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/03_2024/8tj3_41299.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/03_2024/8tj3_41299.pdb" } 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-5265/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: 5.59, per 1000 atoms: 0.43 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: 9.69 Conformation dependent library (CDL) restraints added in 1.2 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: 0.90 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: 4.49 Time building geometry restraints manager: 10.20 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 1.850 nonbonded pdb=" H THR C 630 " pdb=" O LEU C 860 " model vdw 1.739 1.850 nonbonded pdb=" O ILE B 35 " pdb=" HG SER B 39 " model vdw 1.741 1.850 nonbonded pdb=" H ARG C 435 " pdb=" O VAL C 606 " model vdw 1.757 1.850 nonbonded pdb=" OG1 THR C 630 " pdb=" H VAL C 660 " model vdw 1.767 1.850 ... (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 ========== 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: 4.350 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: 0.210 Extract box with map and model: 12.910 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 40.990 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.770 ------------------------------------------------------------------------------- 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 : 1.000 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: 0.4324 time to fit residues: 115.6815 Evaluate side-chains 135 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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: 0.0980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.0050 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6620 Z= 0.223 Angle : 0.643 9.390 9006 Z= 0.330 Chirality : 0.042 0.155 1047 Planarity : 0.006 0.124 1136 Dihedral : 5.456 66.701 910 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.16 % Allowed : 8.67 % Favored : 90.17 % 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: 0.27 (0.31), residues: 821 helix: 1.36 (0.25), residues: 460 sheet: -1.74 (0.74), residues: 43 loop : -1.32 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 873 HIS 0.007 0.001 HIS C 987 PHE 0.020 0.001 PHE B 315 TYR 0.014 0.002 TYR C 916 ARG 0.015 0.001 ARG C 500 *********************** 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 149 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 1.097 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: C 573 LEU cc_start: 0.7853 (mm) cc_final: 0.7471 (pt) REVERT: C 699 THR cc_start: 0.3579 (p) cc_final: 0.3326 (p) REVERT: C 700 GLN cc_start: 0.6639 (OUTLIER) cc_final: 0.6351 (mp10) REVERT: C 839 PRO cc_start: 0.5721 (Cg_exo) cc_final: 0.5134 (Cg_endo) REVERT: C 896 MET cc_start: 0.3388 (mtp) cc_final: 0.2925 (tpt) outliers start: 8 outliers final: 6 residues processed: 147 average time/residue: 0.3224 time to fit residues: 66.5285 Evaluate side-chains 136 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 580 HIS Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 864 THR 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: 2.9990 chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.3980 chunk 20 optimal weight: 0.0970 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 970 ASN ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6620 Z= 0.225 Angle : 0.625 7.080 9006 Z= 0.322 Chirality : 0.041 0.146 1047 Planarity : 0.006 0.109 1136 Dihedral : 5.486 71.154 910 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.45 % Allowed : 11.13 % Favored : 87.43 % 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: 0.33 (0.31), residues: 821 helix: 1.52 (0.25), residues: 460 sheet: -2.10 (0.62), residues: 57 loop : -1.35 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 36 HIS 0.004 0.001 HIS C 859 PHE 0.015 0.001 PHE B 315 TYR 0.014 0.001 TYR C 703 ARG 0.006 0.001 ARG C 397 *********************** 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 145 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 0.929 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: C 573 LEU cc_start: 0.7937 (mm) cc_final: 0.7581 (pt) REVERT: C 700 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6541 (mp10) REVERT: C 862 MET cc_start: 0.6137 (tpp) cc_final: 0.5895 (ttm) REVERT: C 896 MET cc_start: 0.3669 (mtp) cc_final: 0.2847 (tpt) outliers start: 10 outliers final: 9 residues processed: 141 average time/residue: 0.3329 time to fit residues: 65.4064 Evaluate side-chains 142 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL 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 C residue 450 ASP Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 970 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 ** C 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 6620 Z= 0.359 Angle : 0.719 7.356 9006 Z= 0.379 Chirality : 0.044 0.174 1047 Planarity : 0.006 0.069 1136 Dihedral : 5.624 63.764 910 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.43 % Favored : 92.45 % Rotamer: Outliers : 1.73 % Allowed : 13.44 % Favored : 84.83 % 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: -0.29 (0.30), residues: 821 helix: 1.05 (0.24), residues: 459 sheet: -2.14 (0.60), residues: 60 loop : -1.72 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 245 HIS 0.009 0.002 HIS B 247 PHE 0.027 0.002 PHE B 172 TYR 0.016 0.002 TYR C 463 ARG 0.011 0.001 ARG C 802 *********************** 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 148 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 0.986 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: B 306 MET cc_start: 0.8514 (tpt) cc_final: 0.8129 (tpt) REVERT: C 573 LEU cc_start: 0.8172 (mm) cc_final: 0.7844 (tp) REVERT: C 700 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: C 989 MET cc_start: 0.4491 (tmm) cc_final: 0.3511 (ptp) outliers start: 12 outliers final: 10 residues processed: 143 average time/residue: 0.3236 time to fit residues: 65.0145 Evaluate side-chains 133 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 THR 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 C residue 450 ASP Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 911 PHE Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 966 MET 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: 0.8980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 615 GLN C 841 GLN ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.6527 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= 0.229 Angle : 0.606 6.031 9006 Z= 0.311 Chirality : 0.041 0.152 1047 Planarity : 0.004 0.035 1136 Dihedral : 5.441 68.252 910 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.59 % Allowed : 16.47 % Favored : 81.94 % 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: 1.36 (0.25), residues: 462 sheet: -1.68 (0.63), residues: 58 loop : -1.54 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 245 HIS 0.004 0.001 HIS B 360 PHE 0.024 0.001 PHE B 172 TYR 0.018 0.002 TYR C 545 ARG 0.003 0.000 ARG C 982 *********************** 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 141 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 0.959 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: C 573 LEU cc_start: 0.8210 (mm) cc_final: 0.7868 (pt) REVERT: C 700 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6521 (mp10) REVERT: C 802 ARG cc_start: 0.7855 (mtp180) cc_final: 0.7648 (mtp180) outliers start: 11 outliers final: 10 residues processed: 136 average time/residue: 0.3265 time to fit residues: 62.1751 Evaluate side-chains 136 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 471 LYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 911 PHE Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 964 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 841 GLN ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.7184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6620 Z= 0.243 Angle : 0.602 6.573 9006 Z= 0.310 Chirality : 0.041 0.150 1047 Planarity : 0.004 0.036 1136 Dihedral : 5.268 62.167 910 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.88 % Allowed : 17.34 % Favored : 80.78 % 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 (0.30), residues: 821 helix: 1.43 (0.25), residues: 455 sheet: -1.82 (0.60), residues: 62 loop : -1.48 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 873 HIS 0.006 0.001 HIS B 247 PHE 0.031 0.002 PHE B 172 TYR 0.032 0.002 TYR C 910 ARG 0.002 0.000 ARG B 208 *********************** 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 136 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.948 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 306 MET cc_start: 0.8628 (tpt) cc_final: 0.8290 (tpt) REVERT: C 573 LEU cc_start: 0.8236 (mm) cc_final: 0.7842 (tp) REVERT: C 700 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.6821 (mp10) REVERT: C 847 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5753 (ttp) outliers start: 13 outliers final: 9 residues processed: 128 average time/residue: 0.2987 time to fit residues: 54.8938 Evaluate side-chains 128 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ILE 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 471 LYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 952 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 841 GLN ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.7794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6620 Z= 0.236 Angle : 0.599 6.156 9006 Z= 0.309 Chirality : 0.040 0.157 1047 Planarity : 0.005 0.042 1136 Dihedral : 5.204 62.215 910 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 2.17 % Allowed : 17.77 % Favored : 80.06 % 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: 0.24 (0.30), residues: 821 helix: 1.51 (0.25), residues: 455 sheet: -1.65 (0.59), residues: 65 loop : -1.55 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 74 HIS 0.004 0.001 HIS C 859 PHE 0.029 0.002 PHE B 172 TYR 0.021 0.002 TYR C 910 ARG 0.004 0.000 ARG C 982 *********************** 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 136 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.041 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 20 MET cc_start: 0.7641 (ttm) cc_final: 0.7405 (ttm) REVERT: B 46 MET cc_start: 0.8026 (tpt) cc_final: 0.7648 (tpt) REVERT: C 573 LEU cc_start: 0.8356 (mm) cc_final: 0.7999 (pt) REVERT: C 700 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: C 847 MET cc_start: 0.6175 (OUTLIER) cc_final: 0.5827 (ttp) outliers start: 15 outliers final: 11 residues processed: 131 average time/residue: 0.3238 time to fit residues: 59.6823 Evaluate side-chains 127 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 B residue 256 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 471 LYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 964 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 GLN ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.8344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6620 Z= 0.275 Angle : 0.619 7.131 9006 Z= 0.319 Chirality : 0.041 0.148 1047 Planarity : 0.004 0.043 1136 Dihedral : 5.154 60.451 910 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.02 % Allowed : 18.21 % Favored : 79.77 % 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: 0.10 (0.30), residues: 821 helix: 1.38 (0.24), residues: 455 sheet: -1.80 (0.58), residues: 69 loop : -1.55 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 74 HIS 0.005 0.001 HIS B 247 PHE 0.022 0.002 PHE B 172 TYR 0.015 0.002 TYR C 910 ARG 0.003 0.000 ARG C 982 *********************** 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 126 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.033 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: B 20 MET cc_start: 0.7713 (ttm) cc_final: 0.7376 (ttm) REVERT: B 46 MET cc_start: 0.8095 (tpt) cc_final: 0.7561 (tpt) REVERT: B 306 MET cc_start: 0.8635 (tpt) cc_final: 0.8168 (tpt) REVERT: C 573 LEU cc_start: 0.8467 (mm) cc_final: 0.8139 (pt) REVERT: C 951 MET cc_start: 0.6992 (tmm) cc_final: 0.6488 (tpp) outliers start: 14 outliers final: 12 residues processed: 121 average time/residue: 0.3161 time to fit residues: 55.7774 Evaluate side-chains 116 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 B residue 256 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 471 LYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 952 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 70 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 GLN ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.8588 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= 0.216 Angle : 0.585 6.352 9006 Z= 0.299 Chirality : 0.040 0.154 1047 Planarity : 0.004 0.043 1136 Dihedral : 4.362 31.984 907 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.59 % Allowed : 19.80 % Favored : 78.61 % 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: 0.29 (0.30), residues: 821 helix: 1.53 (0.24), residues: 455 sheet: -1.57 (0.60), residues: 65 loop : -1.52 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 74 HIS 0.006 0.001 HIS C 859 PHE 0.024 0.002 PHE B 172 TYR 0.016 0.001 TYR C 910 ARG 0.002 0.000 ARG B 208 *********************** 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 118 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.994 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: B 20 MET cc_start: 0.7647 (ttm) cc_final: 0.7372 (ttm) REVERT: C 573 LEU cc_start: 0.8504 (mm) cc_final: 0.8192 (pt) outliers start: 11 outliers final: 9 residues processed: 116 average time/residue: 0.3273 time to fit residues: 53.3889 Evaluate side-chains 109 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 256 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 471 LYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 863 SER 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: 0.5980 chunk 76 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 20 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.8828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6620 Z= 0.201 Angle : 0.584 6.141 9006 Z= 0.301 Chirality : 0.040 0.135 1047 Planarity : 0.005 0.043 1136 Dihedral : 4.210 19.555 906 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.16 % Allowed : 21.24 % Favored : 77.60 % 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: 0.34 (0.30), residues: 821 helix: 1.55 (0.24), residues: 461 sheet: -1.60 (0.59), residues: 65 loop : -1.50 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 74 HIS 0.006 0.001 HIS C 859 PHE 0.024 0.002 PHE B 172 TYR 0.033 0.001 TYR C 910 ARG 0.005 0.000 ARG B 208 ********************** 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 111 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 1.081 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: C 573 LEU cc_start: 0.8495 (mm) cc_final: 0.8206 (pt) outliers start: 8 outliers final: 6 residues processed: 110 average time/residue: 0.3342 time to fit residues: 51.5592 Evaluate side-chains 109 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 471 LYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 863 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 57 optimal weight: 0.0870 chunk 3 optimal weight: 0.0000 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.0570 overall best weight: 0.1478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 GLN ** 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 = 0.4044 r_free = 0.4044 target = 0.115174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.092051 restraints weight = 51816.577| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.89 r_work: 0.3522 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.8902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6620 Z= 0.171 Angle : 0.584 6.118 9006 Z= 0.296 Chirality : 0.040 0.150 1047 Planarity : 0.005 0.042 1136 Dihedral : 4.157 19.934 906 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.58 % Allowed : 21.97 % Favored : 77.46 % 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: 0.56 (0.31), residues: 821 helix: 1.77 (0.25), residues: 461 sheet: -1.58 (0.59), residues: 65 loop : -1.46 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 181 HIS 0.004 0.001 HIS B 362 PHE 0.024 0.001 PHE B 315 TYR 0.018 0.001 TYR C 910 ARG 0.003 0.000 ARG B 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4071.73 seconds wall clock time: 71 minutes 55.48 seconds (4315.48 seconds total)