Starting phenix.real_space_refine on Sun Dec 10 02:24:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/12_2023/8tj3_41299.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/12_2023/8tj3_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_41299/12_2023/8tj3_41299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/12_2023/8tj3_41299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/12_2023/8tj3_41299.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj3_41299/12_2023/8tj3_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.81, per 1000 atoms: 0.44 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: 10.67 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: 0.92 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: 4.73 Time building geometry restraints manager: 11.12 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: 5418 17.72 - 35.44: 459 35.44 - 53.15: 123 53.15 - 70.87: 27 70.87 - 88.59: 16 Dihedral angle restraints: 6043 sinusoidal: 3243 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 6040 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: 6.080 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: 13.530 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 43.540 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.490 ------------------------------------------------------------------------------- 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 : 0.987 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 outliers start: 8 outliers final: 2 residues processed: 207 average time/residue: 0.4487 time to fit residues: 120.4252 Evaluate side-chains 132 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1693 time to fit residues: 1.7704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0670 chunk 25 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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: 0.6251 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6620 Z= 0.241 Angle : 0.651 9.956 9006 Z= 0.334 Chirality : 0.043 0.157 1047 Planarity : 0.005 0.086 1136 Dihedral : 4.314 25.224 906 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.16 % Allowed : 9.25 % Favored : 89.60 % 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: 0.23 (0.31), residues: 821 helix: 1.36 (0.25), residues: 461 sheet: -2.18 (0.57), residues: 60 loop : -1.22 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 199 HIS 0.007 0.001 HIS C 987 PHE 0.021 0.001 PHE B 315 TYR 0.012 0.002 TYR B 206 ARG 0.014 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 145 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.094 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 outliers start: 8 outliers final: 6 residues processed: 143 average time/residue: 0.3574 time to fit residues: 72.5407 Evaluate side-chains 135 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1988 time to fit residues: 3.4282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 75 optimal weight: 0.0870 chunk 81 optimal weight: 0.0670 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 overall best weight: 0.3014 ------------------------------------------------------------------------------- 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: 0.6340 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6620 Z= 0.195 Angle : 0.593 7.584 9006 Z= 0.304 Chirality : 0.041 0.175 1047 Planarity : 0.004 0.048 1136 Dihedral : 4.199 25.262 906 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.14 % Allowed : 11.85 % Favored : 88.01 % 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: 0.44 (0.31), residues: 821 helix: 1.59 (0.25), residues: 460 sheet: -2.04 (0.59), residues: 57 loop : -1.27 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 873 HIS 0.004 0.001 HIS C 859 PHE 0.018 0.001 PHE B 315 TYR 0.012 0.001 TYR B 206 ARG 0.004 0.000 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 135 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.923 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 outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.3319 time to fit residues: 63.1620 Evaluate side-chains 129 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1448 time to fit residues: 1.4362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.0020 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 C 841 GLN ** C 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 970 ASN C 983 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 6620 Z= 0.275 Angle : 0.648 7.271 9006 Z= 0.329 Chirality : 0.042 0.181 1047 Planarity : 0.005 0.042 1136 Dihedral : 4.331 19.049 906 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 1.59 % Allowed : 11.56 % Favored : 86.85 % 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: 0.37 (0.31), residues: 821 helix: 1.57 (0.25), residues: 461 sheet: -2.08 (0.58), residues: 60 loop : -1.36 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 181 HIS 0.007 0.001 HIS B 247 PHE 0.015 0.002 PHE B 315 TYR 0.020 0.002 TYR C 638 ARG 0.004 0.001 ARG B 259 *********************** 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 145 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 0.909 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 outliers start: 11 outliers final: 9 residues processed: 139 average time/residue: 0.3310 time to fit residues: 64.6723 Evaluate side-chains 133 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1721 time to fit residues: 4.0815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 841 GLN C 970 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6620 Z= 0.303 Angle : 0.671 11.563 9006 Z= 0.345 Chirality : 0.043 0.220 1047 Planarity : 0.005 0.060 1136 Dihedral : 4.385 18.992 906 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.58 % Favored : 93.18 % Rotamer: Outliers : 1.01 % Allowed : 13.44 % Favored : 85.55 % 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: -0.02 (0.30), residues: 821 helix: 1.32 (0.24), residues: 459 sheet: -1.96 (0.61), residues: 59 loop : -1.70 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 245 HIS 0.016 0.002 HIS C 987 PHE 0.014 0.002 PHE B 255 TYR 0.025 0.002 TYR C 545 ARG 0.005 0.001 ARG C 802 *********************** 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: 7 poor density : 134 time to evaluate : 1.028 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 outliers start: 7 outliers final: 4 residues processed: 137 average time/residue: 0.3418 time to fit residues: 66.1029 Evaluate side-chains 122 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1719 time to fit residues: 2.5134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 37 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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: 0.7168 moved from start: 0.7073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6620 Z= 0.234 Angle : 0.619 6.848 9006 Z= 0.317 Chirality : 0.041 0.167 1047 Planarity : 0.004 0.032 1136 Dihedral : 4.294 17.331 906 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.55 % Favored : 92.33 % Rotamer: Outliers : 0.43 % Allowed : 16.91 % Favored : 82.66 % 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: 1.43 (0.25), residues: 460 sheet: -2.02 (0.62), residues: 60 loop : -1.65 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 873 HIS 0.005 0.001 HIS B 247 PHE 0.026 0.002 PHE B 315 TYR 0.014 0.002 TYR C 545 ARG 0.002 0.000 ARG C 982 *********************** 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 121 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.090 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 outliers start: 3 outliers final: 1 residues processed: 121 average time/residue: 0.3594 time to fit residues: 61.2320 Evaluate side-chains 117 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6982 time to fit residues: 2.1239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.0980 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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: 0.7248 moved from start: 0.7672 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= 0.242 Angle : 0.610 6.755 9006 Z= 0.313 Chirality : 0.041 0.168 1047 Planarity : 0.005 0.067 1136 Dihedral : 4.257 17.197 906 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.92 % Favored : 91.96 % Rotamer: Outliers : 0.58 % Allowed : 16.91 % 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: 0.15 (0.30), residues: 821 helix: 1.51 (0.24), residues: 459 sheet: -2.01 (0.60), residues: 63 loop : -1.68 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 873 HIS 0.005 0.001 HIS B 247 PHE 0.019 0.002 PHE B 315 TYR 0.011 0.001 TYR B 317 ARG 0.012 0.001 ARG C 802 *********************** 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 118 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 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 outliers start: 4 outliers final: 1 residues processed: 116 average time/residue: 0.3189 time to fit residues: 53.2586 Evaluate side-chains 111 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2070 time to fit residues: 1.5950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 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 688 ASN ** 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: 0.7285 moved from start: 0.8111 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= 0.226 Angle : 0.613 8.000 9006 Z= 0.311 Chirality : 0.041 0.177 1047 Planarity : 0.004 0.032 1136 Dihedral : 4.222 16.785 906 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.19 % Favored : 92.69 % Rotamer: Outliers : 0.14 % Allowed : 17.05 % Favored : 82.80 % 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: 0.19 (0.31), residues: 821 helix: 1.51 (0.25), residues: 464 sheet: -1.94 (0.58), residues: 65 loop : -1.68 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 873 HIS 0.004 0.001 HIS B 362 PHE 0.021 0.001 PHE B 315 TYR 0.012 0.002 TYR C 427 ARG 0.009 0.000 ARG C 802 *********************** 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 114 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.966 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 outliers start: 1 outliers final: 1 residues processed: 113 average time/residue: 0.3189 time to fit residues: 51.8709 Evaluate side-chains 110 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1597 time to fit residues: 1.5485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 37 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.8520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6620 Z= 0.220 Angle : 0.596 6.059 9006 Z= 0.304 Chirality : 0.041 0.164 1047 Planarity : 0.005 0.044 1136 Dihedral : 4.227 20.497 906 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 17.92 % Favored : 82.08 % 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 (0.31), residues: 821 helix: 1.61 (0.25), residues: 462 sheet: -1.98 (0.58), residues: 65 loop : -1.64 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 245 HIS 0.005 0.001 HIS C 908 PHE 0.019 0.001 PHE B 315 TYR 0.028 0.001 TYR C 910 ARG 0.009 0.000 ARG C 802 *********************** 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 108 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.018 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 outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3110 time to fit residues: 49.2440 Evaluate side-chains 108 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.9068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6620 Z= 0.260 Angle : 0.618 6.280 9006 Z= 0.323 Chirality : 0.042 0.153 1047 Planarity : 0.005 0.034 1136 Dihedral : 4.234 16.855 906 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.92 % Favored : 91.96 % Rotamer: Outliers : 0.14 % Allowed : 18.21 % Favored : 81.65 % 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: 1.47 (0.25), residues: 462 sheet: -1.96 (0.58), residues: 65 loop : -1.63 (0.38), residues: 294 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 0.019 0.002 PHE B 315 TYR 0.014 0.002 TYR C 427 ARG 0.008 0.001 ARG C 802 ********************** 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 106 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.975 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 outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.3145 time to fit residues: 48.2603 Evaluate side-chains 101 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1466 time to fit residues: 1.5408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 8 optimal weight: 0.0870 chunk 12 optimal weight: 0.0980 chunk 57 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 overall best weight: 0.2958 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.114780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.091202 restraints weight = 51168.081| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.85 r_work: 0.3507 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.9145 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= 0.180 Angle : 0.585 6.679 9006 Z= 0.296 Chirality : 0.040 0.157 1047 Planarity : 0.004 0.036 1136 Dihedral : 4.150 16.972 906 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 19.65 % Favored : 80.35 % 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: 0.48 (0.31), residues: 821 helix: 1.74 (0.25), residues: 462 sheet: -1.92 (0.58), residues: 65 loop : -1.49 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 245 HIS 0.006 0.001 HIS C 859 PHE 0.024 0.001 PHE B 315 TYR 0.018 0.001 TYR C 910 ARG 0.008 0.000 ARG C 802 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4132.81 seconds wall clock time: 73 minutes 22.62 seconds (4402.62 seconds total)