Starting phenix.real_space_refine on Thu Nov 14 23:37:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qat_18302/11_2024/8qat_18302.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qat_18302/11_2024/8qat_18302.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/8qat_18302/11_2024/8qat_18302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qat_18302/11_2024/8qat_18302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qat_18302/11_2024/8qat_18302.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qat_18302/11_2024/8qat_18302.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 4978 2.51 5 N 1348 2.21 5 O 1393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7758 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 646 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "B" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 522 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "C" Number of atoms: 4767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4767 Classifications: {'peptide': 606} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 565} Chain breaks: 4 Chain: "D" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1823 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 203} Time building chain proxies: 5.15, per 1000 atoms: 0.66 Number of scatterers: 7758 At special positions: 0 Unit cell: (145.083, 120.726, 83.661, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1393 8.00 N 1348 7.00 C 4978 6.00 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 - 3.00 Amino acid : True - 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: 2.11 Conformation dependent library (CDL) restraints added in 1.4 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 2 sheets defined 69.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 627 through 687 removed outlier: 3.702A pdb=" N ALA A 632 " --> pdb=" O PRO A 628 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 702 Processing helix chain 'B' and resid 628 through 689 removed outlier: 3.832A pdb=" N LYS B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR B 664 " --> pdb=" O MET B 660 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N MET B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 689 " --> pdb=" O LEU B 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 53 removed outlier: 3.614A pdb=" N LEU C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 82 Processing helix chain 'C' and resid 94 through 101 Processing helix chain 'C' and resid 104 through 117 removed outlier: 3.511A pdb=" N TRP C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 122 through 141 removed outlier: 3.789A pdb=" N ALA C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 147 removed outlier: 3.641A pdb=" N ARG C 147 " --> pdb=" O PRO C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 147' Processing helix chain 'C' and resid 148 through 162 removed outlier: 3.616A pdb=" N ARG C 152 " --> pdb=" O HIS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 190 Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.804A pdb=" N ARG C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.744A pdb=" N VAL C 220 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 242 removed outlier: 3.650A pdb=" N GLY C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 255 removed outlier: 3.862A pdb=" N SER C 255 " --> pdb=" O ILE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 269 Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 294 through 314 removed outlier: 3.570A pdb=" N LEU C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 300 " --> pdb=" O ALA C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'C' and resid 334 through 340 removed outlier: 4.007A pdb=" N HIS C 340 " --> pdb=" O GLY C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 361 Processing helix chain 'C' and resid 363 through 377 removed outlier: 3.545A pdb=" N HIS C 377 " --> pdb=" O PHE C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 391 Processing helix chain 'C' and resid 396 through 412 Processing helix chain 'C' and resid 414 through 422 removed outlier: 4.033A pdb=" N LEU C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 436 through 441 removed outlier: 3.587A pdb=" N VAL C 440 " --> pdb=" O LYS C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 455 Processing helix chain 'C' and resid 550 through 568 removed outlier: 3.593A pdb=" N TYR C 554 " --> pdb=" O ASN C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 751 Processing helix chain 'C' and resid 756 through 772 Processing helix chain 'C' and resid 775 through 783 removed outlier: 3.542A pdb=" N PHE C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 814 Processing helix chain 'C' and resid 816 through 835 removed outlier: 3.557A pdb=" N LEU C 828 " --> pdb=" O ALA C 824 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY C 832 " --> pdb=" O LEU C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 945 removed outlier: 3.654A pdb=" N VAL C 929 " --> pdb=" O VAL C 925 " (cutoff:3.500A) Proline residue: C 932 - end of helix Processing helix chain 'D' and resid 70 through 89 Processing helix chain 'D' and resid 159 through 163 removed outlier: 4.097A pdb=" N ARG D 162 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 184 removed outlier: 3.568A pdb=" N VAL D 177 " --> pdb=" O HIS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 203 Processing helix chain 'D' and resid 205 through 223 removed outlier: 3.532A pdb=" N ARG D 223 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 255 removed outlier: 4.841A pdb=" N GLU D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AA2, first strand: chain 'D' and resid 94 through 98 removed outlier: 4.245A pdb=" N GLY D 120 " --> pdb=" O ILE D 112 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU D 140 " --> pdb=" O LEU D 158 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1440 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: 2.25 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2051 1.34 - 1.46: 1475 1.46 - 1.58: 4355 1.58 - 1.70: 1 1.70 - 1.82: 60 Bond restraints: 7942 Sorted by residual: bond pdb=" CB PRO D 193 " pdb=" CG PRO D 193 " ideal model delta sigma weight residual 1.492 1.674 -0.182 5.00e-02 4.00e+02 1.32e+01 bond pdb=" C VAL C 332 " pdb=" N PRO C 333 " ideal model delta sigma weight residual 1.337 1.380 -0.043 1.24e-02 6.50e+03 1.20e+01 bond pdb=" C GLY C 149 " pdb=" N PRO C 150 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.36e-02 5.41e+03 6.89e+00 bond pdb=" C PHE C 817 " pdb=" N PRO C 818 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.28e-02 6.10e+03 4.48e+00 bond pdb=" CB GLU B 682 " pdb=" CG GLU B 682 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.35e+00 ... (remaining 7937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 10623 3.66 - 7.32: 121 7.32 - 10.98: 21 10.98 - 14.65: 2 14.65 - 18.31: 1 Bond angle restraints: 10768 Sorted by residual: angle pdb=" CA PRO D 193 " pdb=" N PRO D 193 " pdb=" CD PRO D 193 " ideal model delta sigma weight residual 112.00 93.69 18.31 1.40e+00 5.10e-01 1.71e+02 angle pdb=" N PRO D 193 " pdb=" CA PRO D 193 " pdb=" C PRO D 193 " ideal model delta sigma weight residual 110.40 120.13 -9.73 1.61e+00 3.86e-01 3.65e+01 angle pdb=" N SER C 270 " pdb=" CA SER C 270 " pdb=" C SER C 270 " ideal model delta sigma weight residual 114.75 108.02 6.73 1.26e+00 6.30e-01 2.85e+01 angle pdb=" CA GLN D 227 " pdb=" CB GLN D 227 " pdb=" CG GLN D 227 " ideal model delta sigma weight residual 114.10 124.73 -10.63 2.00e+00 2.50e-01 2.82e+01 angle pdb=" N HIS C 43 " pdb=" CA HIS C 43 " pdb=" CB HIS C 43 " ideal model delta sigma weight residual 110.12 117.45 -7.33 1.47e+00 4.63e-01 2.49e+01 ... (remaining 10763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4215 17.81 - 35.61: 456 35.61 - 53.42: 132 53.42 - 71.22: 13 71.22 - 89.03: 11 Dihedral angle restraints: 4827 sinusoidal: 1977 harmonic: 2850 Sorted by residual: dihedral pdb=" CA VAL C 313 " pdb=" C VAL C 313 " pdb=" N ALA C 314 " pdb=" CA ALA C 314 " ideal model delta harmonic sigma weight residual -180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA GLU C 933 " pdb=" C GLU C 933 " pdb=" N PHE C 934 " pdb=" CA PHE C 934 " ideal model delta harmonic sigma weight residual 180.00 157.01 22.99 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA GLU C 415 " pdb=" C GLU C 415 " pdb=" N ASP C 416 " pdb=" CA ASP C 416 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 4824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1081 0.090 - 0.180: 117 0.180 - 0.270: 2 0.270 - 0.360: 1 0.360 - 0.450: 1 Chirality restraints: 1202 Sorted by residual: chirality pdb=" CB VAL C 39 " pdb=" CA VAL C 39 " pdb=" CG1 VAL C 39 " pdb=" CG2 VAL C 39 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" CA PRO D 193 " pdb=" N PRO D 193 " pdb=" C PRO D 193 " pdb=" CB PRO D 193 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB VAL C 48 " pdb=" CA VAL C 48 " pdb=" CG1 VAL C 48 " pdb=" CG2 VAL C 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1199 not shown) Planarity restraints: 1382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 192 " 0.088 5.00e-02 4.00e+02 1.18e-01 2.25e+01 pdb=" N PRO D 193 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO D 193 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 193 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 193 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C PRO D 193 " 0.065 2.00e-02 2.50e+03 pdb=" O PRO D 193 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU D 194 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 817 " -0.020 2.00e-02 2.50e+03 2.40e-02 1.01e+01 pdb=" CG PHE C 817 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE C 817 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 817 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE C 817 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 817 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 817 " 0.004 2.00e-02 2.50e+03 ... (remaining 1379 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 385 2.73 - 3.28: 7523 3.28 - 3.82: 12656 3.82 - 4.36: 15120 4.36 - 4.90: 25404 Nonbonded interactions: 61088 Sorted by model distance: nonbonded pdb=" O VAL C 69 " pdb=" OG1 THR C 73 " model vdw 2.192 3.040 nonbonded pdb=" O ARG A 699 " pdb=" OG1 THR A 702 " model vdw 2.348 3.040 nonbonded pdb=" OG SER D 99 " pdb=" OD2 ASP D 232 " model vdw 2.366 3.040 nonbonded pdb=" O TYR D 74 " pdb=" OG SER D 78 " model vdw 2.367 3.040 nonbonded pdb=" O LEU C 339 " pdb=" NH2 ARG C 391 " model vdw 2.368 3.120 ... (remaining 61083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.030 Find NCS groups from input model: 0.070 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:3.190 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.182 7942 Z= 0.327 Angle : 1.029 18.308 10768 Z= 0.569 Chirality : 0.053 0.450 1202 Planarity : 0.009 0.118 1382 Dihedral : 16.201 89.031 2971 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.89 % Favored : 98.01 % Rotamer: Outliers : 0.35 % Allowed : 15.45 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.24), residues: 954 helix: -1.35 (0.17), residues: 626 sheet: -2.60 (0.84), residues: 30 loop : -0.51 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP C 44 HIS 0.020 0.002 HIS A 677 PHE 0.055 0.003 PHE C 817 TYR 0.011 0.002 TYR A 651 ARG 0.007 0.001 ARG C 570 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 671 ASN cc_start: 0.7331 (m110) cc_final: 0.7085 (m110) REVERT: B 652 GLU cc_start: 0.8596 (tp30) cc_final: 0.8386 (tp30) REVERT: C 40 PHE cc_start: 0.8180 (t80) cc_final: 0.7974 (t80) REVERT: C 43 HIS cc_start: 0.8050 (m90) cc_final: 0.7060 (m-70) REVERT: C 76 MET cc_start: 0.8233 (mtp) cc_final: 0.7448 (mmp) REVERT: C 112 TRP cc_start: 0.8685 (t60) cc_final: 0.8453 (t60) REVERT: C 433 MET cc_start: 0.7556 (pmm) cc_final: 0.7111 (pmm) REVERT: C 436 GLN cc_start: 0.7760 (tt0) cc_final: 0.7530 (tt0) outliers start: 3 outliers final: 1 residues processed: 144 average time/residue: 0.2324 time to fit residues: 44.2024 Evaluate side-chains 121 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 318 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.0070 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 636 GLN C 143 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 GLN ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 7942 Z= 0.191 Angle : 0.604 11.503 10768 Z= 0.310 Chirality : 0.041 0.155 1202 Planarity : 0.006 0.056 1382 Dihedral : 4.652 24.687 1057 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 2.24 % Allowed : 15.80 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.35 (0.27), residues: 954 helix: 0.61 (0.20), residues: 636 sheet: -2.37 (0.75), residues: 30 loop : -0.03 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 669 HIS 0.007 0.001 HIS A 677 PHE 0.012 0.001 PHE C 99 TYR 0.015 0.001 TYR C 827 ARG 0.003 0.000 ARG A 640 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 638 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8308 (pp30) REVERT: A 639 GLU cc_start: 0.8274 (tp30) cc_final: 0.7893 (tp30) REVERT: A 671 ASN cc_start: 0.7451 (m110) cc_final: 0.7147 (m110) REVERT: A 698 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6908 (mm-40) REVERT: B 656 SER cc_start: 0.7958 (m) cc_final: 0.7590 (p) REVERT: C 37 LEU cc_start: 0.8494 (mm) cc_final: 0.8197 (tp) REVERT: C 43 HIS cc_start: 0.8443 (m90) cc_final: 0.7814 (m-70) outliers start: 19 outliers final: 8 residues processed: 134 average time/residue: 0.2086 time to fit residues: 38.0807 Evaluate side-chains 124 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 325 TYR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 184 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 29 optimal weight: 0.0980 chunk 69 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7942 Z= 0.240 Angle : 0.601 7.990 10768 Z= 0.303 Chirality : 0.043 0.170 1202 Planarity : 0.005 0.061 1382 Dihedral : 4.394 22.443 1056 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 2.48 % Allowed : 17.81 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.28), residues: 954 helix: 1.27 (0.21), residues: 635 sheet: -2.09 (0.77), residues: 30 loop : 0.19 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 669 HIS 0.006 0.001 HIS D 148 PHE 0.014 0.002 PHE D 209 TYR 0.014 0.001 TYR D 77 ARG 0.003 0.000 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 638 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8354 (pp30) REVERT: A 671 ASN cc_start: 0.7576 (m110) cc_final: 0.7244 (m110) REVERT: A 698 GLN cc_start: 0.7282 (mm-40) cc_final: 0.6981 (mm-40) REVERT: B 656 SER cc_start: 0.7950 (m) cc_final: 0.7586 (p) REVERT: C 43 HIS cc_start: 0.8561 (m90) cc_final: 0.8083 (m-70) REVERT: C 76 MET cc_start: 0.8206 (mtp) cc_final: 0.7353 (mmp) REVERT: C 415 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7476 (tt0) outliers start: 21 outliers final: 15 residues processed: 137 average time/residue: 0.2020 time to fit residues: 37.3076 Evaluate side-chains 129 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 325 TYR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 565 CYS Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 230 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.0060 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7942 Z= 0.150 Angle : 0.551 12.722 10768 Z= 0.276 Chirality : 0.040 0.178 1202 Planarity : 0.005 0.055 1382 Dihedral : 4.132 20.750 1056 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.57 % Favored : 98.32 % Rotamer: Outliers : 2.48 % Allowed : 17.81 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.28), residues: 954 helix: 1.72 (0.21), residues: 634 sheet: -1.63 (0.82), residues: 30 loop : 0.19 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 669 HIS 0.005 0.001 HIS A 677 PHE 0.016 0.001 PHE D 209 TYR 0.014 0.001 TYR C 827 ARG 0.006 0.000 ARG A 697 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 638 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8325 (pp30) REVERT: A 671 ASN cc_start: 0.7408 (m110) cc_final: 0.7072 (m110) REVERT: A 698 GLN cc_start: 0.7316 (mm-40) cc_final: 0.7040 (mm-40) REVERT: B 642 ARG cc_start: 0.7837 (tmm160) cc_final: 0.7464 (tmm-80) REVERT: B 653 LYS cc_start: 0.8822 (mptt) cc_final: 0.8597 (mptt) REVERT: B 656 SER cc_start: 0.7911 (m) cc_final: 0.7567 (p) REVERT: B 660 MET cc_start: 0.7626 (tmm) cc_final: 0.6963 (mmm) REVERT: C 43 HIS cc_start: 0.8561 (m90) cc_final: 0.7985 (m-70) REVERT: C 76 MET cc_start: 0.8264 (mtp) cc_final: 0.7389 (mmp) REVERT: C 209 ARG cc_start: 0.7409 (mtm110) cc_final: 0.7130 (mtm110) REVERT: C 814 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.5901 (tm-30) REVERT: C 822 SER cc_start: 0.8108 (t) cc_final: 0.7729 (m) outliers start: 21 outliers final: 13 residues processed: 137 average time/residue: 0.2122 time to fit residues: 38.9666 Evaluate side-chains 131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 814 GLN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 184 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7942 Z= 0.341 Angle : 0.648 10.902 10768 Z= 0.323 Chirality : 0.045 0.181 1202 Planarity : 0.005 0.068 1382 Dihedral : 4.286 20.149 1056 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.20 % Favored : 97.69 % Rotamer: Outliers : 3.30 % Allowed : 17.92 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.28), residues: 954 helix: 1.57 (0.21), residues: 634 sheet: -1.66 (0.82), residues: 30 loop : 0.14 (0.40), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 669 HIS 0.009 0.001 HIS D 148 PHE 0.016 0.002 PHE D 209 TYR 0.019 0.002 TYR D 77 ARG 0.005 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 638 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8372 (pp30) REVERT: A 671 ASN cc_start: 0.7606 (m110) cc_final: 0.7341 (m110) REVERT: A 698 GLN cc_start: 0.7401 (mm-40) cc_final: 0.7081 (mm-40) REVERT: C 43 HIS cc_start: 0.8653 (m90) cc_final: 0.8092 (m-70) REVERT: C 83 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.6620 (t0) outliers start: 28 outliers final: 21 residues processed: 141 average time/residue: 0.2101 time to fit residues: 40.1144 Evaluate side-chains 133 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 325 TYR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 565 CYS Chi-restraints excluded: chain C residue 761 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 230 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 636 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7942 Z= 0.350 Angle : 0.655 9.588 10768 Z= 0.329 Chirality : 0.045 0.172 1202 Planarity : 0.005 0.069 1382 Dihedral : 4.378 20.907 1056 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.41 % Favored : 97.48 % Rotamer: Outliers : 3.18 % Allowed : 18.99 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.28), residues: 954 helix: 1.44 (0.21), residues: 634 sheet: -1.68 (0.82), residues: 30 loop : 0.03 (0.41), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 669 HIS 0.009 0.001 HIS D 148 PHE 0.018 0.002 PHE C 817 TYR 0.017 0.002 TYR D 77 ARG 0.004 0.000 ARG D 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 671 ASN cc_start: 0.7600 (m110) cc_final: 0.7315 (m110) REVERT: A 698 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7125 (mm-40) REVERT: B 653 LYS cc_start: 0.8816 (mptt) cc_final: 0.8554 (mptt) REVERT: C 43 HIS cc_start: 0.8744 (m90) cc_final: 0.8109 (m-70) REVERT: C 209 ARG cc_start: 0.7712 (mtm110) cc_final: 0.7432 (mtm110) REVERT: C 814 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.6343 (tm-30) outliers start: 27 outliers final: 22 residues processed: 138 average time/residue: 0.2407 time to fit residues: 44.3763 Evaluate side-chains 137 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 565 CYS Chi-restraints excluded: chain C residue 761 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 814 GLN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 230 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 42 optimal weight: 0.0050 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 636 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7942 Z= 0.174 Angle : 0.582 14.377 10768 Z= 0.293 Chirality : 0.041 0.168 1202 Planarity : 0.005 0.054 1382 Dihedral : 4.098 19.878 1056 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.89 % Favored : 98.01 % Rotamer: Outliers : 2.71 % Allowed : 19.58 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.29), residues: 954 helix: 1.84 (0.21), residues: 634 sheet: -1.43 (0.87), residues: 30 loop : 0.14 (0.41), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 669 HIS 0.006 0.001 HIS A 677 PHE 0.023 0.001 PHE C 99 TYR 0.017 0.001 TYR A 670 ARG 0.003 0.000 ARG D 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 657 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7104 (tt0) REVERT: A 671 ASN cc_start: 0.7452 (m110) cc_final: 0.7139 (m110) REVERT: A 698 GLN cc_start: 0.7405 (mm-40) cc_final: 0.7163 (mm-40) REVERT: B 653 LYS cc_start: 0.8839 (mptt) cc_final: 0.8613 (mptt) REVERT: B 656 SER cc_start: 0.7922 (m) cc_final: 0.7566 (p) REVERT: C 43 HIS cc_start: 0.8767 (m90) cc_final: 0.8134 (m-70) REVERT: C 209 ARG cc_start: 0.7655 (mtm110) cc_final: 0.7359 (mtm110) REVERT: C 415 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8109 (tp30) REVERT: C 814 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6118 (tm-30) outliers start: 23 outliers final: 17 residues processed: 133 average time/residue: 0.2051 time to fit residues: 36.9682 Evaluate side-chains 132 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 565 CYS Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 814 GLN Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 184 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 58 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 636 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7942 Z= 0.165 Angle : 0.577 14.013 10768 Z= 0.287 Chirality : 0.041 0.164 1202 Planarity : 0.005 0.051 1382 Dihedral : 3.955 19.270 1056 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.78 % Favored : 98.11 % Rotamer: Outliers : 2.48 % Allowed : 19.69 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.29), residues: 954 helix: 1.96 (0.21), residues: 634 sheet: -1.17 (0.89), residues: 30 loop : 0.24 (0.41), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 669 HIS 0.003 0.001 HIS A 677 PHE 0.011 0.001 PHE C 817 TYR 0.016 0.001 TYR A 670 ARG 0.005 0.000 ARG D 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 640 ARG cc_start: 0.7504 (mmm160) cc_final: 0.7296 (mmm160) REVERT: A 671 ASN cc_start: 0.7432 (m110) cc_final: 0.7122 (m110) REVERT: A 674 MET cc_start: 0.7117 (mmt) cc_final: 0.6276 (mmt) REVERT: A 698 GLN cc_start: 0.7347 (mm-40) cc_final: 0.7109 (mm-40) REVERT: B 656 SER cc_start: 0.7880 (m) cc_final: 0.7550 (p) REVERT: B 682 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7424 (mm-30) REVERT: C 43 HIS cc_start: 0.8776 (m90) cc_final: 0.8235 (m-70) REVERT: C 76 MET cc_start: 0.8213 (mtp) cc_final: 0.7373 (mmp) REVERT: C 209 ARG cc_start: 0.7656 (mtm110) cc_final: 0.7344 (mtm110) REVERT: C 814 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6197 (tm-30) outliers start: 21 outliers final: 16 residues processed: 134 average time/residue: 0.2088 time to fit residues: 38.2528 Evaluate side-chains 128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 565 CYS Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 814 GLN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 184 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 636 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7942 Z= 0.181 Angle : 0.585 13.518 10768 Z= 0.290 Chirality : 0.041 0.170 1202 Planarity : 0.005 0.050 1382 Dihedral : 3.935 19.222 1056 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.89 % Favored : 98.01 % Rotamer: Outliers : 2.71 % Allowed : 19.69 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.28), residues: 954 helix: 1.97 (0.21), residues: 640 sheet: -1.11 (0.88), residues: 30 loop : 0.16 (0.41), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 669 HIS 0.003 0.001 HIS D 148 PHE 0.030 0.001 PHE D 209 TYR 0.010 0.001 TYR C 554 ARG 0.004 0.000 ARG D 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 657 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7073 (tt0) REVERT: A 671 ASN cc_start: 0.7398 (m110) cc_final: 0.7077 (m110) REVERT: A 674 MET cc_start: 0.7183 (mmt) cc_final: 0.6331 (mmt) REVERT: A 698 GLN cc_start: 0.7370 (mm-40) cc_final: 0.7064 (mm-40) REVERT: B 653 LYS cc_start: 0.8814 (mptt) cc_final: 0.8538 (mptt) REVERT: B 656 SER cc_start: 0.7882 (m) cc_final: 0.7559 (p) REVERT: C 43 HIS cc_start: 0.8754 (m90) cc_final: 0.8156 (m-70) REVERT: C 76 MET cc_start: 0.8237 (mtp) cc_final: 0.7359 (mmp) REVERT: C 209 ARG cc_start: 0.7675 (mtm110) cc_final: 0.7411 (mtm110) REVERT: C 814 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6209 (tm-30) outliers start: 23 outliers final: 19 residues processed: 134 average time/residue: 0.2087 time to fit residues: 37.7808 Evaluate side-chains 135 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 565 CYS Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 761 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 814 GLN Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 230 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.0370 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 7 optimal weight: 0.0470 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 80 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 636 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7942 Z= 0.172 Angle : 0.590 15.297 10768 Z= 0.292 Chirality : 0.041 0.173 1202 Planarity : 0.005 0.052 1382 Dihedral : 3.851 18.059 1056 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.99 % Favored : 97.90 % Rotamer: Outliers : 2.48 % Allowed : 20.05 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.28), residues: 954 helix: 1.98 (0.21), residues: 642 sheet: -1.06 (0.87), residues: 30 loop : 0.16 (0.41), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 669 HIS 0.003 0.000 HIS C 43 PHE 0.032 0.001 PHE D 209 TYR 0.009 0.001 TYR C 554 ARG 0.007 0.000 ARG A 697 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.915 Fit side-chains REVERT: A 657 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6995 (tt0) REVERT: A 671 ASN cc_start: 0.7311 (m110) cc_final: 0.6990 (m110) REVERT: A 674 MET cc_start: 0.7074 (mmt) cc_final: 0.6248 (mmt) REVERT: A 698 GLN cc_start: 0.7341 (mm-40) cc_final: 0.7101 (mm-40) REVERT: B 642 ARG cc_start: 0.7855 (tmm160) cc_final: 0.7549 (tmm-80) REVERT: B 656 SER cc_start: 0.7852 (m) cc_final: 0.7533 (p) REVERT: B 682 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7262 (mm-30) REVERT: C 43 HIS cc_start: 0.8798 (m90) cc_final: 0.8231 (m-70) REVERT: C 76 MET cc_start: 0.8236 (mtp) cc_final: 0.7378 (mmp) REVERT: C 209 ARG cc_start: 0.7670 (mtm110) cc_final: 0.7432 (mtm110) REVERT: C 814 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6003 (tm-30) outliers start: 21 outliers final: 17 residues processed: 134 average time/residue: 0.2162 time to fit residues: 38.7685 Evaluate side-chains 131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 565 CYS Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 761 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 814 GLN Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 230 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 0.0370 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 54 optimal weight: 0.0040 overall best weight: 0.4470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 636 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.152066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.108887 restraints weight = 10139.789| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.05 r_work: 0.3414 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7942 Z= 0.178 Angle : 0.605 15.489 10768 Z= 0.299 Chirality : 0.042 0.217 1202 Planarity : 0.005 0.049 1382 Dihedral : 3.833 18.431 1056 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.89 % Favored : 98.01 % Rotamer: Outliers : 2.36 % Allowed : 20.64 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.28), residues: 954 helix: 1.97 (0.21), residues: 641 sheet: -0.96 (0.87), residues: 30 loop : 0.14 (0.40), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 669 HIS 0.003 0.001 HIS C 43 PHE 0.034 0.002 PHE D 209 TYR 0.009 0.001 TYR C 554 ARG 0.007 0.000 ARG A 697 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2168.05 seconds wall clock time: 40 minutes 6.45 seconds (2406.45 seconds total)