Starting phenix.real_space_refine on Wed Mar 12 04:29:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdr_60006/03_2025/8zdr_60006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdr_60006/03_2025/8zdr_60006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zdr_60006/03_2025/8zdr_60006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdr_60006/03_2025/8zdr_60006.map" model { file = "/net/cci-nas-00/data/ceres_data/8zdr_60006/03_2025/8zdr_60006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdr_60006/03_2025/8zdr_60006.cif" } resolution = 2.65 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= -0.001 sd= 0.065 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 187 5.49 5 S 16 5.16 5 C 3966 2.51 5 N 1357 2.21 5 O 1913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7440 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 3062 Classifications: {'RNA': 144} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 68, 'rna3p_pyr': 66} Link IDs: {'rna2p': 10, 'rna3p': 133} Chain breaks: 2 Chain: "B" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 651 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "C" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3497 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 12, 'TRANS': 433} Chain breaks: 12 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 76 Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 229 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4788 SG CYS C 182 32.132 35.295 88.845 1.00 40.09 S ATOM 4823 SG CYS C 187 28.882 36.876 90.200 1.00 51.66 S ATOM 5426 SG CYS C 264 32.260 38.220 91.318 1.00 39.17 S Time building chain proxies: 5.24, per 1000 atoms: 0.70 Number of scatterers: 7440 At special positions: 0 Unit cell: (74.7, 97.11, 118.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 16 16.00 P 187 15.00 O 1913 8.00 N 1357 7.00 C 3966 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: 2.28 Conformation dependent library (CDL) restraints added in 444.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 801 " pdb="ZN ZN C 801 " - pdb=" ND1 HIS C 267 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 187 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 182 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 264 " Number of angles added : 3 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 5 sheets defined 47.5% alpha, 7.6% beta 67 base pairs and 122 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'C' and resid 39 through 74 removed outlier: 3.597A pdb=" N ARG C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 136 through 151 Processing helix chain 'C' and resid 154 through 167 Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 197 through 207 removed outlier: 3.514A pdb=" N ILE C 205 " --> pdb=" O LEU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 229 through 239 removed outlier: 3.509A pdb=" N LYS C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 264 through 275 removed outlier: 3.871A pdb=" N ILE C 268 " --> pdb=" O LYS C 265 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU C 269 " --> pdb=" O GLU C 266 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS C 271 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR C 272 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 302 Processing helix chain 'C' and resid 451 through 460 removed outlier: 3.726A pdb=" N ARG C 460 " --> pdb=" O ARG C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 removed outlier: 3.552A pdb=" N ASP C 500 " --> pdb=" O HIS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 575 No H-bonds generated for 'chain 'C' and resid 573 through 575' Processing helix chain 'C' and resid 579 through 583 Processing helix chain 'C' and resid 585 through 600 removed outlier: 3.911A pdb=" N ARG C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 616 Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing sheet with id=AA1, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.968A pdb=" N ASN C 32 " --> pdb=" O LEU C 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 560 through 562 Processing sheet with id=AA3, first strand: chain 'C' and resid 640 through 643 Processing sheet with id=AA4, first strand: chain 'C' and resid 672 through 673 removed outlier: 3.900A pdb=" N GLY C 656 " --> pdb=" O ARG C 672 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 721 through 722 removed outlier: 4.164A pdb=" N VAL C 735 " --> pdb=" O ILE C 722 " (cutoff:3.500A) 158 hydrogen bonds defined for protein. 432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 166 hydrogen bonds 296 hydrogen bond angles 0 basepair planarities 67 basepair parallelities 122 stacking parallelities Total time for adding SS restraints: 3.14 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 792 1.30 - 1.43: 3109 1.43 - 1.56: 3642 1.56 - 1.68: 372 1.68 - 1.81: 25 Bond restraints: 7940 Sorted by residual: bond pdb=" C GLU C 586 " pdb=" N THR C 587 " ideal model delta sigma weight residual 1.334 1.238 0.096 1.33e-02 5.65e+03 5.23e+01 bond pdb=" C LYS C 597 " pdb=" N ARG C 598 " ideal model delta sigma weight residual 1.332 1.421 -0.089 1.35e-02 5.49e+03 4.39e+01 bond pdb=" C SER C 585 " pdb=" N GLU C 586 " ideal model delta sigma weight residual 1.335 1.424 -0.089 1.36e-02 5.41e+03 4.29e+01 bond pdb=" C PHE C 599 " pdb=" N ASP C 600 " ideal model delta sigma weight residual 1.333 1.241 0.092 1.45e-02 4.76e+03 4.00e+01 bond pdb=" C LYS C 247 " pdb=" O LYS C 247 " ideal model delta sigma weight residual 1.236 1.173 0.064 1.15e-02 7.56e+03 3.06e+01 ... (remaining 7935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 11342 1.98 - 3.96: 203 3.96 - 5.94: 17 5.94 - 7.92: 2 7.92 - 9.90: 2 Bond angle restraints: 11566 Sorted by residual: angle pdb=" CA PHE C 599 " pdb=" C PHE C 599 " pdb=" N ASP C 600 " ideal model delta sigma weight residual 117.82 124.77 -6.95 1.42e+00 4.96e-01 2.39e+01 angle pdb=" O SER C 585 " pdb=" C SER C 585 " pdb=" N GLU C 586 " ideal model delta sigma weight residual 122.93 128.78 -5.85 1.23e+00 6.61e-01 2.26e+01 angle pdb=" O PHE C 599 " pdb=" C PHE C 599 " pdb=" N ASP C 600 " ideal model delta sigma weight residual 122.33 116.04 6.29 1.34e+00 5.57e-01 2.21e+01 angle pdb=" CB LYS C 739 " pdb=" CG LYS C 739 " pdb=" CD LYS C 739 " ideal model delta sigma weight residual 111.30 121.20 -9.90 2.30e+00 1.89e-01 1.85e+01 angle pdb=" CA SER C 585 " pdb=" C SER C 585 " pdb=" N GLU C 586 " ideal model delta sigma weight residual 116.21 110.53 5.68 1.33e+00 5.65e-01 1.82e+01 ... (remaining 11561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 4356 35.22 - 70.44: 502 70.44 - 105.66: 41 105.66 - 140.88: 2 140.88 - 176.10: 6 Dihedral angle restraints: 4907 sinusoidal: 3617 harmonic: 1290 Sorted by residual: dihedral pdb=" O4' U A 94 " pdb=" C1' U A 94 " pdb=" N1 U A 94 " pdb=" C2 U A 94 " ideal model delta sinusoidal sigma weight residual -128.00 31.96 -159.96 1 1.70e+01 3.46e-03 6.44e+01 dihedral pdb=" O4' U A 95 " pdb=" C1' U A 95 " pdb=" N1 U A 95 " pdb=" C2 U A 95 " ideal model delta sinusoidal sigma weight residual 232.00 121.50 110.50 1 1.70e+01 3.46e-03 4.48e+01 dihedral pdb=" O4' U A 68 " pdb=" C1' U A 68 " pdb=" N1 U A 68 " pdb=" C2 U A 68 " ideal model delta sinusoidal sigma weight residual -128.00 -66.98 -61.02 1 1.70e+01 3.46e-03 1.71e+01 ... (remaining 4904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1136 0.042 - 0.084: 223 0.084 - 0.126: 62 0.126 - 0.168: 7 0.168 - 0.210: 2 Chirality restraints: 1430 Sorted by residual: chirality pdb=" C1' G A 14 " pdb=" O4' G A 14 " pdb=" C2' G A 14 " pdb=" N9 G A 14 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ASP C 99 " pdb=" N ASP C 99 " pdb=" C ASP C 99 " pdb=" CB ASP C 99 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA GLU C 586 " pdb=" N GLU C 586 " pdb=" C GLU C 586 " pdb=" CB GLU C 586 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1427 not shown) Planarity restraints: 793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 636 " 0.064 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO C 637 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO C 637 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 637 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 597 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C LYS C 597 " -0.068 2.00e-02 2.50e+03 pdb=" O LYS C 597 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG C 598 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 14 " 0.026 2.00e-02 2.50e+03 1.20e-02 4.30e+00 pdb=" N9 G A 14 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G A 14 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G A 14 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 14 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 14 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G A 14 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G A 14 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G A 14 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 14 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 14 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G A 14 " 0.000 2.00e-02 2.50e+03 ... (remaining 790 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 37 2.50 - 3.10: 5119 3.10 - 3.70: 13988 3.70 - 4.30: 20346 4.30 - 4.90: 27345 Nonbonded interactions: 66835 Sorted by model distance: nonbonded pdb=" O6 G A 90 " pdb=" O2 U A 104 " model vdw 1.902 2.432 nonbonded pdb=" OE2 GLU C 723 " pdb=" N THR C 734 " model vdw 2.062 3.120 nonbonded pdb=" N GLU C 270 " pdb=" OE1 GLU C 270 " model vdw 2.135 3.120 nonbonded pdb=" O ASN C 77 " pdb=" OG1 THR C 80 " model vdw 2.182 3.040 nonbonded pdb=" OP1 U A 51 " pdb=" NZ LYS C 629 " model vdw 2.210 3.120 ... (remaining 66830 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: 1.740 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.640 Find NCS groups from input model: 0.060 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:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 0.096 7940 Z= 0.314 Angle : 0.669 9.899 11566 Z= 0.394 Chirality : 0.038 0.210 1430 Planarity : 0.006 0.098 793 Dihedral : 23.334 176.103 4061 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.55 % Allowed : 13.70 % Favored : 85.75 % 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: -0.52 (0.40), residues: 420 helix: 0.20 (0.37), residues: 180 sheet: 0.48 (1.33), residues: 10 loop : -0.78 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.003 TRP C 452 HIS 0.002 0.001 HIS C 653 PHE 0.025 0.002 PHE C 596 TYR 0.014 0.002 TYR C 70 ARG 0.005 0.001 ARG C 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7285 (mt0) cc_final: 0.6471 (tp-100) REVERT: C 247 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7566 (ttpt) REVERT: C 739 LYS cc_start: 0.5943 (mmmt) cc_final: 0.5666 (mtmm) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 1.1445 time to fit residues: 52.4009 Evaluate side-chains 37 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 184 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.194727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.149999 restraints weight = 6840.598| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 0.95 r_work: 0.3745 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 7940 Z= 0.225 Angle : 0.593 8.592 11566 Z= 0.316 Chirality : 0.036 0.277 1430 Planarity : 0.005 0.055 793 Dihedral : 24.307 172.009 3191 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.19 % Allowed : 13.15 % Favored : 84.66 % 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: 0.02 (0.40), residues: 420 helix: 0.79 (0.38), residues: 175 sheet: 0.21 (1.36), residues: 10 loop : -0.56 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 452 HIS 0.007 0.001 HIS C 239 PHE 0.013 0.001 PHE C 648 TYR 0.012 0.001 TYR C 169 ARG 0.004 0.001 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7242 (mt0) cc_final: 0.6099 (tp-100) REVERT: C 79 SER cc_start: 0.8384 (p) cc_final: 0.8115 (m) REVERT: C 247 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7159 (ttpt) REVERT: C 456 ARG cc_start: 0.7146 (tmm160) cc_final: 0.6908 (tmm160) REVERT: C 739 LYS cc_start: 0.5506 (mmmt) cc_final: 0.4964 (mtmm) outliers start: 8 outliers final: 3 residues processed: 46 average time/residue: 1.0628 time to fit residues: 52.3611 Evaluate side-chains 41 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 654 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.191684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.146684 restraints weight = 6978.172| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 0.96 r_work: 0.3708 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7940 Z= 0.255 Angle : 0.605 8.992 11566 Z= 0.318 Chirality : 0.037 0.282 1430 Planarity : 0.005 0.041 793 Dihedral : 24.088 173.128 3191 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.01 % Allowed : 13.97 % Favored : 83.01 % 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: -0.08 (0.40), residues: 420 helix: 0.73 (0.38), residues: 177 sheet: -0.06 (1.32), residues: 10 loop : -0.64 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 PHE 0.010 0.002 PHE C 648 TYR 0.012 0.002 TYR C 70 ARG 0.004 0.001 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7310 (mt0) cc_final: 0.6112 (tp-100) REVERT: C 79 SER cc_start: 0.8427 (p) cc_final: 0.8165 (m) REVERT: C 247 LYS cc_start: 0.7704 (ttmt) cc_final: 0.7192 (ttpt) outliers start: 11 outliers final: 7 residues processed: 48 average time/residue: 1.1003 time to fit residues: 56.4160 Evaluate side-chains 48 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.1980 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.190361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145395 restraints weight = 6846.774| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 0.96 r_work: 0.3686 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7940 Z= 0.280 Angle : 0.624 9.137 11566 Z= 0.327 Chirality : 0.039 0.288 1430 Planarity : 0.005 0.038 793 Dihedral : 24.010 173.509 3191 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.38 % Allowed : 14.25 % Favored : 81.37 % 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: -0.20 (0.39), residues: 420 helix: 0.69 (0.38), residues: 177 sheet: 0.06 (1.34), residues: 10 loop : -0.77 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 PHE 0.009 0.002 PHE C 648 TYR 0.012 0.002 TYR C 169 ARG 0.005 0.001 ARG C 672 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.556 Fit side-chains REVERT: C 58 GLN cc_start: 0.7289 (mt0) cc_final: 0.6088 (tp-100) REVERT: C 79 SER cc_start: 0.8433 (p) cc_final: 0.8181 (m) REVERT: C 247 LYS cc_start: 0.7728 (ttmt) cc_final: 0.7158 (ttpt) REVERT: C 461 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5321 (tm-30) REVERT: C 633 LYS cc_start: 0.7404 (mttt) cc_final: 0.7184 (mttp) REVERT: C 739 LYS cc_start: 0.5599 (mmmt) cc_final: 0.5062 (ptpt) outliers start: 16 outliers final: 7 residues processed: 52 average time/residue: 1.1608 time to fit residues: 64.2896 Evaluate side-chains 47 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 614 GLU Chi-restraints excluded: chain C residue 702 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 639 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.188924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144001 restraints weight = 6829.491| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.05 r_work: 0.3672 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7940 Z= 0.324 Angle : 0.658 9.144 11566 Z= 0.342 Chirality : 0.040 0.291 1430 Planarity : 0.005 0.039 793 Dihedral : 23.972 174.045 3191 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.74 % Allowed : 16.71 % Favored : 80.55 % 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: -0.42 (0.39), residues: 420 helix: 0.47 (0.38), residues: 177 sheet: -0.02 (1.32), residues: 10 loop : -0.86 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 PHE 0.010 0.002 PHE C 83 TYR 0.012 0.002 TYR C 169 ARG 0.008 0.001 ARG C 556 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.576 Fit side-chains REVERT: C 58 GLN cc_start: 0.7331 (mt0) cc_final: 0.6104 (tp-100) REVERT: C 79 SER cc_start: 0.8424 (p) cc_final: 0.8177 (m) REVERT: C 247 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7301 (ttpt) REVERT: C 461 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.5177 (tm-30) REVERT: C 633 LYS cc_start: 0.7458 (mttt) cc_final: 0.7257 (mttp) REVERT: C 739 LYS cc_start: 0.5594 (mmmt) cc_final: 0.5094 (ptpt) outliers start: 10 outliers final: 8 residues processed: 48 average time/residue: 1.1699 time to fit residues: 59.8037 Evaluate side-chains 46 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.191160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146457 restraints weight = 6809.504| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 0.94 r_work: 0.3699 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7940 Z= 0.249 Angle : 0.600 9.069 11566 Z= 0.315 Chirality : 0.037 0.289 1430 Planarity : 0.004 0.036 793 Dihedral : 23.860 174.427 3191 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.56 % Allowed : 16.44 % Favored : 80.00 % 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: -0.13 (0.40), residues: 420 helix: 0.83 (0.39), residues: 177 sheet: 0.03 (1.39), residues: 10 loop : -0.80 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 PHE 0.008 0.001 PHE C 83 TYR 0.011 0.002 TYR C 169 ARG 0.007 0.001 ARG C 556 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 1.008 Fit side-chains REVERT: C 58 GLN cc_start: 0.7297 (mt0) cc_final: 0.6090 (tp-100) REVERT: C 79 SER cc_start: 0.8439 (p) cc_final: 0.8210 (m) REVERT: C 247 LYS cc_start: 0.7721 (ttmt) cc_final: 0.7195 (ttpt) REVERT: C 263 PHE cc_start: 0.7418 (m-80) cc_final: 0.7150 (m-80) REVERT: C 461 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.5204 (tm-30) REVERT: C 580 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: C 739 LYS cc_start: 0.5699 (mmmt) cc_final: 0.5158 (ptpt) outliers start: 13 outliers final: 8 residues processed: 46 average time/residue: 1.8280 time to fit residues: 88.2563 Evaluate side-chains 47 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.192084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147801 restraints weight = 6781.600| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 0.92 r_work: 0.3714 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7940 Z= 0.214 Angle : 0.580 9.056 11566 Z= 0.306 Chirality : 0.035 0.285 1430 Planarity : 0.004 0.034 793 Dihedral : 23.849 174.587 3191 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.01 % Allowed : 16.71 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.40), residues: 420 helix: 0.90 (0.39), residues: 182 sheet: -0.03 (1.39), residues: 10 loop : -0.79 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 PHE 0.006 0.001 PHE C 648 TYR 0.010 0.001 TYR C 169 ARG 0.006 0.001 ARG C 556 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 1.221 Fit side-chains REVERT: C 46 ASP cc_start: 0.7202 (m-30) cc_final: 0.6960 (m-30) REVERT: C 58 GLN cc_start: 0.7301 (mt0) cc_final: 0.6161 (tp-100) REVERT: C 79 SER cc_start: 0.8415 (p) cc_final: 0.8198 (m) REVERT: C 247 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7261 (ttpt) REVERT: C 461 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5206 (tm-30) REVERT: C 580 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7336 (pt0) outliers start: 11 outliers final: 7 residues processed: 46 average time/residue: 1.1778 time to fit residues: 58.6013 Evaluate side-chains 47 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.188779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144100 restraints weight = 6876.847| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.03 r_work: 0.3673 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7940 Z= 0.327 Angle : 0.666 9.571 11566 Z= 0.344 Chirality : 0.040 0.290 1430 Planarity : 0.005 0.040 793 Dihedral : 23.860 174.350 3191 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.56 % Allowed : 17.53 % Favored : 78.90 % 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 (0.39), residues: 420 helix: 0.58 (0.38), residues: 182 sheet: -0.14 (1.37), residues: 10 loop : -0.92 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 452 HIS 0.004 0.001 HIS C 680 PHE 0.011 0.002 PHE C 83 TYR 0.012 0.002 TYR C 169 ARG 0.006 0.001 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.958 Fit side-chains REVERT: C 58 GLN cc_start: 0.7337 (mt0) cc_final: 0.6181 (tp-100) REVERT: C 79 SER cc_start: 0.8421 (p) cc_final: 0.8194 (m) REVERT: C 247 LYS cc_start: 0.7811 (ttmt) cc_final: 0.7287 (ttpt) REVERT: C 461 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5270 (tm-30) REVERT: C 576 GLU cc_start: 0.5254 (mt-10) cc_final: 0.4828 (mp0) REVERT: C 580 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7318 (pt0) REVERT: C 739 LYS cc_start: 0.5575 (mmmt) cc_final: 0.4603 (ptpt) outliers start: 13 outliers final: 9 residues processed: 49 average time/residue: 1.6271 time to fit residues: 84.6743 Evaluate side-chains 48 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.191534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146890 restraints weight = 6912.579| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 0.95 r_work: 0.3709 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7940 Z= 0.234 Angle : 0.589 9.069 11566 Z= 0.309 Chirality : 0.036 0.287 1430 Planarity : 0.004 0.034 793 Dihedral : 23.766 174.873 3191 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.74 % Allowed : 18.63 % Favored : 78.63 % 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: -0.07 (0.40), residues: 420 helix: 0.90 (0.39), residues: 182 sheet: 0.00 (1.41), residues: 10 loop : -0.83 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 452 HIS 0.002 0.001 HIS C 680 PHE 0.012 0.001 PHE C 263 TYR 0.010 0.001 TYR C 169 ARG 0.005 0.001 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.609 Fit side-chains REVERT: C 46 ASP cc_start: 0.7193 (m-30) cc_final: 0.6950 (m-30) REVERT: C 58 GLN cc_start: 0.7291 (mt0) cc_final: 0.6082 (tp-100) REVERT: C 79 SER cc_start: 0.8408 (p) cc_final: 0.8201 (m) REVERT: C 247 LYS cc_start: 0.7727 (ttmt) cc_final: 0.7165 (ttpt) REVERT: C 461 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5276 (tm-30) REVERT: C 576 GLU cc_start: 0.5258 (mt-10) cc_final: 0.4769 (mp0) REVERT: C 739 LYS cc_start: 0.5408 (mmmt) cc_final: 0.4502 (ptpt) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 1.8217 time to fit residues: 90.9576 Evaluate side-chains 49 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 58 optimal weight: 0.0050 chunk 25 optimal weight: 0.0370 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.193539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.149230 restraints weight = 6887.720| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 0.95 r_work: 0.3738 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7940 Z= 0.200 Angle : 0.569 8.867 11566 Z= 0.299 Chirality : 0.034 0.281 1430 Planarity : 0.004 0.034 793 Dihedral : 23.688 174.904 3191 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.74 % Allowed : 19.73 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.41), residues: 420 helix: 1.14 (0.39), residues: 182 sheet: -0.28 (1.32), residues: 10 loop : -0.71 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 452 HIS 0.002 0.001 HIS C 145 PHE 0.018 0.001 PHE C 263 TYR 0.009 0.001 TYR C 169 ARG 0.006 0.001 ARG C 556 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.607 Fit side-chains REVERT: C 46 ASP cc_start: 0.7083 (m-30) cc_final: 0.6844 (m-30) REVERT: C 79 SER cc_start: 0.8395 (p) cc_final: 0.8189 (m) REVERT: C 247 LYS cc_start: 0.7712 (ttmt) cc_final: 0.7153 (ttpt) REVERT: C 461 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5275 (tm-30) REVERT: C 576 GLU cc_start: 0.5188 (mt-10) cc_final: 0.4781 (mp0) REVERT: C 739 LYS cc_start: 0.5500 (mmmt) cc_final: 0.4579 (ptpt) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 1.1473 time to fit residues: 58.8036 Evaluate side-chains 50 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.191753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147153 restraints weight = 6793.100| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 0.95 r_work: 0.3712 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7940 Z= 0.239 Angle : 0.589 9.020 11566 Z= 0.308 Chirality : 0.036 0.279 1430 Planarity : 0.005 0.059 793 Dihedral : 23.631 174.847 3191 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.01 % Allowed : 18.90 % Favored : 78.08 % 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: 0.09 (0.40), residues: 420 helix: 1.06 (0.38), residues: 182 sheet: -0.17 (1.36), residues: 10 loop : -0.74 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 PHE 0.017 0.001 PHE C 263 TYR 0.011 0.002 TYR C 169 ARG 0.008 0.001 ARG C 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5675.40 seconds wall clock time: 101 minutes 18.35 seconds (6078.35 seconds total)