Starting phenix.real_space_refine on Sun May 11 01:45:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdr_60006/05_2025/8zdr_60006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdr_60006/05_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_60006/05_2025/8zdr_60006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdr_60006/05_2025/8zdr_60006.map" model { file = "/net/cci-nas-00/data/ceres_data/8zdr_60006/05_2025/8zdr_60006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdr_60006/05_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-5687/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: 5.16, per 1000 atoms: 0.69 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: 2.04 Conformation dependent library (CDL) restraints added in 414.2 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: 3.70 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: 3.18 Time building geometry restraints manager: 2.34 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: 2.070 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.840 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.190 ------------------------------------------------------------------------------- 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 7944 Z= 0.329 Angle : 0.669 9.899 11569 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 Details of bonding type rmsd hydrogen bonds : bond 0.11473 ( 324) hydrogen bonds : angle 4.61892 ( 728) metal coordination : bond 0.00486 ( 4) metal coordination : angle 1.10530 ( 3) covalent geometry : bond 0.00527 ( 7940) covalent geometry : angle 0.66885 (11566) *********************** 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 : 0.507 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: 1.0688 time to fit residues: 49.2791 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 : 0.515 ------------------------------------------------------------------------------- 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 = 57)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150027 restraints weight = 6840.598| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 0.95 r_work: 0.3745 rms_B_bonded: 1.84 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 7944 Z= 0.173 Angle : 0.593 8.592 11569 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 Details of bonding type rmsd hydrogen bonds : bond 0.05691 ( 324) hydrogen bonds : angle 3.15049 ( 728) metal coordination : bond 0.00623 ( 4) metal coordination : angle 1.44380 ( 3) covalent geometry : bond 0.00368 ( 7940) covalent geometry : angle 0.59295 (11566) *********************** 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 : 0.491 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7243 (mt0) cc_final: 0.6100 (tp-100) REVERT: C 79 SER cc_start: 0.8384 (p) cc_final: 0.8115 (m) REVERT: C 247 LYS cc_start: 0.7693 (ttmt) cc_final: 0.7156 (ttpt) REVERT: C 456 ARG cc_start: 0.7144 (tmm160) cc_final: 0.6907 (tmm160) REVERT: C 739 LYS cc_start: 0.5517 (mmmt) cc_final: 0.4977 (mtmm) outliers start: 8 outliers final: 3 residues processed: 46 average time/residue: 1.0375 time to fit residues: 51.3122 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 : 0.571 ------------------------------------------------------------------------------- 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: 2.9990 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: 3.9990 chunk 25 optimal weight: 0.1980 chunk 44 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.190200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.144998 restraints weight = 6969.433| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.06 r_work: 0.3686 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7944 Z= 0.238 Angle : 0.643 9.056 11569 Z= 0.336 Chirality : 0.040 0.285 1430 Planarity : 0.005 0.044 793 Dihedral : 24.172 173.209 3191 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: -0.26 (0.39), residues: 420 helix: 0.54 (0.38), residues: 177 sheet: -0.13 (1.28), residues: 10 loop : -0.71 (0.40), residues: 233 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 648 TYR 0.013 0.002 TYR C 70 ARG 0.005 0.001 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.07172 ( 324) hydrogen bonds : angle 3.13113 ( 728) metal coordination : bond 0.01483 ( 4) metal coordination : angle 1.64055 ( 3) covalent geometry : bond 0.00494 ( 7940) covalent geometry : angle 0.64245 (11566) *********************** 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 : 0.483 Fit side-chains REVERT: C 58 GLN cc_start: 0.7299 (mt0) cc_final: 0.6096 (tp-100) REVERT: C 79 SER cc_start: 0.8438 (p) cc_final: 0.8176 (m) REVERT: C 247 LYS cc_start: 0.7716 (ttmt) cc_final: 0.7182 (ttpt) REVERT: C 696 LEU cc_start: 0.7486 (mp) cc_final: 0.7247 (tp) outliers start: 11 outliers final: 7 residues processed: 48 average time/residue: 1.5007 time to fit residues: 76.2121 Evaluate side-chains 45 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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: 0.6980 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.192760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.148250 restraints weight = 6852.826| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 0.95 r_work: 0.3721 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7944 Z= 0.179 Angle : 0.579 9.013 11569 Z= 0.306 Chirality : 0.036 0.287 1430 Planarity : 0.004 0.037 793 Dihedral : 23.960 173.631 3191 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.84 % Allowed : 13.97 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.40), residues: 420 helix: 0.93 (0.39), residues: 177 sheet: -0.06 (1.38), residues: 10 loop : -0.71 (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 0.008 0.001 PHE C 648 TYR 0.011 0.001 TYR C 169 ARG 0.007 0.001 ARG C 556 Details of bonding type rmsd hydrogen bonds : bond 0.05450 ( 324) hydrogen bonds : angle 2.96264 ( 728) metal coordination : bond 0.01138 ( 4) metal coordination : angle 1.47728 ( 3) covalent geometry : bond 0.00372 ( 7940) covalent geometry : angle 0.57831 (11566) *********************** 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 57 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.486 Fit side-chains REVERT: C 58 GLN cc_start: 0.7268 (mt0) cc_final: 0.6103 (tp-100) REVERT: C 79 SER cc_start: 0.8420 (p) cc_final: 0.8194 (m) REVERT: C 247 LYS cc_start: 0.7756 (ttmt) cc_final: 0.7225 (ttpt) REVERT: C 461 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5376 (tm-30) REVERT: C 580 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7254 (pt0) REVERT: C 739 LYS cc_start: 0.5464 (mmmt) cc_final: 0.4870 (ptpt) outliers start: 14 outliers final: 7 residues processed: 51 average time/residue: 1.1282 time to fit residues: 61.2637 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 : 0.499 ------------------------------------------------------------------------------- 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 580 GLU Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 54 optimal weight: 0.2980 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 0.0770 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- 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 = 0.4317 r_free = 0.4317 target = 0.190939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.145960 restraints weight = 6834.129| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 0.95 r_work: 0.3697 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7944 Z= 0.211 Angle : 0.604 9.069 11569 Z= 0.317 Chirality : 0.037 0.285 1430 Planarity : 0.005 0.036 793 Dihedral : 23.894 173.899 3191 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.84 % Allowed : 13.97 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.40), residues: 420 helix: 0.85 (0.39), residues: 177 sheet: 0.01 (1.36), residues: 10 loop : -0.73 (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 0.001 PHE C 83 TYR 0.011 0.002 TYR C 70 ARG 0.012 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.06303 ( 324) hydrogen bonds : angle 3.06721 ( 728) metal coordination : bond 0.01415 ( 4) metal coordination : angle 1.60741 ( 3) covalent geometry : bond 0.00442 ( 7940) covalent geometry : angle 0.60354 (11566) *********************** 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 54 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.509 Fit side-chains REVERT: C 58 GLN cc_start: 0.7306 (mt0) cc_final: 0.6097 (tp-100) REVERT: C 79 SER cc_start: 0.8440 (p) cc_final: 0.8205 (m) REVERT: C 247 LYS cc_start: 0.7796 (ttmt) cc_final: 0.7316 (ttpt) REVERT: C 461 GLU cc_start: 0.6082 (OUTLIER) cc_final: 0.5301 (tm-30) REVERT: C 580 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: C 739 LYS cc_start: 0.5621 (mmmt) cc_final: 0.5062 (ptpt) outliers start: 14 outliers final: 9 residues processed: 48 average time/residue: 1.0976 time to fit residues: 56.2063 Evaluate side-chains 49 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 702 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 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: 2.9990 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.188882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143764 restraints weight = 6818.925| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.05 r_work: 0.3669 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7944 Z= 0.268 Angle : 0.665 9.160 11569 Z= 0.345 Chirality : 0.041 0.291 1430 Planarity : 0.005 0.040 793 Dihedral : 23.899 174.192 3191 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.56 % Allowed : 16.16 % 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: -0.40 (0.39), residues: 420 helix: 0.46 (0.37), residues: 182 sheet: 0.00 (1.31), residues: 10 loop : -0.85 (0.39), 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 70 ARG 0.008 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.07636 ( 324) hydrogen bonds : angle 3.18733 ( 728) metal coordination : bond 0.02024 ( 4) metal coordination : angle 1.94818 ( 3) covalent geometry : bond 0.00559 ( 7940) covalent geometry : angle 0.66466 (11566) *********************** 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 51 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.477 Fit side-chains REVERT: C 58 GLN cc_start: 0.7323 (mt0) cc_final: 0.6113 (tp-100) REVERT: C 79 SER cc_start: 0.8436 (p) cc_final: 0.8191 (m) REVERT: C 247 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7236 (ttpt) REVERT: C 461 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5193 (tm-30) REVERT: C 580 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7235 (pt0) REVERT: C 739 LYS cc_start: 0.5599 (mmmt) cc_final: 0.5082 (ptpt) outliers start: 13 outliers final: 8 residues processed: 47 average time/residue: 1.0534 time to fit residues: 53.0074 Evaluate side-chains 46 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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: 8.9990 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.190307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.145484 restraints weight = 6780.115| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 0.95 r_work: 0.3691 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7944 Z= 0.216 Angle : 0.612 9.080 11569 Z= 0.321 Chirality : 0.038 0.289 1430 Planarity : 0.004 0.037 793 Dihedral : 23.828 174.498 3191 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.01 % Allowed : 16.99 % 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: -0.27 (0.39), residues: 420 helix: 0.65 (0.38), residues: 182 sheet: 0.02 (1.40), residues: 10 loop : -0.87 (0.39), 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 0.009 0.001 PHE C 83 TYR 0.011 0.002 TYR C 169 ARG 0.009 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.06478 ( 324) hydrogen bonds : angle 3.08094 ( 728) metal coordination : bond 0.01476 ( 4) metal coordination : angle 1.80250 ( 3) covalent geometry : bond 0.00451 ( 7940) covalent geometry : angle 0.61186 (11566) *********************** 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 49 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.585 Fit side-chains REVERT: C 58 GLN cc_start: 0.7291 (mt0) cc_final: 0.6100 (tp-100) REVERT: C 79 SER cc_start: 0.8420 (p) cc_final: 0.8182 (m) REVERT: C 247 LYS cc_start: 0.7757 (ttmt) cc_final: 0.7204 (ttpt) REVERT: C 461 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5240 (tm-30) REVERT: C 739 LYS cc_start: 0.5670 (mmmt) cc_final: 0.5153 (ptpt) outliers start: 11 outliers final: 8 residues processed: 46 average time/residue: 1.1853 time to fit residues: 58.3604 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 : 0.463 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 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: 0.9990 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4313 r_free = 0.4313 target = 0.190777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.145928 restraints weight = 6874.165| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 0.94 r_work: 0.3699 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7944 Z= 0.204 Angle : 0.601 9.065 11569 Z= 0.315 Chirality : 0.037 0.286 1430 Planarity : 0.004 0.036 793 Dihedral : 23.770 174.748 3191 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.74 % Allowed : 17.53 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.40), residues: 420 helix: 0.79 (0.38), residues: 182 sheet: 0.00 (1.38), residues: 10 loop : -0.84 (0.39), 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 0.008 0.001 PHE C 83 TYR 0.011 0.002 TYR C 169 ARG 0.009 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.06066 ( 324) hydrogen bonds : angle 3.04697 ( 728) metal coordination : bond 0.01574 ( 4) metal coordination : angle 1.51911 ( 3) covalent geometry : bond 0.00425 ( 7940) covalent geometry : angle 0.60065 (11566) *********************** 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 52 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.612 Fit side-chains REVERT: C 46 ASP cc_start: 0.7224 (m-30) cc_final: 0.6978 (m-30) REVERT: C 58 GLN cc_start: 0.7290 (mt0) cc_final: 0.6103 (tp-100) REVERT: C 79 SER cc_start: 0.8420 (p) cc_final: 0.8206 (m) REVERT: C 247 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7176 (ttpt) REVERT: C 263 PHE cc_start: 0.7397 (m-80) cc_final: 0.7173 (m-80) REVERT: C 461 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5271 (tm-30) REVERT: C 576 GLU cc_start: 0.5237 (mt-10) cc_final: 0.4876 (mp0) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 1.1527 time to fit residues: 59.6609 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 : 0.775 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 9.9990 chunk 60 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 0.0170 chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0022 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.191966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147353 restraints weight = 6912.371| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 0.94 r_work: 0.3713 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7944 Z= 0.173 Angle : 0.585 9.914 11569 Z= 0.307 Chirality : 0.035 0.283 1430 Planarity : 0.004 0.034 793 Dihedral : 23.754 174.942 3191 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.74 % Allowed : 18.08 % Favored : 79.18 % 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: 0.01 (0.40), residues: 420 helix: 0.96 (0.39), residues: 182 sheet: -0.06 (1.37), residues: 10 loop : -0.76 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 452 HIS 0.002 0.001 HIS C 680 PHE 0.006 0.001 PHE C 648 TYR 0.011 0.001 TYR C 169 ARG 0.008 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.05628 ( 324) hydrogen bonds : angle 2.99762 ( 728) metal coordination : bond 0.01266 ( 4) metal coordination : angle 1.43046 ( 3) covalent geometry : bond 0.00364 ( 7940) covalent geometry : angle 0.58418 (11566) *********************** 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 52 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.528 Fit side-chains REVERT: C 46 ASP cc_start: 0.7168 (m-30) cc_final: 0.6920 (m-30) REVERT: C 58 GLN cc_start: 0.7283 (mt0) cc_final: 0.6088 (tp-100) REVERT: C 79 SER cc_start: 0.8404 (p) cc_final: 0.8195 (m) REVERT: C 247 LYS cc_start: 0.7715 (ttmt) cc_final: 0.7149 (ttpt) REVERT: C 461 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5245 (tm-30) REVERT: C 576 GLU cc_start: 0.5204 (mt-10) cc_final: 0.4882 (mp0) REVERT: C 739 LYS cc_start: 0.5491 (mmmt) cc_final: 0.4471 (ptpt) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 1.0480 time to fit residues: 53.9199 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 : 0.497 ------------------------------------------------------------------------------- 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 52 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 0.0050 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.7400 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.189451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144512 restraints weight = 6897.561| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 0.97 r_work: 0.3681 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7944 Z= 0.240 Angle : 0.642 9.892 11569 Z= 0.332 Chirality : 0.039 0.280 1430 Planarity : 0.005 0.037 793 Dihedral : 23.761 174.644 3191 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.47 % Allowed : 18.08 % Favored : 79.45 % 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: -0.22 (0.39), residues: 420 helix: 0.74 (0.38), residues: 182 sheet: -0.10 (1.38), residues: 10 loop : -0.88 (0.39), 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 0.014 0.002 PHE C 263 TYR 0.012 0.002 TYR C 169 ARG 0.008 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.06832 ( 324) hydrogen bonds : angle 3.09425 ( 728) metal coordination : bond 0.01846 ( 4) metal coordination : angle 1.73999 ( 3) covalent geometry : bond 0.00501 ( 7940) covalent geometry : angle 0.64110 (11566) ********************** 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 47 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.556 Fit side-chains REVERT: C 58 GLN cc_start: 0.7318 (mt0) cc_final: 0.6113 (tp-100) REVERT: C 79 SER cc_start: 0.8422 (p) cc_final: 0.8212 (m) REVERT: C 247 LYS cc_start: 0.7729 (ttmt) cc_final: 0.7187 (ttpt) REVERT: C 461 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5270 (tm-30) REVERT: C 576 GLU cc_start: 0.5335 (mt-10) cc_final: 0.4909 (mp0) REVERT: C 739 LYS cc_start: 0.5404 (mmmt) cc_final: 0.4416 (ptpt) outliers start: 9 outliers final: 8 residues processed: 44 average time/residue: 1.0843 time to fit residues: 51.1822 Evaluate side-chains 48 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 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 = 0.4324 r_free = 0.4324 target = 0.191890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147380 restraints weight = 6796.815| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 0.93 r_work: 0.3713 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7944 Z= 0.182 Angle : 0.591 9.026 11569 Z= 0.309 Chirality : 0.036 0.279 1430 Planarity : 0.004 0.035 793 Dihedral : 23.683 174.883 3191 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.74 % Allowed : 17.81 % Favored : 79.45 % 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: -0.00 (0.40), residues: 420 helix: 0.97 (0.38), residues: 182 sheet: -0.01 (1.36), residues: 10 loop : -0.80 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 452 HIS 0.002 0.001 HIS C 680 PHE 0.017 0.001 PHE C 263 TYR 0.011 0.001 TYR C 169 ARG 0.008 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.05610 ( 324) hydrogen bonds : angle 3.00266 ( 728) metal coordination : bond 0.01353 ( 4) metal coordination : angle 1.68395 ( 3) covalent geometry : bond 0.00384 ( 7940) covalent geometry : angle 0.59012 (11566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5343.96 seconds wall clock time: 92 minutes 49.61 seconds (5569.61 seconds total)