Starting phenix.real_space_refine on Mon Apr 28 08:26:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdr_60006/04_2025/8zdr_60006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdr_60006/04_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_60006/04_2025/8zdr_60006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdr_60006/04_2025/8zdr_60006.map" model { file = "/net/cci-nas-00/data/ceres_data/8zdr_60006/04_2025/8zdr_60006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdr_60006/04_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-5669/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: 5.29, per 1000 atoms: 0.71 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: 2.41 Conformation dependent library (CDL) restraints added in 422.7 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: 3.49 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: 3.12 Time building geometry restraints manager: 2.67 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.920 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:16.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.300 ------------------------------------------------------------------------------- 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 : 0.565 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: 1.1410 time to fit residues: 52.4316 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 : 0.496 ------------------------------------------------------------------------------- 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 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 : 0.496 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: 1.0535 time to fit residues: 51.9880 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 : 0.495 ------------------------------------------------------------------------------- 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 7944 Z= 0.204 Angle : 0.605 8.992 11569 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 Details of bonding type rmsd hydrogen bonds : bond 0.06229 ( 324) hydrogen bonds : angle 3.02923 ( 728) metal coordination : bond 0.01231 ( 4) metal coordination : angle 1.44511 ( 3) covalent geometry : bond 0.00425 ( 7940) covalent geometry : angle 0.60474 (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 : 0.839 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: 1.4350 time to fit residues: 73.2488 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 : 0.527 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4360 r_free = 0.4360 target = 0.195513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.151100 restraints weight = 6883.872| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 0.95 r_work: 0.3758 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7944 Z= 0.145 Angle : 0.548 8.847 11569 Z= 0.291 Chirality : 0.034 0.280 1430 Planarity : 0.004 0.034 793 Dihedral : 23.910 173.557 3191 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.29 % Allowed : 15.07 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.41), residues: 420 helix: 1.16 (0.39), residues: 177 sheet: -0.02 (1.35), residues: 10 loop : -0.62 (0.41), residues: 233 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 0.008 0.001 PHE C 648 TYR 0.010 0.001 TYR C 169 ARG 0.006 0.001 ARG C 672 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 324) hydrogen bonds : angle 2.88943 ( 728) metal coordination : bond 0.00730 ( 4) metal coordination : angle 1.12115 ( 3) covalent geometry : bond 0.00302 ( 7940) covalent geometry : angle 0.54737 (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 59 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: C 46 ASP cc_start: 0.7045 (m-30) cc_final: 0.6810 (m-30) REVERT: C 58 GLN cc_start: 0.7256 (mt0) cc_final: 0.6099 (tp-100) REVERT: C 79 SER cc_start: 0.8390 (p) cc_final: 0.8164 (m) REVERT: C 247 LYS cc_start: 0.7744 (ttmt) cc_final: 0.7250 (ttpt) REVERT: C 461 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5292 (tm-30) REVERT: C 739 LYS cc_start: 0.5398 (mmmt) cc_final: 0.4799 (ptpt) outliers start: 12 outliers final: 6 residues processed: 54 average time/residue: 1.4768 time to fit residues: 84.5590 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 : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 MET 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 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: 0.9980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 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 651 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.190579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.145626 restraints weight = 6842.527| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.04 r_work: 0.3690 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7944 Z= 0.236 Angle : 0.626 9.151 11569 Z= 0.326 Chirality : 0.039 0.284 1430 Planarity : 0.005 0.035 793 Dihedral : 23.909 173.559 3191 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.84 % Allowed : 14.25 % Favored : 81.92 % 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: 0.85 (0.38), residues: 177 sheet: 0.04 (1.35), 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 0.011 0.002 PHE C 83 TYR 0.012 0.002 TYR C 70 ARG 0.012 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.06699 ( 324) hydrogen bonds : angle 3.05042 ( 728) metal coordination : bond 0.01599 ( 4) metal coordination : angle 1.69713 ( 3) covalent geometry : bond 0.00493 ( 7940) covalent geometry : angle 0.62503 (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 : 1.134 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7313 (mt0) cc_final: 0.6128 (tp-100) REVERT: C 79 SER cc_start: 0.8432 (p) cc_final: 0.8197 (m) REVERT: C 247 LYS cc_start: 0.7786 (ttmt) cc_final: 0.7296 (ttpt) REVERT: C 461 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5394 (tm-30) REVERT: C 580 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7357 (pt0) REVERT: C 739 LYS cc_start: 0.5628 (mmmt) cc_final: 0.5067 (ptpt) outliers start: 14 outliers final: 8 residues processed: 48 average time/residue: 1.6717 time to fit residues: 85.4048 Evaluate side-chains 49 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 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: 1.9990 chunk 39 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.188737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143614 restraints weight = 6837.059| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.05 r_work: 0.3664 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7944 Z= 0.268 Angle : 0.662 9.166 11569 Z= 0.344 Chirality : 0.041 0.292 1430 Planarity : 0.005 0.041 793 Dihedral : 23.929 174.326 3191 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.29 % Allowed : 14.79 % Favored : 81.92 % 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: -0.31 (0.39), residues: 420 helix: 0.62 (0.38), residues: 177 sheet: 0.08 (1.34), 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 0.004 0.001 HIS C 680 PHE 0.011 0.002 PHE C 83 TYR 0.012 0.002 TYR C 70 ARG 0.011 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.07695 ( 324) hydrogen bonds : angle 3.17574 ( 728) metal coordination : bond 0.01960 ( 4) metal coordination : angle 2.08793 ( 3) covalent geometry : bond 0.00556 ( 7940) covalent geometry : angle 0.66084 (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 50 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.528 Fit side-chains REVERT: C 58 GLN cc_start: 0.7304 (mt0) cc_final: 0.6094 (tp-100) REVERT: C 79 SER cc_start: 0.8426 (p) cc_final: 0.8185 (m) REVERT: C 247 LYS cc_start: 0.7774 (ttmt) cc_final: 0.7207 (ttpt) REVERT: C 461 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.5205 (tm-30) REVERT: C 739 LYS cc_start: 0.5649 (mmmt) cc_final: 0.5161 (ptpt) outliers start: 12 outliers final: 8 residues processed: 47 average time/residue: 1.4395 time to fit residues: 73.7267 Evaluate side-chains 44 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.189462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144542 restraints weight = 6784.344| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 0.95 r_work: 0.3679 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1972 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= 0.242 Angle : 0.638 9.122 11569 Z= 0.333 Chirality : 0.039 0.292 1430 Planarity : 0.005 0.037 793 Dihedral : 23.862 174.449 3191 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.01 % Allowed : 16.44 % 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: -0.39 (0.39), residues: 420 helix: 0.56 (0.38), residues: 182 sheet: 0.02 (1.37), residues: 10 loop : -0.94 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 PHE 0.010 0.001 PHE C 83 TYR 0.011 0.002 TYR C 169 ARG 0.010 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.06922 ( 324) hydrogen bonds : angle 3.12230 ( 728) metal coordination : bond 0.01715 ( 4) metal coordination : angle 1.83069 ( 3) covalent geometry : bond 0.00505 ( 7940) covalent geometry : angle 0.63778 (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 : 0.518 Fit side-chains REVERT: C 58 GLN cc_start: 0.7316 (mt0) cc_final: 0.6097 (tp-100) REVERT: C 79 SER cc_start: 0.8448 (p) cc_final: 0.8231 (m) REVERT: C 247 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7158 (ttpt) REVERT: C 263 PHE cc_start: 0.7446 (m-80) cc_final: 0.7176 (m-80) REVERT: C 461 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5260 (tm-30) REVERT: C 576 GLU cc_start: 0.5327 (mt-10) cc_final: 0.4860 (mp0) REVERT: C 739 LYS cc_start: 0.5595 (mmmt) cc_final: 0.5147 (ptpt) outliers start: 11 outliers final: 8 residues processed: 46 average time/residue: 1.9465 time to fit residues: 95.2578 Evaluate side-chains 45 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.188258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.143098 restraints weight = 6884.370| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.06 r_work: 0.3661 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7944 Z= 0.279 Angle : 0.678 9.194 11569 Z= 0.350 Chirality : 0.041 0.291 1430 Planarity : 0.005 0.042 793 Dihedral : 23.882 174.632 3191 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.47 % Allowed : 16.99 % 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: -0.55 (0.39), residues: 420 helix: 0.41 (0.37), residues: 182 sheet: -0.12 (1.32), residues: 10 loop : -1.00 (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 0.013 0.002 TYR C 70 ARG 0.011 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.07796 ( 324) hydrogen bonds : angle 3.20051 ( 728) metal coordination : bond 0.01977 ( 4) metal coordination : angle 2.18158 ( 3) covalent geometry : bond 0.00581 ( 7940) covalent geometry : angle 0.67686 (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 46 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.625 Fit side-chains REVERT: C 58 GLN cc_start: 0.7333 (mt0) cc_final: 0.6112 (tp-100) REVERT: C 79 SER cc_start: 0.8429 (p) cc_final: 0.8211 (m) REVERT: C 247 LYS cc_start: 0.7732 (ttmt) cc_final: 0.7168 (ttpt) REVERT: C 461 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5316 (tm-30) REVERT: C 576 GLU cc_start: 0.5395 (mt-10) cc_final: 0.4925 (mp0) REVERT: C 739 LYS cc_start: 0.5612 (mmmt) cc_final: 0.5126 (ptpt) outliers start: 9 outliers final: 8 residues processed: 44 average time/residue: 1.1883 time to fit residues: 56.1865 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 : 0.565 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.0050 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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 = 0.192220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.148003 restraints weight = 6910.570| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 0.92 r_work: 0.3723 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7944 Z= 0.172 Angle : 0.577 8.984 11569 Z= 0.305 Chirality : 0.035 0.287 1430 Planarity : 0.004 0.036 793 Dihedral : 23.759 175.048 3191 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.01 % Allowed : 17.26 % 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: -0.14 (0.40), residues: 420 helix: 0.90 (0.39), residues: 182 sheet: -0.06 (1.39), residues: 10 loop : -0.91 (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 145 PHE 0.007 0.001 PHE C 83 TYR 0.011 0.001 TYR C 169 ARG 0.009 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.05410 ( 324) hydrogen bonds : angle 3.00333 ( 728) metal coordination : bond 0.01184 ( 4) metal coordination : angle 1.51693 ( 3) covalent geometry : bond 0.00360 ( 7940) covalent geometry : angle 0.57621 (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 53 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.541 Fit side-chains REVERT: C 46 ASP cc_start: 0.7185 (m-30) cc_final: 0.6945 (m-30) REVERT: C 58 GLN cc_start: 0.7284 (mt0) cc_final: 0.6169 (tp-100) REVERT: C 247 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7245 (ttpt) REVERT: C 461 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5287 (tm-30) REVERT: C 576 GLU cc_start: 0.5277 (mt-10) cc_final: 0.4994 (mp0) outliers start: 11 outliers final: 7 residues processed: 49 average time/residue: 1.0844 time to fit residues: 56.9046 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 : 0.516 ------------------------------------------------------------------------------- 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 614 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 58 optimal weight: 0.2980 chunk 25 optimal weight: 0.0030 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- 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 = 0.190540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.146047 restraints weight = 6891.316| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 0.93 r_work: 0.3698 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2158 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= 0.210 Angle : 0.620 9.957 11569 Z= 0.323 Chirality : 0.037 0.281 1430 Planarity : 0.004 0.036 793 Dihedral : 23.724 174.854 3191 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.19 % Allowed : 18.63 % 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: -0.20 (0.40), residues: 420 helix: 0.80 (0.38), residues: 182 sheet: -0.12 (1.37), residues: 10 loop : -0.91 (0.40), 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 0.010 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.06126 ( 324) hydrogen bonds : angle 3.12444 ( 728) metal coordination : bond 0.01669 ( 4) metal coordination : angle 1.68517 ( 3) covalent geometry : bond 0.00446 ( 7940) covalent geometry : angle 0.61939 (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: 8 poor density : 39 time to evaluate : 0.494 Fit side-chains REVERT: C 46 ASP cc_start: 0.7236 (m-30) cc_final: 0.6989 (m-30) REVERT: C 58 GLN cc_start: 0.7340 (mt0) cc_final: 0.6214 (tp-100) REVERT: C 247 LYS cc_start: 0.7833 (ttmt) cc_final: 0.7344 (ttpt) REVERT: C 461 GLU cc_start: 0.6112 (OUTLIER) cc_final: 0.5296 (tm-30) REVERT: C 576 GLU cc_start: 0.5346 (mt-10) cc_final: 0.5009 (mp0) REVERT: C 739 LYS cc_start: 0.5505 (mmmt) cc_final: 0.4585 (ptpt) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 1.3122 time to fit residues: 61.1617 Evaluate side-chains 46 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 461 GLU 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: 0.4980 chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4333 r_free = 0.4333 target = 0.192823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.148386 restraints weight = 6797.845| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 0.94 r_work: 0.3728 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7944 Z= 0.163 Angle : 0.585 9.791 11569 Z= 0.307 Chirality : 0.035 0.278 1430 Planarity : 0.004 0.034 793 Dihedral : 23.690 175.229 3191 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.19 % Allowed : 18.36 % 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: 0.02 (0.41), residues: 420 helix: 1.02 (0.39), residues: 182 sheet: -0.36 (1.32), residues: 10 loop : -0.80 (0.41), 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 0.006 0.001 PHE C 648 TYR 0.012 0.001 TYR C 169 ARG 0.008 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.05318 ( 324) hydrogen bonds : angle 3.06257 ( 728) metal coordination : bond 0.01400 ( 4) metal coordination : angle 1.70411 ( 3) covalent geometry : bond 0.00346 ( 7940) covalent geometry : angle 0.58489 (11566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6222.81 seconds wall clock time: 111 minutes 54.91 seconds (6714.91 seconds total)