Starting phenix.real_space_refine on Wed Sep 17 08:40:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdr_60006/09_2025/8zdr_60006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdr_60006/09_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_60006/09_2025/8zdr_60006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdr_60006/09_2025/8zdr_60006.map" model { file = "/net/cci-nas-00/data/ceres_data/8zdr_60006/09_2025/8zdr_60006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdr_60006/09_2025/8zdr_60006.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'TYR:plan': 3, 'ARG:plan': 5, 'GLU:plan': 4, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1} 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: 1.87, per 1000 atoms: 0.25 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: 0.64 Conformation dependent library (CDL) restraints added in 293.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.27 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: 1.59 Time building geometry restraints manager: 0.87 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: 2.540 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.690 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:8.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG C 47 TYR 0.014 0.002 TYR C 70 PHE 0.025 0.002 PHE C 596 TRP 0.006 0.003 TRP C 452 HIS 0.002 0.001 HIS C 653 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 7940) covalent geometry : angle 0.66885 (11566) hydrogen bonds : bond 0.11473 ( 324) hydrogen bonds : angle 4.61892 ( 728) metal coordination : bond 0.00486 ( 4) metal coordination : angle 1.10530 ( 3) *********************** 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 : 0.208 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: 0.5489 time to fit residues: 25.1439 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 : 0.212 ------------------------------------------------------------------------------- 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 54 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.191938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.146810 restraints weight = 6879.626| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 0.96 r_work: 0.3705 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 7944 Z= 0.216 Angle : 0.637 8.795 11569 Z= 0.335 Chirality : 0.039 0.283 1430 Planarity : 0.005 0.057 793 Dihedral : 24.368 171.614 3191 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.47 % Allowed : 13.42 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.39), residues: 420 helix: 0.57 (0.38), residues: 175 sheet: 0.10 (1.32), residues: 10 loop : -0.66 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 137 TYR 0.013 0.002 TYR C 169 PHE 0.014 0.002 PHE C 648 TRP 0.004 0.002 TRP C 452 HIS 0.007 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 7940) covalent geometry : angle 0.63657 (11566) hydrogen bonds : bond 0.06593 ( 324) hydrogen bonds : angle 3.22951 ( 728) metal coordination : bond 0.01164 ( 4) metal coordination : angle 1.63366 ( 3) *********************** 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: 9 poor density : 41 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7283 (mt0) cc_final: 0.6161 (tp-100) REVERT: C 79 SER cc_start: 0.8404 (p) cc_final: 0.8134 (m) REVERT: C 247 LYS cc_start: 0.7727 (ttmt) cc_final: 0.7189 (ttpt) REVERT: C 456 ARG cc_start: 0.7170 (tmm160) cc_final: 0.6908 (tmm160) REVERT: C 739 LYS cc_start: 0.5513 (mmmt) cc_final: 0.4994 (mtmm) outliers start: 9 outliers final: 4 residues processed: 46 average time/residue: 0.5542 time to fit residues: 27.1308 Evaluate side-chains 43 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 621 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.0030 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.4376 r_free = 0.4376 target = 0.197305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.159609 restraints weight = 6900.377| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 0.89 r_work: 0.3768 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1478 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= 0.135 Angle : 0.543 8.639 11569 Z= 0.289 Chirality : 0.034 0.281 1430 Planarity : 0.004 0.039 793 Dihedral : 23.973 173.229 3191 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.92 % Allowed : 15.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.41), residues: 420 helix: 1.06 (0.39), residues: 177 sheet: 0.32 (1.42), residues: 10 loop : -0.54 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.010 0.001 TYR C 169 PHE 0.007 0.001 PHE C 648 TRP 0.003 0.001 TRP C 452 HIS 0.002 0.001 HIS C 680 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7940) covalent geometry : angle 0.54301 (11566) hydrogen bonds : bond 0.04389 ( 324) hydrogen bonds : angle 2.89536 ( 728) metal coordination : bond 0.00712 ( 4) metal coordination : angle 1.10997 ( 3) *********************** 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 53 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7297 (mt0) cc_final: 0.6197 (tp-100) REVERT: C 79 SER cc_start: 0.8388 (p) cc_final: 0.8150 (m) REVERT: C 247 LYS cc_start: 0.7762 (ttmt) cc_final: 0.7298 (ttpt) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.5547 time to fit residues: 29.4974 Evaluate side-chains 45 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 269 LEU 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 21 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.191479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146573 restraints weight = 6926.491| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 0.96 r_work: 0.3704 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: 0.7336 moved from start: 0.1551 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= 0.214 Angle : 0.608 9.059 11569 Z= 0.318 Chirality : 0.037 0.281 1430 Planarity : 0.004 0.036 793 Dihedral : 23.952 173.315 3191 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.11 % Allowed : 13.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.40), residues: 420 helix: 0.90 (0.38), residues: 177 sheet: 0.08 (1.35), residues: 10 loop : -0.63 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 65 TYR 0.012 0.002 TYR C 70 PHE 0.010 0.002 PHE C 83 TRP 0.002 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 7940) covalent geometry : angle 0.60757 (11566) hydrogen bonds : bond 0.06228 ( 324) hydrogen bonds : angle 2.99914 ( 728) metal coordination : bond 0.01492 ( 4) metal coordination : angle 1.52717 ( 3) *********************** 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: 15 poor density : 42 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7322 (mt0) cc_final: 0.6126 (tp-100) REVERT: C 79 SER cc_start: 0.8424 (p) cc_final: 0.8185 (m) REVERT: C 247 LYS cc_start: 0.7762 (ttmt) cc_final: 0.7266 (ttpt) REVERT: C 739 LYS cc_start: 0.5283 (mmmt) cc_final: 0.4634 (ptpt) outliers start: 15 outliers final: 8 residues processed: 51 average time/residue: 0.5834 time to fit residues: 31.4355 Evaluate side-chains 46 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.192148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147240 restraints weight = 6909.512| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 0.96 r_work: 0.3712 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 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 0.061 7944 Z= 0.194 Angle : 0.587 9.053 11569 Z= 0.308 Chirality : 0.036 0.283 1430 Planarity : 0.004 0.034 793 Dihedral : 23.849 173.961 3191 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.40), residues: 420 helix: 0.94 (0.39), residues: 177 sheet: 0.10 (1.39), residues: 10 loop : -0.66 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 556 TYR 0.010 0.002 TYR C 169 PHE 0.009 0.001 PHE C 83 TRP 0.002 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 7940) covalent geometry : angle 0.58610 (11566) hydrogen bonds : bond 0.05784 ( 324) hydrogen bonds : angle 2.99394 ( 728) metal coordination : bond 0.01344 ( 4) metal coordination : angle 1.50436 ( 3) *********************** 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 53 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7263 (mt0) cc_final: 0.6073 (tp-100) REVERT: C 79 SER cc_start: 0.8407 (p) cc_final: 0.8167 (m) REVERT: C 247 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7266 (ttpt) REVERT: C 461 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5239 (tm-30) REVERT: C 739 LYS cc_start: 0.5610 (mmmt) cc_final: 0.5017 (ptpt) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 0.5152 time to fit residues: 25.2170 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 : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 571 MET Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.190649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.145669 restraints weight = 6866.430| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 0.96 r_work: 0.3693 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1890 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= 0.215 Angle : 0.604 9.064 11569 Z= 0.317 Chirality : 0.038 0.284 1430 Planarity : 0.005 0.035 793 Dihedral : 23.805 174.260 3191 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.29 % Allowed : 15.34 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.39), residues: 420 helix: 0.73 (0.38), residues: 182 sheet: -0.04 (1.34), residues: 10 loop : -0.76 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 556 TYR 0.012 0.002 TYR C 70 PHE 0.009 0.001 PHE C 83 TRP 0.003 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 7940) covalent geometry : angle 0.60335 (11566) hydrogen bonds : bond 0.06439 ( 324) hydrogen bonds : angle 3.04388 ( 728) metal coordination : bond 0.01567 ( 4) metal coordination : angle 1.28832 ( 3) *********************** 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 53 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: C 58 GLN cc_start: 0.7319 (mt0) cc_final: 0.6109 (tp-100) REVERT: C 79 SER cc_start: 0.8426 (p) cc_final: 0.8184 (m) REVERT: C 247 LYS cc_start: 0.7741 (ttmt) cc_final: 0.7211 (ttpt) REVERT: C 461 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5222 (tm-30) REVERT: C 577 CYS cc_start: 0.7402 (t) cc_final: 0.7183 (t) REVERT: C 739 LYS cc_start: 0.5652 (mmmt) cc_final: 0.5137 (ptpt) outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 0.5297 time to fit residues: 27.0600 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 : 0.184 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 626 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.189088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.143952 restraints weight = 6862.029| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.05 r_work: 0.3670 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2002 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= 0.254 Angle : 0.648 9.190 11569 Z= 0.337 Chirality : 0.040 0.290 1430 Planarity : 0.005 0.038 793 Dihedral : 23.824 174.415 3191 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.29 % Allowed : 16.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.39), residues: 420 helix: 0.59 (0.38), residues: 182 sheet: -0.03 (1.31), residues: 10 loop : -0.81 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 65 TYR 0.012 0.002 TYR C 70 PHE 0.011 0.002 PHE C 83 TRP 0.004 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 7940) covalent geometry : angle 0.64818 (11566) hydrogen bonds : bond 0.07287 ( 324) hydrogen bonds : angle 3.15240 ( 728) metal coordination : bond 0.01997 ( 4) metal coordination : angle 1.31144 ( 3) *********************** 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 52 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.129 Fit side-chains REVERT: C 58 GLN cc_start: 0.7327 (mt0) cc_final: 0.6117 (tp-100) REVERT: C 79 SER cc_start: 0.8424 (p) cc_final: 0.8184 (m) REVERT: C 247 LYS cc_start: 0.7755 (ttmt) cc_final: 0.7177 (ttpt) REVERT: C 461 GLU cc_start: 0.6082 (OUTLIER) cc_final: 0.5300 (tm-30) REVERT: C 576 GLU cc_start: 0.5480 (mt-10) cc_final: 0.5054 (mp0) REVERT: C 577 CYS cc_start: 0.7475 (t) cc_final: 0.7265 (t) REVERT: C 580 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7185 (pt0) REVERT: C 739 LYS cc_start: 0.5610 (mmmt) cc_final: 0.5139 (ptpt) outliers start: 12 outliers final: 9 residues processed: 49 average time/residue: 0.5218 time to fit residues: 27.2222 Evaluate side-chains 50 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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 626 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.188801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143580 restraints weight = 6892.824| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.05 r_work: 0.3666 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7944 Z= 0.259 Angle : 0.656 9.141 11569 Z= 0.340 Chirality : 0.040 0.291 1430 Planarity : 0.005 0.037 793 Dihedral : 23.818 174.562 3191 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.29 % Allowed : 16.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.39), residues: 420 helix: 0.50 (0.38), residues: 182 sheet: -0.09 (1.32), residues: 10 loop : -0.81 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 65 TYR 0.012 0.002 TYR C 169 PHE 0.011 0.002 PHE C 83 TRP 0.002 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 7940) covalent geometry : angle 0.65549 (11566) hydrogen bonds : bond 0.07325 ( 324) hydrogen bonds : angle 3.18283 ( 728) metal coordination : bond 0.01982 ( 4) metal coordination : angle 1.78965 ( 3) *********************** 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 53 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.209 Fit side-chains REVERT: C 58 GLN cc_start: 0.7329 (mt0) cc_final: 0.6093 (tp-100) REVERT: C 79 SER cc_start: 0.8438 (p) cc_final: 0.8223 (m) REVERT: C 247 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7127 (ttpt) REVERT: C 461 GLU cc_start: 0.6092 (OUTLIER) cc_final: 0.5304 (tm-30) REVERT: C 576 GLU cc_start: 0.5638 (mt-10) cc_final: 0.5000 (mp0) REVERT: C 739 LYS cc_start: 0.5675 (mmmt) cc_final: 0.5242 (ptpt) outliers start: 12 outliers final: 9 residues processed: 50 average time/residue: 0.4906 time to fit residues: 26.2291 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 : 0.211 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 626 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.193247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.148832 restraints weight = 6799.708| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 0.94 r_work: 0.3732 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7944 Z= 0.162 Angle : 0.576 9.527 11569 Z= 0.304 Chirality : 0.035 0.283 1430 Planarity : 0.004 0.035 793 Dihedral : 23.673 175.034 3191 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.47 % Allowed : 18.63 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.41), residues: 420 helix: 0.90 (0.39), residues: 182 sheet: 0.02 (1.40), residues: 10 loop : -0.70 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 65 TYR 0.010 0.001 TYR C 169 PHE 0.006 0.001 PHE C 83 TRP 0.003 0.001 TRP C 452 HIS 0.002 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7940) covalent geometry : angle 0.57570 (11566) hydrogen bonds : bond 0.05033 ( 324) hydrogen bonds : angle 3.09443 ( 728) metal coordination : bond 0.01256 ( 4) metal coordination : angle 1.49183 ( 3) *********************** 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: 9 poor density : 43 time to evaluate : 0.188 Fit side-chains REVERT: C 36 MET cc_start: 0.5096 (mtm) cc_final: 0.2138 (mmm) REVERT: C 46 ASP cc_start: 0.7128 (m-30) cc_final: 0.6886 (m-30) REVERT: C 58 GLN cc_start: 0.7276 (mt0) cc_final: 0.6079 (tp-100) REVERT: C 247 LYS cc_start: 0.7715 (ttmt) cc_final: 0.7202 (ttpt) REVERT: C 461 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5247 (tm-30) REVERT: C 576 GLU cc_start: 0.5304 (mt-10) cc_final: 0.4991 (mp0) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.5037 time to fit residues: 25.2337 Evaluate side-chains 47 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 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 32 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.194320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.149974 restraints weight = 6847.408| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 0.94 r_work: 0.3746 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7944 Z= 0.157 Angle : 0.567 10.360 11569 Z= 0.299 Chirality : 0.034 0.274 1430 Planarity : 0.004 0.034 793 Dihedral : 23.508 175.109 3191 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.64 % Allowed : 20.00 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.41), residues: 420 helix: 1.11 (0.39), residues: 182 sheet: -0.17 (1.37), residues: 10 loop : -0.67 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 672 TYR 0.010 0.001 TYR C 169 PHE 0.006 0.001 PHE C 648 TRP 0.002 0.001 TRP C 452 HIS 0.002 0.001 HIS C 680 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7940) covalent geometry : angle 0.56704 (11566) hydrogen bonds : bond 0.04771 ( 324) hydrogen bonds : angle 3.00658 ( 728) metal coordination : bond 0.00950 ( 4) metal coordination : angle 1.51928 ( 3) ********************** 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: 6 poor density : 41 time to evaluate : 0.184 Fit side-chains REVERT: C 46 ASP cc_start: 0.7029 (m-30) cc_final: 0.6781 (m-30) REVERT: C 247 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7243 (ttpt) REVERT: C 461 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5277 (tm-30) REVERT: C 576 GLU cc_start: 0.5216 (mt-10) cc_final: 0.4978 (mp0) REVERT: C 739 LYS cc_start: 0.5507 (mmmt) cc_final: 0.4672 (mtmm) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 0.5409 time to fit residues: 25.3656 Evaluate side-chains 46 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.192004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147290 restraints weight = 6871.844| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 0.96 r_work: 0.3714 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7944 Z= 0.189 Angle : 0.597 9.301 11569 Z= 0.314 Chirality : 0.036 0.275 1430 Planarity : 0.004 0.036 793 Dihedral : 23.505 175.043 3191 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.19 % Allowed : 19.73 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.41), residues: 420 helix: 1.04 (0.39), residues: 182 sheet: -0.10 (1.35), residues: 10 loop : -0.69 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 672 TYR 0.011 0.001 TYR C 169 PHE 0.007 0.001 PHE C 83 TRP 0.002 0.001 TRP C 452 HIS 0.003 0.001 HIS C 680 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7940) covalent geometry : angle 0.59670 (11566) hydrogen bonds : bond 0.05594 ( 324) hydrogen bonds : angle 3.06922 ( 728) metal coordination : bond 0.01234 ( 4) metal coordination : angle 1.66764 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2531.90 seconds wall clock time: 43 minutes 55.42 seconds (2635.42 seconds total)