Starting phenix.real_space_refine on Wed Sep 17 04:53:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnz_27585/09_2025/8dnz_27585_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnz_27585/09_2025/8dnz_27585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dnz_27585/09_2025/8dnz_27585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnz_27585/09_2025/8dnz_27585.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnz_27585/09_2025/8dnz_27585_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnz_27585/09_2025/8dnz_27585_trim.cif" } resolution = 2.57 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= 0.003 sd= 0.055 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: 5 Type Number sf(0) Gaussians S 27 5.16 5 C 2872 2.51 5 N 694 2.21 5 O 744 1.98 5 H 38 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 4375 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 251 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3548 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'T69': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'NMTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="T69 D 1 " pdbres="0A1 D 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'T69:plan-1': 1, '0A1:plan-2': 1, 'MAA:plan-1': 2, 'IML:plan-1': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.51, per 1000 atoms: 0.35 Number of scatterers: 4375 At special positions: 0 Unit cell: (93.45, 80.85, 78.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 O 744 8.00 N 694 7.00 C 2872 6.00 H 38 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 186.1 milliseconds Enol-peptide restraints added in 1.4 microseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1018 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 73.7% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 66 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 69 through 96 Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.539A pdb=" N VAL A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 9 " --> pdb=" O PHE A 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4 through 9' Processing helix chain 'A' and resid 9 through 14 Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.577A pdb=" N ARG A 66 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 105 through 134 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 144 through 171 Processing helix chain 'A' and resid 177 through 197 Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 241 through 260 Processing helix chain 'A' and resid 288 through 312 Processing helix chain 'A' and resid 315 through 322 Processing helix chain 'A' and resid 340 through 345 removed outlier: 3.752A pdb=" N TYR A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 381 removed outlier: 3.591A pdb=" N ALA A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 409 through 438 Proline residue: A 418 - end of helix removed outlier: 3.543A pdb=" N SER A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 468 removed outlier: 3.583A pdb=" N GLY A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 202 Processing sheet with id=AA3, first strand: chain 'A' and resid 276 through 282 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.477A pdb=" N THR A 323 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR A 336 " --> pdb=" O SER A 325 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.73 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.16: 38 1.16 - 1.33: 746 1.33 - 1.49: 1721 1.49 - 1.65: 1916 1.65 - 1.82: 46 Bond restraints: 4467 Sorted by residual: bond pdb=" CD1 0A1 D 2 " pdb=" HD1 0A1 D 2 " ideal model delta sigma weight residual 0.930 1.158 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" CE1 0A1 D 2 " pdb=" HE1 0A1 D 2 " ideal model delta sigma weight residual 0.930 1.156 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" CD2 0A1 D 2 " pdb=" HD2 0A1 D 2 " ideal model delta sigma weight residual 0.930 1.150 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CE2 0A1 D 2 " pdb=" HE2 0A1 D 2 " ideal model delta sigma weight residual 0.930 1.122 -0.192 2.00e-02 2.50e+03 9.23e+01 bond pdb=" CA MAA D 3 " pdb=" HA MAA D 3 " ideal model delta sigma weight residual 0.970 1.149 -0.179 2.00e-02 2.50e+03 7.98e+01 ... (remaining 4462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 6042 4.34 - 8.67: 31 8.67 - 13.01: 4 13.01 - 17.34: 1 17.34 - 21.68: 1 Bond angle restraints: 6079 Sorted by residual: angle pdb=" CA MAA D 5 " pdb=" C MAA D 5 " pdb=" O MAA D 5 " ideal model delta sigma weight residual 120.80 107.21 13.59 1.70e+00 3.46e-01 6.39e+01 angle pdb=" C25 T69 D 1 " pdb=" C26 T69 D 1 " pdb=" N12 T69 D 1 " ideal model delta sigma weight residual 111.50 133.18 -21.68 3.00e+00 1.11e-01 5.22e+01 angle pdb=" N GLY A 442 " pdb=" CA GLY A 442 " pdb=" C GLY A 442 " ideal model delta sigma weight residual 113.58 106.52 7.06 1.07e+00 8.73e-01 4.35e+01 angle pdb=" CA 0A1 D 2 " pdb=" C 0A1 D 2 " pdb=" N MAA D 3 " ideal model delta sigma weight residual 116.20 127.09 -10.89 2.00e+00 2.50e-01 2.97e+01 angle pdb=" N 0A1 D 2 " pdb=" CA 0A1 D 2 " pdb=" CB 0A1 D 2 " ideal model delta sigma weight residual 110.50 119.64 -9.14 1.70e+00 3.46e-01 2.89e+01 ... (remaining 6074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 2398 17.01 - 34.02: 215 34.02 - 51.02: 32 51.02 - 68.03: 9 68.03 - 85.04: 6 Dihedral angle restraints: 2660 sinusoidal: 1074 harmonic: 1586 Sorted by residual: dihedral pdb=" CB MET A 77 " pdb=" CG MET A 77 " pdb=" SD MET A 77 " pdb=" CE MET A 77 " ideal model delta sinusoidal sigma weight residual 180.00 123.52 56.48 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA ASP A 389 " pdb=" CB ASP A 389 " pdb=" CG ASP A 389 " pdb=" OD1 ASP A 389 " ideal model delta sinusoidal sigma weight residual -30.00 -81.14 51.14 1 2.00e+01 2.50e-03 8.94e+00 dihedral pdb=" CB MET C 86 " pdb=" CG MET C 86 " pdb=" SD MET C 86 " pdb=" CE MET C 86 " ideal model delta sinusoidal sigma weight residual 180.00 129.24 50.76 3 1.50e+01 4.44e-03 8.94e+00 ... (remaining 2657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.424: 709 0.424 - 0.847: 0 0.847 - 1.271: 0 1.271 - 1.694: 0 1.694 - 2.118: 1 Chirality restraints: 710 Sorted by residual: chirality pdb=" C26 T69 D 1 " pdb=" C25 T69 D 1 " pdb=" N12 T69 D 1 " pdb=" S01 T69 D 1 " both_signs ideal model delta sigma weight residual False 3.12 1.00 2.12 2.00e-01 2.50e+01 1.12e+02 chirality pdb=" CA IML D 4 " pdb=" N IML D 4 " pdb=" C IML D 4 " pdb=" CB IML D 4 " both_signs ideal model delta sigma weight residual False 2.43 2.84 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA MAA D 5 " pdb=" N MAA D 5 " pdb=" C MAA D 5 " pdb=" CB MAA D 5 " both_signs ideal model delta sigma weight residual False 2.48 2.78 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 707 not shown) Planarity restraints: 732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 439 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C GLY A 439 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY A 439 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 440 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 60 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A 61 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 21 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 22 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " -0.024 5.00e-02 4.00e+02 ... (remaining 729 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 14 2.35 - 2.91: 1830 2.91 - 3.47: 5353 3.47 - 4.04: 8575 4.04 - 4.60: 12554 Nonbonded interactions: 28326 Sorted by model distance: nonbonded pdb=" OD1 ASN A 300 " pdb=" HN1 0A1 D 2 " model vdw 1.783 2.450 nonbonded pdb=" HA IML D 4 " pdb=" HM3 MAA D 5 " model vdw 2.042 2.440 nonbonded pdb=" OD2 ASP A 139 " pdb=" OG SER A 141 " model vdw 2.177 2.800 nonbonded pdb=" O ILE A 68 " pdb=" HE2 0A1 D 2 " model vdw 2.177 2.450 nonbonded pdb=" HB1 MAA D 5 " pdb=" HM2 MAA D 5 " model vdw 2.201 2.440 ... (remaining 28321 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.960 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:9.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 : 0.006 0.156 4431 Z= 0.347 Angle : 0.708 21.675 5997 Z= 0.370 Chirality : 0.091 2.118 710 Planarity : 0.005 0.049 732 Dihedral : 13.188 85.038 1621 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.55 (0.35), residues: 543 helix: 1.69 (0.25), residues: 388 sheet: -1.32 (1.44), residues: 12 loop : -0.50 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 311 TYR 0.007 0.001 TYR A 137 PHE 0.017 0.001 PHE A 217 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.000 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00622 ( 4429) covalent geometry : angle 0.70836 ( 5997) hydrogen bonds : bond 0.20065 ( 316) hydrogen bonds : angle 6.43995 ( 945) Misc. bond : bond 0.01311 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.169 Fit side-chains REVERT: B 31 LYS cc_start: 0.8113 (mppt) cc_final: 0.7711 (mppt) REVERT: A 27 GLN cc_start: 0.7407 (mm110) cc_final: 0.7001 (mm110) REVERT: A 117 LYS cc_start: 0.7491 (mttt) cc_final: 0.7201 (mtmm) REVERT: A 167 GLU cc_start: 0.7900 (tt0) cc_final: 0.7670 (tt0) REVERT: A 268 ARG cc_start: 0.6814 (ptp-110) cc_final: 0.6438 (ptm-80) REVERT: A 307 MET cc_start: 0.6089 (mmt) cc_final: 0.5278 (ttt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.8341 time to fit residues: 61.6409 Evaluate side-chains 62 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109300 restraints weight = 4814.561| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.89 r_work: 0.3310 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4431 Z= 0.151 Angle : 0.486 6.156 5997 Z= 0.253 Chirality : 0.038 0.131 710 Planarity : 0.004 0.034 732 Dihedral : 5.667 89.089 627 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.43 % Allowed : 7.76 % Favored : 91.81 % 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: 2.63 (0.36), residues: 543 helix: 2.49 (0.25), residues: 398 sheet: -0.63 (1.63), residues: 12 loop : -0.38 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 388 TYR 0.011 0.001 TYR A 137 PHE 0.011 0.001 PHE B 49 TRP 0.009 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4429) covalent geometry : angle 0.48626 ( 5997) hydrogen bonds : bond 0.04569 ( 316) hydrogen bonds : angle 4.14487 ( 945) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.180 Fit side-chains REVERT: B 34 GLN cc_start: 0.8009 (mt0) cc_final: 0.7793 (mt0) REVERT: A 15 ILE cc_start: 0.7785 (pt) cc_final: 0.7120 (mm) REVERT: A 27 GLN cc_start: 0.7658 (mm110) cc_final: 0.7408 (mm110) REVERT: A 268 ARG cc_start: 0.7517 (ptp-110) cc_final: 0.6841 (ptm-80) outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 0.6425 time to fit residues: 44.5249 Evaluate side-chains 63 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 241 ASN A 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.142843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108660 restraints weight = 4816.389| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.88 r_work: 0.3298 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4431 Z= 0.138 Angle : 0.436 5.138 5997 Z= 0.225 Chirality : 0.037 0.129 710 Planarity : 0.003 0.030 732 Dihedral : 5.430 86.148 627 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.65 % Allowed : 10.78 % Favored : 88.58 % 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: 2.99 (0.37), residues: 543 helix: 2.74 (0.26), residues: 400 sheet: -1.16 (1.51), residues: 14 loop : -0.12 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 388 TYR 0.010 0.001 TYR A 137 PHE 0.009 0.001 PHE B 49 TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4429) covalent geometry : angle 0.43552 ( 5997) hydrogen bonds : bond 0.04162 ( 316) hydrogen bonds : angle 3.83284 ( 945) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.200 Fit side-chains REVERT: A 15 ILE cc_start: 0.7713 (pt) cc_final: 0.7178 (mm) REVERT: A 27 GLN cc_start: 0.7465 (mm110) cc_final: 0.7210 (mm110) REVERT: A 139 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7871 (t70) REVERT: A 268 ARG cc_start: 0.7580 (ptp-110) cc_final: 0.7259 (ptm160) REVERT: A 273 ARG cc_start: 0.7921 (mtt180) cc_final: 0.6930 (mtp85) REVERT: A 405 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6788 (mtt-85) outliers start: 3 outliers final: 0 residues processed: 61 average time/residue: 0.7452 time to fit residues: 46.8659 Evaluate side-chains 63 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 405 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.141931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107593 restraints weight = 4767.307| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.87 r_work: 0.3283 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4431 Z= 0.161 Angle : 0.456 5.886 5997 Z= 0.234 Chirality : 0.037 0.130 710 Planarity : 0.003 0.029 732 Dihedral : 5.448 84.844 627 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.08 % Allowed : 11.21 % Favored : 87.72 % 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: 3.05 (0.36), residues: 543 helix: 2.75 (0.26), residues: 400 sheet: -1.33 (1.52), residues: 14 loop : 0.02 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.010 0.001 TYR A 137 PHE 0.010 0.001 PHE B 49 TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4429) covalent geometry : angle 0.45643 ( 5997) hydrogen bonds : bond 0.04141 ( 316) hydrogen bonds : angle 3.80351 ( 945) Misc. bond : bond 0.00047 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.161 Fit side-chains REVERT: A 15 ILE cc_start: 0.7675 (pt) cc_final: 0.7303 (mt) REVERT: A 27 GLN cc_start: 0.7437 (mm110) cc_final: 0.7213 (mm110) REVERT: A 139 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7904 (t70) REVERT: A 268 ARG cc_start: 0.7724 (ptp-110) cc_final: 0.7447 (ptm160) REVERT: A 273 ARG cc_start: 0.7963 (mtt180) cc_final: 0.6966 (mtp85) REVERT: A 405 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6788 (mtt-85) outliers start: 5 outliers final: 2 residues processed: 62 average time/residue: 0.7410 time to fit residues: 47.4086 Evaluate side-chains 65 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 465 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.0570 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 0.0270 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110215 restraints weight = 4812.240| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.88 r_work: 0.3318 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4431 Z= 0.103 Angle : 0.394 4.467 5997 Z= 0.202 Chirality : 0.036 0.127 710 Planarity : 0.003 0.029 732 Dihedral : 5.216 84.615 627 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.86 % Allowed : 12.07 % Favored : 87.07 % 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: 3.44 (0.37), residues: 543 helix: 3.02 (0.26), residues: 402 sheet: -0.91 (1.66), residues: 12 loop : 0.11 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 388 TYR 0.006 0.001 TYR A 137 PHE 0.006 0.001 PHE B 49 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 4429) covalent geometry : angle 0.39446 ( 5997) hydrogen bonds : bond 0.03582 ( 316) hydrogen bonds : angle 3.58719 ( 945) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.113 Fit side-chains REVERT: A 15 ILE cc_start: 0.7705 (pt) cc_final: 0.7150 (mm) REVERT: A 27 GLN cc_start: 0.7446 (mm110) cc_final: 0.7220 (mm110) REVERT: A 139 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7809 (t70) REVERT: A 268 ARG cc_start: 0.7727 (ptp-110) cc_final: 0.7426 (ptm160) REVERT: A 273 ARG cc_start: 0.7949 (mtt180) cc_final: 0.6922 (mtp85) outliers start: 4 outliers final: 0 residues processed: 66 average time/residue: 0.7156 time to fit residues: 48.6846 Evaluate side-chains 63 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108186 restraints weight = 4878.352| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.90 r_work: 0.3289 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4431 Z= 0.138 Angle : 0.428 5.430 5997 Z= 0.219 Chirality : 0.037 0.131 710 Planarity : 0.003 0.028 732 Dihedral : 5.258 84.022 627 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.29 % Allowed : 12.93 % Favored : 85.78 % 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: 3.38 (0.37), residues: 543 helix: 2.99 (0.26), residues: 402 sheet: -1.57 (1.47), residues: 14 loop : 0.15 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 236 TYR 0.008 0.001 TYR A 137 PHE 0.009 0.001 PHE B 49 TRP 0.006 0.001 TRP A 324 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4429) covalent geometry : angle 0.42805 ( 5997) hydrogen bonds : bond 0.03843 ( 316) hydrogen bonds : angle 3.62105 ( 945) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.188 Fit side-chains REVERT: A 15 ILE cc_start: 0.7705 (pt) cc_final: 0.7319 (mt) REVERT: A 27 GLN cc_start: 0.7370 (mm110) cc_final: 0.7161 (mm110) REVERT: A 139 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7816 (t70) REVERT: A 268 ARG cc_start: 0.7724 (ptp-110) cc_final: 0.7407 (ptm160) REVERT: A 273 ARG cc_start: 0.8016 (mtt180) cc_final: 0.6969 (mtp85) outliers start: 6 outliers final: 2 residues processed: 67 average time/residue: 0.6350 time to fit residues: 43.9702 Evaluate side-chains 66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 465 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108570 restraints weight = 4803.214| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.88 r_work: 0.3296 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4431 Z= 0.128 Angle : 0.417 4.966 5997 Z= 0.213 Chirality : 0.036 0.129 710 Planarity : 0.003 0.029 732 Dihedral : 5.230 83.826 627 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.29 % Allowed : 12.72 % Favored : 85.99 % 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: 3.43 (0.37), residues: 543 helix: 3.02 (0.26), residues: 402 sheet: -1.21 (1.59), residues: 12 loop : 0.11 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.007 0.001 TYR A 137 PHE 0.008 0.001 PHE B 49 TRP 0.006 0.001 TRP A 324 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4429) covalent geometry : angle 0.41719 ( 5997) hydrogen bonds : bond 0.03752 ( 316) hydrogen bonds : angle 3.60281 ( 945) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.177 Fit side-chains REVERT: A 15 ILE cc_start: 0.7729 (pt) cc_final: 0.7343 (mt) REVERT: A 27 GLN cc_start: 0.7413 (mm110) cc_final: 0.7184 (mm110) REVERT: A 139 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7803 (t70) REVERT: A 268 ARG cc_start: 0.7745 (ptp-110) cc_final: 0.7400 (ptm160) REVERT: A 273 ARG cc_start: 0.8050 (mtt180) cc_final: 0.6982 (mtp85) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 0.7141 time to fit residues: 47.9790 Evaluate side-chains 66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 465 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 chunk 4 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.110094 restraints weight = 4809.391| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.87 r_work: 0.3319 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4431 Z= 0.098 Angle : 0.384 4.353 5997 Z= 0.197 Chirality : 0.035 0.127 710 Planarity : 0.003 0.029 732 Dihedral : 5.068 83.668 627 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.86 % Allowed : 12.07 % Favored : 87.07 % 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: 3.66 (0.37), residues: 543 helix: 3.21 (0.26), residues: 403 sheet: -1.18 (1.57), residues: 12 loop : 0.09 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.006 0.001 TYR A 137 PHE 0.006 0.001 PHE B 49 TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 4429) covalent geometry : angle 0.38401 ( 5997) hydrogen bonds : bond 0.03448 ( 316) hydrogen bonds : angle 3.48467 ( 945) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.178 Fit side-chains REVERT: A 15 ILE cc_start: 0.7720 (pt) cc_final: 0.7334 (mt) REVERT: A 27 GLN cc_start: 0.7433 (mm110) cc_final: 0.7165 (mm110) REVERT: A 139 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7765 (t70) REVERT: A 268 ARG cc_start: 0.7743 (ptp-110) cc_final: 0.6931 (ptt90) REVERT: A 273 ARG cc_start: 0.8009 (mtt180) cc_final: 0.6975 (mtp85) outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 0.6761 time to fit residues: 45.4375 Evaluate side-chains 68 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 465 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.0570 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109105 restraints weight = 4809.463| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.87 r_work: 0.3313 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4431 Z= 0.120 Angle : 0.408 5.126 5997 Z= 0.209 Chirality : 0.036 0.129 710 Planarity : 0.003 0.029 732 Dihedral : 5.109 83.459 627 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.08 % Allowed : 12.28 % Favored : 86.64 % 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: 3.64 (0.37), residues: 543 helix: 3.20 (0.25), residues: 402 sheet: -1.28 (1.57), residues: 12 loop : 0.10 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.007 0.001 TYR A 137 PHE 0.008 0.001 PHE B 49 TRP 0.006 0.001 TRP A 324 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 4429) covalent geometry : angle 0.40818 ( 5997) hydrogen bonds : bond 0.03626 ( 316) hydrogen bonds : angle 3.52300 ( 945) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.273 Fit side-chains REVERT: A 15 ILE cc_start: 0.7797 (pt) cc_final: 0.7419 (mt) REVERT: A 27 GLN cc_start: 0.7431 (mm110) cc_final: 0.7201 (mm110) REVERT: A 139 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7772 (t70) REVERT: A 268 ARG cc_start: 0.7688 (ptp-110) cc_final: 0.6908 (ptt90) REVERT: A 273 ARG cc_start: 0.8007 (mtt180) cc_final: 0.6975 (mtp85) REVERT: A 405 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6702 (mtt-85) outliers start: 5 outliers final: 2 residues processed: 65 average time/residue: 0.7057 time to fit residues: 47.2439 Evaluate side-chains 67 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.0010 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 46 optimal weight: 0.0270 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN A 402 ASN A 456 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.144312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110546 restraints weight = 4759.462| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.85 r_work: 0.3335 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4431 Z= 0.096 Angle : 0.380 4.321 5997 Z= 0.195 Chirality : 0.035 0.128 710 Planarity : 0.003 0.029 732 Dihedral : 5.000 83.379 627 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.86 % Allowed : 11.85 % Favored : 87.28 % 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: 3.77 (0.37), residues: 543 helix: 3.31 (0.26), residues: 404 sheet: -1.19 (1.57), residues: 12 loop : 0.03 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.005 0.001 TYR A 131 PHE 0.006 0.001 PHE B 49 TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 4429) covalent geometry : angle 0.38022 ( 5997) hydrogen bonds : bond 0.03408 ( 316) hydrogen bonds : angle 3.44073 ( 945) Misc. bond : bond 0.00004 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.181 Fit side-chains REVERT: A 15 ILE cc_start: 0.7789 (pt) cc_final: 0.7423 (mt) REVERT: A 27 GLN cc_start: 0.7430 (mm110) cc_final: 0.7214 (mm110) REVERT: A 139 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7752 (t70) REVERT: A 268 ARG cc_start: 0.7697 (ptp-110) cc_final: 0.6950 (ptt90) REVERT: A 273 ARG cc_start: 0.7964 (mtt180) cc_final: 0.6961 (mtp85) REVERT: A 405 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6681 (mtt-85) outliers start: 4 outliers final: 2 residues processed: 67 average time/residue: 0.7084 time to fit residues: 48.9729 Evaluate side-chains 69 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 0.0470 chunk 40 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109855 restraints weight = 4866.615| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.89 r_work: 0.3327 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4431 Z= 0.112 Angle : 0.404 4.846 5997 Z= 0.207 Chirality : 0.036 0.129 710 Planarity : 0.003 0.028 732 Dihedral : 5.017 83.180 627 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.86 % Allowed : 12.72 % Favored : 86.42 % 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: 3.71 (0.37), residues: 543 helix: 3.27 (0.25), residues: 404 sheet: -1.40 (1.53), residues: 12 loop : 0.04 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.006 0.001 TYR A 137 PHE 0.007 0.001 PHE B 49 TRP 0.005 0.001 TRP A 324 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 4429) covalent geometry : angle 0.40380 ( 5997) hydrogen bonds : bond 0.03518 ( 316) hydrogen bonds : angle 3.46408 ( 945) Misc. bond : bond 0.00013 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1976.56 seconds wall clock time: 34 minutes 30.54 seconds (2070.54 seconds total)