Starting phenix.real_space_refine on Wed Jul 23 23:06:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnz_27585/07_2025/8dnz_27585_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnz_27585/07_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_27585/07_2025/8dnz_27585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnz_27585/07_2025/8dnz_27585.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnz_27585/07_2025/8dnz_27585_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnz_27585/07_2025/8dnz_27585_trim.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'IML:plan-1': 1, 'MAA:plan-1': 2, '0A1:plan-2': 1, 'T69:plan-1': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 3.54, per 1000 atoms: 0.81 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: 1.45 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.43 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: 1.29 Time building geometry restraints manager: 1.43 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: 2.030 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: 0.120 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.680 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.100 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.000 HIS C 88 PHE 0.017 0.001 PHE A 217 TYR 0.007 0.001 TYR A 137 ARG 0.006 0.001 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.20065 ( 316) hydrogen bonds : angle 6.43995 ( 945) covalent geometry : bond 0.00622 ( 4429) covalent geometry : angle 0.70836 ( 5997) 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 : 0.447 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: 1.5831 time to fit residues: 117.4558 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 : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.0020 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.0050 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.146359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112546 restraints weight = 4729.506| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.87 r_work: 0.3352 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4431 Z= 0.103 Angle : 0.443 4.628 5997 Z= 0.233 Chirality : 0.036 0.132 710 Planarity : 0.004 0.033 732 Dihedral : 5.524 89.781 627 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.43 % Allowed : 6.90 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.36), residues: 543 helix: 2.66 (0.26), residues: 398 sheet: -0.71 (1.63), residues: 12 loop : -0.36 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 90 HIS 0.003 0.001 HIS A 360 PHE 0.006 0.001 PHE A 112 TYR 0.007 0.001 TYR A 455 ARG 0.002 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 316) hydrogen bonds : angle 4.07580 ( 945) covalent geometry : bond 0.00199 ( 4429) covalent geometry : angle 0.44316 ( 5997) Misc. bond : bond 0.00084 ( 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 : 0.463 Fit side-chains REVERT: A 27 GLN cc_start: 0.7756 (mm110) cc_final: 0.7487 (mm110) REVERT: A 268 ARG cc_start: 0.7541 (ptp-110) cc_final: 0.6839 (ptm-80) outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 1.2226 time to fit residues: 85.1051 Evaluate side-chains 61 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.0030 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 0.0050 chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.4404 ------------------------------------------------------------------------------- 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 A 241 ASN A 244 ASN A 275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.145626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111782 restraints weight = 4771.335| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.87 r_work: 0.3351 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4431 Z= 0.103 Angle : 0.403 4.570 5997 Z= 0.208 Chirality : 0.036 0.128 710 Planarity : 0.003 0.029 732 Dihedral : 5.233 86.726 627 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.86 % Allowed : 9.70 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.37), residues: 543 helix: 2.96 (0.26), residues: 401 sheet: -0.91 (1.54), residues: 12 loop : -0.16 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE B 49 TYR 0.009 0.001 TYR A 137 ARG 0.002 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 316) hydrogen bonds : angle 3.64944 ( 945) covalent geometry : bond 0.00213 ( 4429) covalent geometry : angle 0.40303 ( 5997) Misc. bond : bond 0.00035 ( 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 68 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.454 Fit side-chains REVERT: A 15 ILE cc_start: 0.8037 (pt) cc_final: 0.7685 (mt) REVERT: A 27 GLN cc_start: 0.7641 (mm110) cc_final: 0.7403 (mm110) REVERT: A 139 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7885 (t70) REVERT: A 268 ARG cc_start: 0.7604 (ptp-110) cc_final: 0.6895 (ptm-80) REVERT: A 405 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6709 (mtt-85) outliers start: 4 outliers final: 0 residues processed: 65 average time/residue: 1.2247 time to fit residues: 82.6389 Evaluate side-chains 62 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.141910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107418 restraints weight = 4750.275| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.87 r_work: 0.3289 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4431 Z= 0.177 Angle : 0.471 6.515 5997 Z= 0.242 Chirality : 0.038 0.133 710 Planarity : 0.003 0.027 732 Dihedral : 5.422 84.861 627 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.08 % Allowed : 11.42 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.36), residues: 543 helix: 2.75 (0.26), residues: 402 sheet: -1.32 (1.51), residues: 14 loop : -0.00 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.003 0.001 HIS C 88 PHE 0.011 0.001 PHE B 49 TYR 0.012 0.001 TYR A 137 ARG 0.002 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 316) hydrogen bonds : angle 3.80235 ( 945) covalent geometry : bond 0.00406 ( 4429) covalent geometry : angle 0.47124 ( 5997) Misc. bond : bond 0.00051 ( 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 61 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.469 Fit side-chains REVERT: A 15 ILE cc_start: 0.8014 (pt) cc_final: 0.7623 (mt) REVERT: A 20 GLN cc_start: 0.7716 (mt0) cc_final: 0.7474 (mt0) REVERT: A 27 GLN cc_start: 0.7454 (mm110) cc_final: 0.7237 (mm110) REVERT: A 139 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7912 (t70) REVERT: A 268 ARG cc_start: 0.7747 (ptp-110) cc_final: 0.7503 (ptm160) REVERT: A 273 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7003 (mtp85) REVERT: A 405 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6737 (mtt-85) outliers start: 5 outliers final: 2 residues processed: 58 average time/residue: 1.4614 time to fit residues: 87.5649 Evaluate side-chains 60 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.109246 restraints weight = 4852.550| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.90 r_work: 0.3303 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2142 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= 0.119 Angle : 0.412 4.638 5997 Z= 0.212 Chirality : 0.036 0.128 710 Planarity : 0.003 0.028 732 Dihedral : 5.273 84.653 627 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.08 % Allowed : 12.07 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.37), residues: 543 helix: 2.97 (0.26), residues: 402 sheet: -0.72 (1.68), residues: 12 loop : -0.01 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.008 0.001 PHE A 261 TYR 0.006 0.001 TYR A 137 ARG 0.001 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 316) hydrogen bonds : angle 3.63147 ( 945) covalent geometry : bond 0.00260 ( 4429) covalent geometry : angle 0.41202 ( 5997) Misc. bond : bond 0.00015 ( 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 67 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.523 Fit side-chains REVERT: A 15 ILE cc_start: 0.8014 (pt) cc_final: 0.7624 (mt) REVERT: A 20 GLN cc_start: 0.7661 (mt0) cc_final: 0.7348 (mt0) REVERT: A 27 GLN cc_start: 0.7460 (mm110) cc_final: 0.7232 (mm110) REVERT: A 139 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7795 (t70) REVERT: A 268 ARG cc_start: 0.7739 (ptp-110) cc_final: 0.7465 (ptm160) REVERT: A 273 ARG cc_start: 0.7946 (mtt180) cc_final: 0.6970 (mtp85) outliers start: 5 outliers final: 2 residues processed: 64 average time/residue: 1.4033 time to fit residues: 92.8200 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 : 0.477 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108527 restraints weight = 4766.074| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.88 r_work: 0.3297 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2244 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= 0.133 Angle : 0.424 5.281 5997 Z= 0.217 Chirality : 0.036 0.131 710 Planarity : 0.003 0.028 732 Dihedral : 5.252 84.158 627 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.08 % Allowed : 13.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.37), residues: 543 helix: 3.00 (0.26), residues: 402 sheet: -1.53 (1.47), residues: 14 loop : 0.09 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.009 0.001 PHE B 49 TYR 0.006 0.001 TYR A 137 ARG 0.001 0.000 ARG A 236 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 316) hydrogen bonds : angle 3.61025 ( 945) covalent geometry : bond 0.00296 ( 4429) covalent geometry : angle 0.42396 ( 5997) Misc. bond : bond 0.00028 ( 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 68 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.487 Fit side-chains REVERT: A 15 ILE cc_start: 0.8006 (pt) cc_final: 0.7615 (mt) REVERT: A 20 GLN cc_start: 0.7631 (mt0) cc_final: 0.7330 (mt0) REVERT: A 27 GLN cc_start: 0.7387 (mm110) cc_final: 0.7171 (mm110) REVERT: A 139 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7770 (t70) REVERT: A 268 ARG cc_start: 0.7735 (ptp-110) cc_final: 0.7403 (ptm160) REVERT: A 273 ARG cc_start: 0.8039 (mtt180) cc_final: 0.6992 (mtp85) outliers start: 5 outliers final: 2 residues processed: 63 average time/residue: 1.3008 time to fit residues: 84.8602 Evaluate side-chains 63 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109949 restraints weight = 4738.487| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.87 r_work: 0.3314 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4431 Z= 0.109 Angle : 0.398 4.379 5997 Z= 0.204 Chirality : 0.036 0.129 710 Planarity : 0.003 0.029 732 Dihedral : 5.138 84.065 627 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.22 % Allowed : 14.44 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.37), residues: 543 helix: 3.22 (0.26), residues: 399 sheet: -0.94 (1.66), residues: 12 loop : 0.08 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.007 0.001 PHE B 49 TYR 0.005 0.001 TYR A 455 ARG 0.001 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 316) hydrogen bonds : angle 3.52214 ( 945) covalent geometry : bond 0.00236 ( 4429) covalent geometry : angle 0.39811 ( 5997) Misc. bond : bond 0.00011 ( 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 64 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.494 Fit side-chains REVERT: A 15 ILE cc_start: 0.8009 (pt) cc_final: 0.7590 (mt) REVERT: A 20 GLN cc_start: 0.7602 (mt0) cc_final: 0.7356 (mt0) REVERT: A 27 GLN cc_start: 0.7396 (mm110) cc_final: 0.7176 (mm110) REVERT: A 139 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7754 (t70) REVERT: A 268 ARG cc_start: 0.7751 (ptp-110) cc_final: 0.7419 (ptm160) REVERT: A 273 ARG cc_start: 0.7988 (mtt180) cc_final: 0.6956 (mtp85) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 1.3124 time to fit residues: 85.6782 Evaluate side-chains 64 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 0.0010 chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.143746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109573 restraints weight = 4730.182| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.87 r_work: 0.3318 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4431 Z= 0.112 Angle : 0.399 4.700 5997 Z= 0.204 Chirality : 0.036 0.130 710 Planarity : 0.003 0.028 732 Dihedral : 5.106 83.794 627 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.86 % Allowed : 13.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.37), residues: 543 helix: 3.26 (0.26), residues: 399 sheet: -1.00 (1.66), residues: 12 loop : 0.10 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.008 0.001 PHE B 49 TYR 0.005 0.001 TYR A 137 ARG 0.001 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 316) hydrogen bonds : angle 3.50747 ( 945) covalent geometry : bond 0.00245 ( 4429) covalent geometry : angle 0.39928 ( 5997) Misc. bond : bond 0.00014 ( 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 66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.483 Fit side-chains REVERT: A 15 ILE cc_start: 0.8038 (pt) cc_final: 0.7636 (mt) REVERT: A 20 GLN cc_start: 0.7616 (mt0) cc_final: 0.7368 (mt0) REVERT: A 27 GLN cc_start: 0.7416 (mm110) cc_final: 0.7192 (mm110) REVERT: A 139 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7781 (t70) REVERT: A 268 ARG cc_start: 0.7747 (ptp-110) cc_final: 0.7403 (ptm160) REVERT: A 273 ARG cc_start: 0.8000 (mtt180) cc_final: 0.6976 (mtp85) outliers start: 4 outliers final: 1 residues processed: 62 average time/residue: 1.3488 time to fit residues: 86.7029 Evaluate side-chains 64 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.0870 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.143667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.109540 restraints weight = 4720.705| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.86 r_work: 0.3324 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4431 Z= 0.117 Angle : 0.407 4.736 5997 Z= 0.208 Chirality : 0.036 0.130 710 Planarity : 0.003 0.028 732 Dihedral : 5.105 83.655 627 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.86 % Allowed : 13.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.37), residues: 543 helix: 3.19 (0.26), residues: 402 sheet: -1.21 (1.60), residues: 12 loop : 0.11 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.007 0.001 PHE B 49 TYR 0.005 0.001 TYR A 137 ARG 0.001 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 316) hydrogen bonds : angle 3.50811 ( 945) covalent geometry : bond 0.00258 ( 4429) covalent geometry : angle 0.40735 ( 5997) Misc. bond : bond 0.00018 ( 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 66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.503 Fit side-chains REVERT: A 15 ILE cc_start: 0.8067 (pt) cc_final: 0.7657 (mt) REVERT: A 20 GLN cc_start: 0.7624 (mt0) cc_final: 0.7378 (mt0) REVERT: A 27 GLN cc_start: 0.7415 (mm110) cc_final: 0.7194 (mm110) REVERT: A 139 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7761 (t70) REVERT: A 268 ARG cc_start: 0.7722 (ptp-110) cc_final: 0.7369 (ptm160) REVERT: A 273 ARG cc_start: 0.7975 (mtt180) cc_final: 0.6979 (mtp85) REVERT: A 405 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6684 (mtt-85) outliers start: 4 outliers final: 1 residues processed: 64 average time/residue: 1.3005 time to fit residues: 86.2667 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 : 0.451 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 8 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109621 restraints weight = 4694.589| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.86 r_work: 0.3310 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2386 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= 0.116 Angle : 0.403 4.750 5997 Z= 0.206 Chirality : 0.036 0.129 710 Planarity : 0.003 0.028 732 Dihedral : 5.085 83.544 627 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.65 % Allowed : 13.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.37), residues: 543 helix: 3.21 (0.26), residues: 402 sheet: -1.79 (1.41), residues: 14 loop : 0.14 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 324 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE B 49 TYR 0.005 0.001 TYR A 63 ARG 0.001 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 316) hydrogen bonds : angle 3.50264 ( 945) covalent geometry : bond 0.00256 ( 4429) covalent geometry : angle 0.40289 ( 5997) Misc. bond : bond 0.00020 ( 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 66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.494 Fit side-chains REVERT: A 15 ILE cc_start: 0.8072 (pt) cc_final: 0.7676 (mt) REVERT: A 20 GLN cc_start: 0.7623 (mt0) cc_final: 0.7381 (mt0) REVERT: A 27 GLN cc_start: 0.7442 (mm110) cc_final: 0.7211 (mm110) REVERT: A 139 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7751 (t70) REVERT: A 268 ARG cc_start: 0.7714 (ptp-110) cc_final: 0.7462 (ptm160) REVERT: A 273 ARG cc_start: 0.7963 (mtt180) cc_final: 0.6965 (mtp85) REVERT: A 405 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6682 (mtt-85) outliers start: 3 outliers final: 1 residues processed: 64 average time/residue: 1.5374 time to fit residues: 101.9717 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 : 0.819 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109349 restraints weight = 4774.119| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.88 r_work: 0.3307 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4431 Z= 0.121 Angle : 0.417 4.834 5997 Z= 0.214 Chirality : 0.036 0.130 710 Planarity : 0.003 0.028 732 Dihedral : 5.081 83.451 627 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.65 % Allowed : 13.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.37), residues: 543 helix: 3.23 (0.25), residues: 403 sheet: -1.83 (1.41), residues: 14 loop : 0.05 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE B 49 TYR 0.006 0.001 TYR A 63 ARG 0.001 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 316) hydrogen bonds : angle 3.50896 ( 945) covalent geometry : bond 0.00269 ( 4429) covalent geometry : angle 0.41700 ( 5997) Misc. bond : bond 0.00021 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3852.57 seconds wall clock time: 67 minutes 14.99 seconds (4034.99 seconds total)