Starting phenix.real_space_refine on Wed Jun 4 22:26:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yni_33962/06_2025/7yni_33962.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yni_33962/06_2025/7yni_33962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yni_33962/06_2025/7yni_33962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yni_33962/06_2025/7yni_33962.map" model { file = "/net/cci-nas-00/data/ceres_data/7yni_33962/06_2025/7yni_33962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yni_33962/06_2025/7yni_33962.cif" } resolution = 3.26 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= 0.009 sd= 0.146 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 32 5.16 5 C 2926 2.51 5 N 694 2.21 5 O 734 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4387 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4182 Classifications: {'peptide': 566} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 21, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "B" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 193 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 26} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'KQC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.60, per 1000 atoms: 0.82 Number of scatterers: 4387 At special positions: 0 Unit cell: (85.068, 75.06, 77.562, 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 32 16.00 F 1 9.00 O 734 8.00 N 694 7.00 C 2926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.04 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 514.6 milliseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1100 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 83.8% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 21 through 24 Processing helix chain 'A' and resid 25 through 48 removed outlier: 3.594A pdb=" N ILE A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 80 through 94 Processing helix chain 'A' and resid 96 through 115 removed outlier: 3.609A pdb=" N GLY A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 107 " --> pdb=" O TRP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 139 through 173 removed outlier: 4.477A pdb=" N ILE A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 Processing helix chain 'A' and resid 201 through 227 Processing helix chain 'A' and resid 227 through 237 removed outlier: 4.017A pdb=" N ALA A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.837A pdb=" N TYR A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 293 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.506A pdb=" N VAL A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 323 through 339 removed outlier: 4.696A pdb=" N MET A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 375 through 409 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 418 through 445 Proline residue: A 442 - end of helix removed outlier: 3.641A pdb=" N GLN A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 464 through 477 Processing helix chain 'A' and resid 481 through 507 Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 525 through 548 removed outlier: 3.729A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 Processing helix chain 'A' and resid 638 through 663 Processing helix chain 'B' and resid 28 through 54 Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 246 355 hydrogen bonds defined for protein. 1059 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: 1.26 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1215 1.34 - 1.45: 776 1.45 - 1.57: 2452 1.57 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 4494 Sorted by residual: bond pdb=" C1 KQC A 701 " pdb=" O1 KQC A 701 " ideal model delta sigma weight residual 1.375 1.432 -0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CA VAL A 441 " pdb=" C VAL A 441 " ideal model delta sigma weight residual 1.524 1.502 0.023 1.11e-02 8.12e+03 4.12e+00 bond pdb=" N VAL A 441 " pdb=" CA VAL A 441 " ideal model delta sigma weight residual 1.463 1.486 -0.023 1.18e-02 7.18e+03 3.85e+00 bond pdb=" CA TYR A 366 " pdb=" C TYR A 366 " ideal model delta sigma weight residual 1.520 1.500 0.021 1.23e-02 6.61e+03 2.80e+00 bond pdb=" C LEU A 387 " pdb=" O LEU A 387 " ideal model delta sigma weight residual 1.237 1.218 0.018 1.17e-02 7.31e+03 2.48e+00 ... (remaining 4489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 5925 1.48 - 2.95: 171 2.95 - 4.43: 34 4.43 - 5.90: 14 5.90 - 7.38: 2 Bond angle restraints: 6146 Sorted by residual: angle pdb=" N ARG A 135 " pdb=" CA ARG A 135 " pdb=" C ARG A 135 " ideal model delta sigma weight residual 111.36 117.03 -5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" N PRO A 552 " pdb=" CA PRO A 552 " pdb=" C PRO A 552 " ideal model delta sigma weight residual 112.47 118.72 -6.25 2.06e+00 2.36e-01 9.21e+00 angle pdb=" N VAL A 441 " pdb=" CA VAL A 441 " pdb=" CB VAL A 441 " ideal model delta sigma weight residual 110.52 108.56 1.96 6.70e-01 2.23e+00 8.58e+00 angle pdb=" CA TRP A 68 " pdb=" CB TRP A 68 " pdb=" CG TRP A 68 " ideal model delta sigma weight residual 113.60 119.11 -5.51 1.90e+00 2.77e-01 8.41e+00 angle pdb=" C ILE A 364 " pdb=" CA ILE A 364 " pdb=" CB ILE A 364 " ideal model delta sigma weight residual 112.19 109.29 2.90 1.15e+00 7.56e-01 6.37e+00 ... (remaining 6141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 2427 15.76 - 31.52: 131 31.52 - 47.28: 32 47.28 - 63.04: 3 63.04 - 78.80: 3 Dihedral angle restraints: 2596 sinusoidal: 886 harmonic: 1710 Sorted by residual: dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -135.79 49.79 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 133.53 -40.53 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" CB CYS A 345 " pdb=" SG CYS A 345 " pdb=" SG CYS A 351 " pdb=" CB CYS A 351 " ideal model delta sinusoidal sigma weight residual 93.00 126.08 -33.08 1 1.00e+01 1.00e-02 1.56e+01 ... (remaining 2593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 540 0.039 - 0.078: 163 0.078 - 0.117: 47 0.117 - 0.156: 8 0.156 - 0.195: 3 Chirality restraints: 761 Sorted by residual: chirality pdb=" CA PRO A 552 " pdb=" N PRO A 552 " pdb=" C PRO A 552 " pdb=" CB PRO A 552 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA ARG A 135 " pdb=" N ARG A 135 " pdb=" C ARG A 135 " pdb=" CB ARG A 135 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA PRO A 324 " pdb=" N PRO A 324 " pdb=" C PRO A 324 " pdb=" CB PRO A 324 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 758 not shown) Planarity restraints: 734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 154 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE A 154 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE A 154 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 155 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 155 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C PHE A 155 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE A 155 " -0.022 2.00e-02 2.50e+03 pdb=" N THR A 156 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 551 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A 552 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 552 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 552 " -0.036 5.00e-02 4.00e+02 ... (remaining 731 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 602 2.75 - 3.28: 4879 3.28 - 3.82: 7903 3.82 - 4.36: 8927 4.36 - 4.90: 15620 Nonbonded interactions: 37931 Sorted by model distance: nonbonded pdb=" NE2 HIS A 83 " pdb=" O1 KQC A 701 " model vdw 2.206 3.120 nonbonded pdb=" NE2 GLN A 207 " pdb=" CA ALA A 388 " model vdw 2.233 3.550 nonbonded pdb=" OH TYR A 35 " pdb=" NE2 GLN A 207 " model vdw 2.287 3.120 nonbonded pdb=" OH TYR A 557 " pdb=" OE1 GLU A 568 " model vdw 2.295 3.040 nonbonded pdb=" O GLN A 448 " pdb=" OG SER A 449 " model vdw 2.296 3.040 ... (remaining 37926 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.400 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 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 : 0.004 0.057 4497 Z= 0.238 Angle : 0.661 7.378 6152 Z= 0.374 Chirality : 0.042 0.195 761 Planarity : 0.006 0.067 734 Dihedral : 10.917 78.797 1487 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.98 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.35), residues: 582 helix: 1.18 (0.24), residues: 442 sheet: None (None), residues: 0 loop : -1.54 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 68 HIS 0.005 0.001 HIS A 83 PHE 0.011 0.002 PHE A 663 TYR 0.020 0.002 TYR A 144 ARG 0.009 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.12490 ( 355) hydrogen bonds : angle 6.45847 ( 1059) SS BOND : bond 0.00360 ( 3) SS BOND : angle 0.89248 ( 6) covalent geometry : bond 0.00448 ( 4494) covalent geometry : angle 0.66120 ( 6146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.7696 (tpt) cc_final: 0.7003 (tpt) REVERT: A 328 MET cc_start: 0.7002 (mtt) cc_final: 0.5502 (mtt) REVERT: A 526 TYR cc_start: 0.6157 (p90) cc_final: 0.4766 (p90) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1859 time to fit residues: 11.5819 Evaluate side-chains 43 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 481 ASN ** 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 = 0.4312 r_free = 0.4312 target = 0.192050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.160689 restraints weight = 4238.528| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 1.68 r_work: 0.3927 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4497 Z= 0.188 Angle : 0.693 7.463 6152 Z= 0.362 Chirality : 0.046 0.209 761 Planarity : 0.006 0.062 734 Dihedral : 4.585 20.783 646 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.64 % Favored : 94.85 % Rotamer: Outliers : 0.70 % Allowed : 5.81 % Favored : 93.49 % 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: 1.05 (0.35), residues: 582 helix: 1.32 (0.24), residues: 450 sheet: None (None), residues: 0 loop : -1.39 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 30 HIS 0.008 0.002 HIS A 83 PHE 0.017 0.002 PHE A 663 TYR 0.013 0.002 TYR A 236 ARG 0.005 0.001 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 355) hydrogen bonds : angle 5.64548 ( 1059) SS BOND : bond 0.00241 ( 3) SS BOND : angle 0.76664 ( 6) covalent geometry : bond 0.00430 ( 4494) covalent geometry : angle 0.69277 ( 6146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.453 Fit side-chains REVERT: A 283 MET cc_start: 0.8006 (tpt) cc_final: 0.7217 (tpt) REVERT: A 300 ARG cc_start: 0.7011 (mpt180) cc_final: 0.6476 (mpt180) REVERT: A 328 MET cc_start: 0.7136 (mtt) cc_final: 0.5983 (mtt) REVERT: A 501 ILE cc_start: 0.7669 (mm) cc_final: 0.7458 (mm) outliers start: 3 outliers final: 1 residues processed: 48 average time/residue: 0.1521 time to fit residues: 10.1009 Evaluate side-chains 44 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** 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 = 0.4267 r_free = 0.4267 target = 0.190580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.157444 restraints weight = 4216.338| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 1.87 r_work: 0.3814 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4497 Z= 0.162 Angle : 0.640 7.253 6152 Z= 0.336 Chirality : 0.044 0.215 761 Planarity : 0.006 0.059 734 Dihedral : 4.422 20.039 646 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.64 % Favored : 94.85 % Rotamer: Outliers : 1.40 % Allowed : 9.53 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.35), residues: 582 helix: 1.45 (0.24), residues: 450 sheet: None (None), residues: 0 loop : -1.40 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 30 HIS 0.005 0.001 HIS A 83 PHE 0.014 0.001 PHE A 232 TYR 0.012 0.001 TYR A 236 ARG 0.004 0.001 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 355) hydrogen bonds : angle 5.50306 ( 1059) SS BOND : bond 0.00227 ( 3) SS BOND : angle 0.61305 ( 6) covalent geometry : bond 0.00362 ( 4494) covalent geometry : angle 0.64023 ( 6146) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.7814 (tpt) cc_final: 0.7077 (tpt) REVERT: A 300 ARG cc_start: 0.6971 (mpt180) cc_final: 0.6462 (mpt180) REVERT: A 328 MET cc_start: 0.7127 (mtt) cc_final: 0.5792 (mtt) REVERT: A 501 ILE cc_start: 0.7533 (mm) cc_final: 0.7275 (mm) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.1706 time to fit residues: 10.8349 Evaluate side-chains 47 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 0.0870 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** 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 = 0.4288 r_free = 0.4288 target = 0.192686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.159770 restraints weight = 4211.530| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.89 r_work: 0.3821 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4497 Z= 0.148 Angle : 0.602 7.232 6152 Z= 0.319 Chirality : 0.043 0.220 761 Planarity : 0.006 0.056 734 Dihedral : 4.279 18.865 646 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.15 % Favored : 94.33 % Rotamer: Outliers : 1.86 % Allowed : 11.40 % Favored : 86.74 % 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: 1.45 (0.36), residues: 582 helix: 1.68 (0.25), residues: 449 sheet: None (None), residues: 0 loop : -1.53 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 30 HIS 0.004 0.001 HIS A 83 PHE 0.015 0.001 PHE A 232 TYR 0.009 0.001 TYR A 236 ARG 0.004 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 355) hydrogen bonds : angle 5.36943 ( 1059) SS BOND : bond 0.00227 ( 3) SS BOND : angle 0.52342 ( 6) covalent geometry : bond 0.00324 ( 4494) covalent geometry : angle 0.60190 ( 6146) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 233 MET cc_start: 0.6384 (mtm) cc_final: 0.6166 (mtm) REVERT: A 300 ARG cc_start: 0.6938 (mpt180) cc_final: 0.6628 (mpt180) REVERT: A 328 MET cc_start: 0.7190 (mtt) cc_final: 0.5903 (mtt) REVERT: A 501 ILE cc_start: 0.7505 (mm) cc_final: 0.7235 (mm) outliers start: 8 outliers final: 3 residues processed: 48 average time/residue: 0.1453 time to fit residues: 9.5887 Evaluate side-chains 44 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.0020 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** 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 = 0.4257 r_free = 0.4257 target = 0.190158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.157618 restraints weight = 4340.716| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.86 r_work: 0.3828 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4497 Z= 0.148 Angle : 0.607 7.207 6152 Z= 0.319 Chirality : 0.043 0.218 761 Planarity : 0.006 0.056 734 Dihedral : 4.203 18.328 646 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.64 % Favored : 94.85 % Rotamer: Outliers : 1.63 % Allowed : 12.79 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.49 (0.36), residues: 582 helix: 1.71 (0.24), residues: 449 sheet: None (None), residues: 0 loop : -1.53 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 30 HIS 0.003 0.001 HIS A 83 PHE 0.015 0.001 PHE A 232 TYR 0.010 0.001 TYR A 236 ARG 0.003 0.001 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 355) hydrogen bonds : angle 5.31290 ( 1059) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.50468 ( 6) covalent geometry : bond 0.00327 ( 4494) covalent geometry : angle 0.60712 ( 6146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 300 ARG cc_start: 0.6949 (mpt180) cc_final: 0.6668 (mpt180) REVERT: A 328 MET cc_start: 0.7267 (mtt) cc_final: 0.6011 (mtt) REVERT: A 501 ILE cc_start: 0.7523 (mm) cc_final: 0.7242 (mm) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.1385 time to fit residues: 9.3022 Evaluate side-chains 48 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 0.0270 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 0.0060 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 overall best weight: 0.4654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.197374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.166808 restraints weight = 4241.073| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.66 r_work: 0.3990 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4497 Z= 0.138 Angle : 0.588 7.185 6152 Z= 0.311 Chirality : 0.042 0.219 761 Planarity : 0.006 0.057 734 Dihedral : 4.121 17.101 646 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.33 % Favored : 94.16 % Rotamer: Outliers : 2.33 % Allowed : 13.72 % Favored : 83.95 % 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: 1.60 (0.36), residues: 582 helix: 1.74 (0.25), residues: 454 sheet: None (None), residues: 0 loop : -1.42 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 30 HIS 0.003 0.001 HIS A 83 PHE 0.014 0.001 PHE A 232 TYR 0.009 0.001 TYR A 236 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 355) hydrogen bonds : angle 5.22081 ( 1059) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.45790 ( 6) covalent geometry : bond 0.00299 ( 4494) covalent geometry : angle 0.58825 ( 6146) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 300 ARG cc_start: 0.7136 (mpt180) cc_final: 0.6884 (mpt180) REVERT: A 328 MET cc_start: 0.7272 (mtt) cc_final: 0.6064 (mtt) REVERT: A 501 ILE cc_start: 0.7578 (mm) cc_final: 0.7328 (mm) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.1291 time to fit residues: 9.4635 Evaluate side-chains 52 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 38 optimal weight: 9.9990 chunk 42 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN ** A 481 ASN ** 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 = 0.4245 r_free = 0.4245 target = 0.188918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.158851 restraints weight = 4121.089| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.74 r_work: 0.3853 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4497 Z= 0.151 Angle : 0.613 7.206 6152 Z= 0.321 Chirality : 0.042 0.217 761 Planarity : 0.006 0.059 734 Dihedral : 4.160 16.860 646 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.98 % Favored : 94.50 % Rotamer: Outliers : 1.86 % Allowed : 15.12 % Favored : 83.02 % 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: 1.52 (0.36), residues: 582 helix: 1.69 (0.24), residues: 455 sheet: None (None), residues: 0 loop : -1.49 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 30 HIS 0.003 0.001 HIS A 83 PHE 0.015 0.001 PHE A 232 TYR 0.011 0.001 TYR A 229 ARG 0.002 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 355) hydrogen bonds : angle 5.23869 ( 1059) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.49789 ( 6) covalent geometry : bond 0.00339 ( 4494) covalent geometry : angle 0.61269 ( 6146) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.459 Fit side-chains REVERT: A 283 MET cc_start: 0.7846 (tpt) cc_final: 0.7373 (tpt) REVERT: A 300 ARG cc_start: 0.7146 (mpt180) cc_final: 0.6806 (mpt180) REVERT: A 328 MET cc_start: 0.7346 (mtt) cc_final: 0.6075 (mtt) REVERT: A 501 ILE cc_start: 0.7417 (mm) cc_final: 0.7150 (mm) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.1318 time to fit residues: 9.0466 Evaluate side-chains 49 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.193533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.162050 restraints weight = 4150.852| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.77 r_work: 0.3843 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4497 Z= 0.149 Angle : 0.615 7.386 6152 Z= 0.320 Chirality : 0.042 0.218 761 Planarity : 0.006 0.060 734 Dihedral : 4.140 17.989 646 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.67 % Favored : 93.81 % Rotamer: Outliers : 1.86 % Allowed : 15.12 % Favored : 83.02 % 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: 1.49 (0.36), residues: 582 helix: 1.66 (0.25), residues: 455 sheet: None (None), residues: 0 loop : -1.51 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 30 HIS 0.003 0.001 HIS A 83 PHE 0.017 0.001 PHE A 232 TYR 0.017 0.001 TYR A 229 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 355) hydrogen bonds : angle 5.21609 ( 1059) SS BOND : bond 0.00197 ( 3) SS BOND : angle 0.49161 ( 6) covalent geometry : bond 0.00334 ( 4494) covalent geometry : angle 0.61482 ( 6146) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.444 Fit side-chains REVERT: A 328 MET cc_start: 0.7152 (mtt) cc_final: 0.6427 (mtt) REVERT: A 501 ILE cc_start: 0.7377 (mm) cc_final: 0.7081 (mm) outliers start: 8 outliers final: 7 residues processed: 47 average time/residue: 0.1270 time to fit residues: 8.3836 Evaluate side-chains 51 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.191712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.161057 restraints weight = 4088.802| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.74 r_work: 0.3857 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4497 Z= 0.150 Angle : 0.631 8.758 6152 Z= 0.327 Chirality : 0.043 0.215 761 Planarity : 0.006 0.061 734 Dihedral : 4.205 21.888 646 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.15 % Favored : 94.50 % Rotamer: Outliers : 1.63 % Allowed : 15.35 % Favored : 83.02 % 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: 1.46 (0.36), residues: 582 helix: 1.66 (0.25), residues: 454 sheet: None (None), residues: 0 loop : -1.54 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 30 HIS 0.003 0.001 HIS A 83 PHE 0.014 0.001 PHE A 232 TYR 0.016 0.001 TYR A 229 ARG 0.002 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 355) hydrogen bonds : angle 5.20150 ( 1059) SS BOND : bond 0.00197 ( 3) SS BOND : angle 0.48130 ( 6) covalent geometry : bond 0.00331 ( 4494) covalent geometry : angle 0.63078 ( 6146) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.493 Fit side-chains REVERT: A 283 MET cc_start: 0.7816 (tpt) cc_final: 0.7429 (tpt) REVERT: A 328 MET cc_start: 0.7136 (mtt) cc_final: 0.6468 (mtt) REVERT: A 501 ILE cc_start: 0.7511 (mm) cc_final: 0.7224 (mm) outliers start: 7 outliers final: 7 residues processed: 48 average time/residue: 0.1484 time to fit residues: 9.7368 Evaluate side-chains 50 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 3 optimal weight: 0.0000 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 40 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.193801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.163150 restraints weight = 4064.649| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 1.75 r_work: 0.3914 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4497 Z= 0.138 Angle : 0.642 10.997 6152 Z= 0.326 Chirality : 0.043 0.215 761 Planarity : 0.006 0.060 734 Dihedral : 4.169 19.475 646 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.15 % Favored : 94.50 % Rotamer: Outliers : 0.93 % Allowed : 16.74 % Favored : 82.33 % 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: 1.58 (0.36), residues: 582 helix: 1.71 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -1.44 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 30 HIS 0.002 0.001 HIS A 83 PHE 0.014 0.001 PHE A 232 TYR 0.016 0.001 TYR A 229 ARG 0.006 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 355) hydrogen bonds : angle 5.14534 ( 1059) SS BOND : bond 0.00182 ( 3) SS BOND : angle 0.38539 ( 6) covalent geometry : bond 0.00294 ( 4494) covalent geometry : angle 0.64215 ( 6146) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.438 Fit side-chains REVERT: A 283 MET cc_start: 0.7774 (tpt) cc_final: 0.7397 (tpt) REVERT: A 328 MET cc_start: 0.7014 (mtt) cc_final: 0.6240 (mtt) REVERT: A 501 ILE cc_start: 0.7431 (mm) cc_final: 0.7147 (mm) outliers start: 4 outliers final: 4 residues processed: 46 average time/residue: 0.1327 time to fit residues: 8.5736 Evaluate side-chains 46 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.192714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.161591 restraints weight = 4112.197| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.76 r_work: 0.3857 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4497 Z= 0.149 Angle : 0.642 10.525 6152 Z= 0.328 Chirality : 0.043 0.223 761 Planarity : 0.006 0.060 734 Dihedral : 4.176 19.677 646 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.33 % Favored : 94.33 % Rotamer: Outliers : 1.86 % Allowed : 16.05 % Favored : 82.09 % 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: 1.47 (0.36), residues: 582 helix: 1.65 (0.25), residues: 455 sheet: None (None), residues: 0 loop : -1.50 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 30 HIS 0.003 0.001 HIS A 83 PHE 0.014 0.001 PHE A 232 TYR 0.014 0.001 TYR A 229 ARG 0.006 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 355) hydrogen bonds : angle 5.16033 ( 1059) SS BOND : bond 0.00206 ( 3) SS BOND : angle 0.45389 ( 6) covalent geometry : bond 0.00332 ( 4494) covalent geometry : angle 0.64221 ( 6146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3094.47 seconds wall clock time: 54 minutes 3.66 seconds (3243.66 seconds total)