Starting phenix.real_space_refine on Fri Aug 22 14:43:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yni_33962/08_2025/7yni_33962.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yni_33962/08_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_33962/08_2025/7yni_33962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yni_33962/08_2025/7yni_33962.map" model { file = "/net/cci-nas-00/data/ceres_data/7yni_33962/08_2025/7yni_33962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yni_33962/08_2025/7yni_33962.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 11, 'ASN:plan1': 6, 'ASP:plan': 6, 'ARG:plan': 6, 'TYR:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 2} 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, 'HIS:plan': 1, 'PHE:plan': 1, 'TRP: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: 1.12, per 1000 atoms: 0.26 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: 0.45 Conformation dependent library (CDL) restraints added in 121.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.08 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: 0.67 Time building geometry restraints manager: 0.59 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: 0.830 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: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.690 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.940 ------------------------------------------------------------------------------- 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 : 19.14 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (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 ARG 0.009 0.001 ARG A 300 TYR 0.020 0.002 TYR A 144 PHE 0.011 0.002 PHE A 663 TRP 0.016 0.002 TRP A 68 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 4494) covalent geometry : angle 0.66120 ( 6146) SS BOND : bond 0.00360 ( 3) SS BOND : angle 0.89248 ( 6) hydrogen bonds : bond 0.12490 ( 355) hydrogen bonds : angle 6.45847 ( 1059) *********************** 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 : 0.183 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: 0.0889 time to fit residues: 5.4870 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 : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.4337 r_free = 0.4337 target = 0.194792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.163385 restraints weight = 4286.439| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.69 r_work: 0.3932 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4497 Z= 0.173 Angle : 0.672 7.463 6152 Z= 0.352 Chirality : 0.045 0.210 761 Planarity : 0.006 0.061 734 Dihedral : 4.501 20.643 646 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.18 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.35), residues: 582 helix: 1.48 (0.24), residues: 449 sheet: None (None), residues: 0 loop : -1.44 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 267 TYR 0.012 0.001 TYR A 236 PHE 0.017 0.002 PHE A 663 TRP 0.018 0.002 TRP B 30 HIS 0.008 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 4494) covalent geometry : angle 0.67147 ( 6146) SS BOND : bond 0.00240 ( 3) SS BOND : angle 0.75211 ( 6) hydrogen bonds : bond 0.04604 ( 355) hydrogen bonds : angle 5.61210 ( 1059) *********************** 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 : 0.162 Fit side-chains REVERT: A 300 ARG cc_start: 0.6962 (mpt180) cc_final: 0.6464 (mpt180) REVERT: A 328 MET cc_start: 0.7076 (mtt) cc_final: 0.5943 (mtt) outliers start: 3 outliers final: 0 residues processed: 47 average time/residue: 0.0721 time to fit residues: 4.5171 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 : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.185971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153871 restraints weight = 4295.158| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.77 r_work: 0.3790 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4497 Z= 0.184 Angle : 0.665 7.277 6152 Z= 0.348 Chirality : 0.045 0.215 761 Planarity : 0.006 0.059 734 Dihedral : 4.461 20.073 646 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.81 % Favored : 94.67 % Rotamer: Outliers : 1.16 % Allowed : 9.53 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.35), residues: 582 helix: 1.41 (0.24), residues: 449 sheet: None (None), residues: 0 loop : -1.44 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 267 TYR 0.011 0.001 TYR A 236 PHE 0.016 0.002 PHE A 232 TRP 0.012 0.002 TRP B 30 HIS 0.005 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 4494) covalent geometry : angle 0.66459 ( 6146) SS BOND : bond 0.00252 ( 3) SS BOND : angle 0.64661 ( 6) hydrogen bonds : bond 0.04465 ( 355) hydrogen bonds : angle 5.54678 ( 1059) *********************** 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 51 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 233 MET cc_start: 0.6642 (mtm) cc_final: 0.6389 (mtm) REVERT: A 300 ARG cc_start: 0.7172 (mpt180) cc_final: 0.6531 (mpt180) REVERT: A 328 MET cc_start: 0.7328 (mtt) cc_final: 0.5942 (mtt) outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.0654 time to fit residues: 4.1282 Evaluate side-chains 46 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 270 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.188820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.156493 restraints weight = 4245.697| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.82 r_work: 0.3811 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.1802 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= 0.155 Angle : 0.614 7.225 6152 Z= 0.325 Chirality : 0.043 0.216 761 Planarity : 0.006 0.058 734 Dihedral : 4.326 19.438 646 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.33 % Favored : 94.16 % Rotamer: Outliers : 1.86 % Allowed : 11.63 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.36), residues: 582 helix: 1.56 (0.24), residues: 449 sheet: None (None), residues: 0 loop : -1.46 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 336 TYR 0.012 0.001 TYR A 236 PHE 0.015 0.001 PHE A 232 TRP 0.015 0.001 TRP B 30 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 4494) covalent geometry : angle 0.61401 ( 6146) SS BOND : bond 0.00226 ( 3) SS BOND : angle 0.53864 ( 6) hydrogen bonds : bond 0.04125 ( 355) hydrogen bonds : angle 5.42799 ( 1059) *********************** 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 51 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 133 ARG cc_start: 0.7629 (ttt180) cc_final: 0.7393 (ttm-80) REVERT: A 233 MET cc_start: 0.6627 (mtm) cc_final: 0.6390 (mtm) REVERT: A 300 ARG cc_start: 0.7173 (mpt180) cc_final: 0.6768 (mpt180) REVERT: A 325 MET cc_start: 0.7602 (ttt) cc_final: 0.7398 (ttt) REVERT: A 328 MET cc_start: 0.7309 (mtt) cc_final: 0.6023 (mtt) outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 0.0615 time to fit residues: 4.0688 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 : 0.103 ------------------------------------------------------------------------------- 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 270 LEU 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 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.189525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.157518 restraints weight = 4276.805| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.81 r_work: 0.3842 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.2026 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 : 0.607 7.215 6152 Z= 0.319 Chirality : 0.043 0.218 761 Planarity : 0.006 0.056 734 Dihedral : 4.212 18.535 646 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.81 % Favored : 94.67 % Rotamer: Outliers : 1.63 % Allowed : 13.02 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.36), residues: 582 helix: 1.65 (0.25), residues: 449 sheet: None (None), residues: 0 loop : -1.57 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 336 TYR 0.011 0.001 TYR A 236 PHE 0.014 0.001 PHE A 232 TRP 0.015 0.001 TRP B 30 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4494) covalent geometry : angle 0.60659 ( 6146) SS BOND : bond 0.00220 ( 3) SS BOND : angle 0.51258 ( 6) hydrogen bonds : bond 0.03992 ( 355) hydrogen bonds : angle 5.34441 ( 1059) *********************** 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 51 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 233 MET cc_start: 0.6581 (mtm) cc_final: 0.6352 (mtm) REVERT: A 300 ARG cc_start: 0.7129 (mpt180) cc_final: 0.6737 (mpt180) REVERT: A 328 MET cc_start: 0.7304 (mtt) cc_final: 0.5996 (mtt) REVERT: A 407 MET cc_start: 0.7067 (mtp) cc_final: 0.6849 (ttm) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.0485 time to fit residues: 3.3052 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 : 0.155 ------------------------------------------------------------------------------- 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 8 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 = 0.4297 r_free = 0.4297 target = 0.193622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.160338 restraints weight = 4269.556| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.90 r_work: 0.3837 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.2239 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= 0.145 Angle : 0.598 7.206 6152 Z= 0.313 Chirality : 0.042 0.219 761 Planarity : 0.006 0.057 734 Dihedral : 4.146 17.493 646 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.15 % Favored : 94.33 % Rotamer: Outliers : 2.09 % Allowed : 14.65 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.36), residues: 582 helix: 1.71 (0.24), residues: 449 sheet: None (None), residues: 0 loop : -1.58 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 336 TYR 0.010 0.001 TYR A 236 PHE 0.013 0.001 PHE A 232 TRP 0.017 0.001 TRP B 30 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4494) covalent geometry : angle 0.59779 ( 6146) SS BOND : bond 0.00216 ( 3) SS BOND : angle 0.47282 ( 6) hydrogen bonds : bond 0.03896 ( 355) hydrogen bonds : angle 5.26897 ( 1059) *********************** 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 54 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: A 233 MET cc_start: 0.6546 (mtm) cc_final: 0.6315 (mtm) REVERT: A 300 ARG cc_start: 0.6907 (mpt180) cc_final: 0.6659 (mpt180) REVERT: A 325 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6993 (ttt) REVERT: A 328 MET cc_start: 0.7252 (mtt) cc_final: 0.5989 (mtt) outliers start: 9 outliers final: 5 residues processed: 49 average time/residue: 0.0501 time to fit residues: 3.4291 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 : 0.147 ------------------------------------------------------------------------------- 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 325 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 53 optimal weight: 0.0270 chunk 28 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.191601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.161266 restraints weight = 4102.410| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.75 r_work: 0.3870 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2421 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 : 0.604 7.179 6152 Z= 0.314 Chirality : 0.042 0.217 761 Planarity : 0.006 0.057 734 Dihedral : 4.081 16.598 646 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.81 % Favored : 94.67 % Rotamer: Outliers : 1.63 % Allowed : 16.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.36), residues: 582 helix: 1.74 (0.25), residues: 455 sheet: None (None), residues: 0 loop : -1.52 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.009 0.001 TYR A 236 PHE 0.013 0.001 PHE A 232 TRP 0.020 0.001 TRP B 30 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4494) covalent geometry : angle 0.60409 ( 6146) SS BOND : bond 0.00199 ( 3) SS BOND : angle 0.44678 ( 6) hydrogen bonds : bond 0.03833 ( 355) hydrogen bonds : angle 5.18939 ( 1059) *********************** 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 52 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.151 Fit side-chains REVERT: A 233 MET cc_start: 0.6620 (mtm) cc_final: 0.6359 (mtm) REVERT: A 283 MET cc_start: 0.7743 (tpt) cc_final: 0.7531 (tpt) REVERT: A 300 ARG cc_start: 0.7127 (mpt180) cc_final: 0.6858 (mpt180) REVERT: A 328 MET cc_start: 0.7344 (mtt) cc_final: 0.6304 (mtt) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.0463 time to fit residues: 3.2032 Evaluate side-chains 50 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 325 MET Chi-restraints excluded: chain A residue 387 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.189426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.158970 restraints weight = 4103.845| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.73 r_work: 0.3837 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4497 Z= 0.157 Angle : 0.616 8.164 6152 Z= 0.321 Chirality : 0.043 0.215 761 Planarity : 0.006 0.059 734 Dihedral : 4.165 17.347 646 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.33 % Favored : 94.16 % Rotamer: Outliers : 1.86 % Allowed : 15.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.36), residues: 582 helix: 1.64 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -1.59 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.010 0.001 TYR A 236 PHE 0.014 0.001 PHE A 232 TRP 0.022 0.001 TRP B 30 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 4494) covalent geometry : angle 0.61582 ( 6146) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.50232 ( 6) hydrogen bonds : bond 0.03973 ( 355) hydrogen bonds : angle 5.22166 ( 1059) *********************** 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 52 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.128 Fit side-chains REVERT: A 233 MET cc_start: 0.6703 (mtm) cc_final: 0.6462 (mtm) REVERT: A 300 ARG cc_start: 0.7169 (mpt180) cc_final: 0.6895 (mpt180) REVERT: A 328 MET cc_start: 0.7151 (mtt) cc_final: 0.6520 (mtt) outliers start: 8 outliers final: 7 residues processed: 48 average time/residue: 0.0550 time to fit residues: 3.6453 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 : 0.098 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 0.4980 chunk 52 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.190835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.160690 restraints weight = 4137.784| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.73 r_work: 0.3858 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2589 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 : 0.631 9.754 6152 Z= 0.324 Chirality : 0.043 0.214 761 Planarity : 0.006 0.059 734 Dihedral : 4.195 21.762 646 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.15 % Favored : 94.50 % Rotamer: Outliers : 1.86 % Allowed : 15.58 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.36), residues: 582 helix: 1.75 (0.25), residues: 450 sheet: None (None), residues: 0 loop : -1.61 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.010 0.001 TYR A 236 PHE 0.013 0.001 PHE A 232 TRP 0.027 0.002 TRP B 30 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4494) covalent geometry : angle 0.63095 ( 6146) SS BOND : bond 0.00197 ( 3) SS BOND : angle 0.45800 ( 6) hydrogen bonds : bond 0.03901 ( 355) hydrogen bonds : angle 5.19644 ( 1059) *********************** 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: 8 poor density : 43 time to evaluate : 0.160 Fit side-chains REVERT: A 233 MET cc_start: 0.6669 (mtm) cc_final: 0.6405 (mtm) REVERT: A 283 MET cc_start: 0.7822 (tpt) cc_final: 0.7405 (tpt) REVERT: A 300 ARG cc_start: 0.7187 (mpt180) cc_final: 0.6920 (mpt180) REVERT: A 328 MET cc_start: 0.7137 (mtt) cc_final: 0.6507 (mtt) outliers start: 8 outliers final: 7 residues processed: 47 average time/residue: 0.0551 time to fit residues: 3.6159 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 : 0.113 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.190564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.157510 restraints weight = 4251.980| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.90 r_work: 0.3844 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4497 Z= 0.168 Angle : 0.654 10.314 6152 Z= 0.336 Chirality : 0.043 0.212 761 Planarity : 0.006 0.062 734 Dihedral : 4.252 19.907 646 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.50 % Favored : 94.16 % Rotamer: Outliers : 1.40 % Allowed : 15.81 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.35), residues: 582 helix: 1.61 (0.24), residues: 449 sheet: None (None), residues: 0 loop : -1.75 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.011 0.001 TYR A 236 PHE 0.015 0.001 PHE A 232 TRP 0.025 0.002 TRP B 30 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 4494) covalent geometry : angle 0.65391 ( 6146) SS BOND : bond 0.00228 ( 3) SS BOND : angle 0.53352 ( 6) hydrogen bonds : bond 0.04064 ( 355) hydrogen bonds : angle 5.24358 ( 1059) ********************** 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 52 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.150 Fit side-chains REVERT: A 233 MET cc_start: 0.6700 (mtm) cc_final: 0.6429 (mtm) REVERT: A 283 MET cc_start: 0.7855 (tpt) cc_final: 0.7376 (tpt) REVERT: A 328 MET cc_start: 0.7122 (mtt) cc_final: 0.6586 (mtt) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.0783 time to fit residues: 4.9508 Evaluate side-chains 49 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.191080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.158563 restraints weight = 4222.946| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.83 r_work: 0.3845 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.2694 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= 0.153 Angle : 0.658 11.733 6152 Z= 0.336 Chirality : 0.043 0.217 761 Planarity : 0.006 0.061 734 Dihedral : 4.205 19.991 646 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.15 % Favored : 94.50 % Rotamer: Outliers : 1.40 % Allowed : 15.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.36), residues: 582 helix: 1.67 (0.25), residues: 450 sheet: None (None), residues: 0 loop : -1.72 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 336 TYR 0.010 0.001 TYR A 236 PHE 0.014 0.001 PHE A 232 TRP 0.026 0.002 TRP B 30 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4494) covalent geometry : angle 0.65854 ( 6146) SS BOND : bond 0.00214 ( 3) SS BOND : angle 0.44984 ( 6) hydrogen bonds : bond 0.03960 ( 355) hydrogen bonds : angle 5.19800 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1450.81 seconds wall clock time: 25 minutes 24.83 seconds (1524.83 seconds total)