Starting phenix.real_space_refine on Sat Aug 23 07:33:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e2h_27836/08_2025/8e2h_27836.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2h_27836/08_2025/8e2h_27836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e2h_27836/08_2025/8e2h_27836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2h_27836/08_2025/8e2h_27836.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e2h_27836/08_2025/8e2h_27836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2h_27836/08_2025/8e2h_27836.map" } resolution = 2.3 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= -0.004 sd= 0.068 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 37 5.16 5 C 3280 2.51 5 N 863 2.21 5 O 952 1.98 5 H 5280 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s 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: 10412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 10372 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 36, 'TRANS': 619} Chain breaks: 12 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Time building chain proxies: 2.39, per 1000 atoms: 0.23 Number of scatterers: 10412 At special positions: 0 Unit cell: (77.44, 101.2, 113.52, 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 37 16.00 O 952 8.00 N 863 7.00 C 3280 6.00 H 5280 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 274.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1256 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 1 sheets defined 74.2% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 3428 through 3441 Processing helix chain 'A' and resid 3445 through 3469 Processing helix chain 'A' and resid 3484 through 3488 Processing helix chain 'A' and resid 3490 through 3507 Processing helix chain 'A' and resid 3512 through 3517 removed outlier: 3.563A pdb=" N LEU A3516 " --> pdb=" O ASP A3512 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A3517 " --> pdb=" O LEU A3513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3512 through 3517' Processing helix chain 'A' and resid 3518 through 3532 Processing helix chain 'A' and resid 3536 through 3553 Processing helix chain 'A' and resid 3553 through 3565 removed outlier: 3.953A pdb=" N PHE A3557 " --> pdb=" O HIS A3553 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A3558 " --> pdb=" O PRO A3554 " (cutoff:3.500A) Processing helix chain 'A' and resid 3606 through 3617 Processing helix chain 'A' and resid 3619 through 3629 Processing helix chain 'A' and resid 3630 through 3644 Processing helix chain 'A' and resid 3679 through 3695 removed outlier: 4.316A pdb=" N ALA A3684 " --> pdb=" O ALA A3680 " (cutoff:3.500A) Proline residue: A3685 - end of helix Processing helix chain 'A' and resid 3696 through 3704 Processing helix chain 'A' and resid 3708 through 3720 removed outlier: 3.740A pdb=" N TRP A3712 " --> pdb=" O VAL A3708 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A3713 " --> pdb=" O ASN A3709 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3772 Processing helix chain 'A' and resid 3774 through 3790 Processing helix chain 'A' and resid 3806 through 3816 Processing helix chain 'A' and resid 3846 through 3850 Processing helix chain 'A' and resid 3865 through 3874 Processing helix chain 'A' and resid 3982 through 3993 Processing helix chain 'A' and resid 4069 through 4077 Processing helix chain 'A' and resid 4078 through 4085 Processing helix chain 'A' and resid 4154 through 4165 Processing helix chain 'A' and resid 4169 through 4175 Processing helix chain 'A' and resid 4177 through 4189 Processing helix chain 'A' and resid 4208 through 4210 No H-bonds generated for 'chain 'A' and resid 4208 through 4210' Processing helix chain 'A' and resid 4211 through 4223 Processing helix chain 'A' and resid 4228 through 4242 Processing helix chain 'A' and resid 4242 through 4256 Processing helix chain 'A' and resid 4306 through 4332 Processing helix chain 'A' and resid 4359 through 4367 Processing helix chain 'A' and resid 4368 through 4378 Processing helix chain 'A' and resid 4381 through 4386 Processing helix chain 'A' and resid 4388 through 4404 Processing helix chain 'A' and resid 4408 through 4412 Processing helix chain 'A' and resid 4432 through 4455 Processing helix chain 'A' and resid 4474 through 4499 Proline residue: A4479 - end of helix removed outlier: 3.739A pdb=" N GLN A4482 " --> pdb=" O VAL A4478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3855 through 3861 343 hydrogen bonds defined for protein. 1014 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: 2.43 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5263 1.03 - 1.23: 17 1.23 - 1.42: 2034 1.42 - 1.61: 3095 1.61 - 1.81: 57 Bond restraints: 10466 Sorted by residual: bond pdb=" CB THR A4484 " pdb=" CG2 THR A4484 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.92e+00 bond pdb=" CB GLU A4063 " pdb=" CG GLU A4063 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CA VAL A4389 " pdb=" CB VAL A4389 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 1.04e+00 bond pdb=" CA ASP A3443 " pdb=" C ASP A3443 " ideal model delta sigma weight residual 1.517 1.527 -0.010 1.02e-02 9.61e+03 9.49e-01 bond pdb=" CA VAL A4006 " pdb=" CB VAL A4006 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 8.69e-01 ... (remaining 10461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 18404 1.36 - 2.72: 566 2.72 - 4.08: 53 4.08 - 5.44: 6 5.44 - 6.80: 2 Bond angle restraints: 19031 Sorted by residual: angle pdb=" CA ASP A3443 " pdb=" C ASP A3443 " pdb=" N PRO A3444 " ideal model delta sigma weight residual 117.59 120.93 -3.34 9.90e-01 1.02e+00 1.14e+01 angle pdb=" C ASP A3443 " pdb=" CA ASP A3443 " pdb=" CB ASP A3443 " ideal model delta sigma weight residual 109.56 114.15 -4.59 1.51e+00 4.39e-01 9.24e+00 angle pdb=" N ASN A3535 " pdb=" CA ASN A3535 " pdb=" CB ASN A3535 " ideal model delta sigma weight residual 114.17 110.87 3.30 1.14e+00 7.69e-01 8.36e+00 angle pdb=" N ILE A4370 " pdb=" CA ILE A4370 " pdb=" C ILE A4370 " ideal model delta sigma weight residual 112.35 109.10 3.25 1.20e+00 6.94e-01 7.33e+00 angle pdb=" N ILE A4331 " pdb=" CA ILE A4331 " pdb=" C ILE A4331 " ideal model delta sigma weight residual 111.67 109.42 2.25 9.50e-01 1.11e+00 5.59e+00 ... (remaining 19026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.34: 4301 15.34 - 30.67: 397 30.67 - 46.01: 141 46.01 - 61.35: 53 61.35 - 76.68: 8 Dihedral angle restraints: 4900 sinusoidal: 2715 harmonic: 2185 Sorted by residual: dihedral pdb=" CA GLY A3694 " pdb=" C GLY A3694 " pdb=" N ASN A3695 " pdb=" CA ASN A3695 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU A3815 " pdb=" C LEU A3815 " pdb=" N MET A3816 " pdb=" CA MET A3816 " ideal model delta harmonic sigma weight residual -180.00 -163.78 -16.22 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CG ARG A4166 " pdb=" CD ARG A4166 " pdb=" NE ARG A4166 " pdb=" CZ ARG A4166 " ideal model delta sinusoidal sigma weight residual 90.00 134.18 -44.18 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 4897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 553 0.027 - 0.053: 217 0.053 - 0.080: 57 0.080 - 0.106: 29 0.106 - 0.133: 8 Chirality restraints: 864 Sorted by residual: chirality pdb=" CA ILE A4153 " pdb=" N ILE A4153 " pdb=" C ILE A4153 " pdb=" CB ILE A4153 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE A3678 " pdb=" N ILE A3678 " pdb=" C ILE A3678 " pdb=" CB ILE A3678 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA PRO A3775 " pdb=" N PRO A3775 " pdb=" C PRO A3775 " pdb=" CB PRO A3775 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 861 not shown) Planarity restraints: 1476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A4409 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO A4410 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A4410 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A4410 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A4389 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A4390 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A4390 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A4390 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A3684 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO A3685 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A3685 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A3685 " 0.020 5.00e-02 4.00e+02 ... (remaining 1473 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 130 2.03 - 2.67: 16210 2.67 - 3.32: 33200 3.32 - 3.96: 42794 3.96 - 4.60: 66147 Nonbonded interactions: 158481 Sorted by model distance: nonbonded pdb=" OE1 GLU A4063 " pdb=" H GLU A4063 " model vdw 1.390 2.450 nonbonded pdb="HH11 ARG A3809 " pdb=" O LEU A4189 " model vdw 1.561 2.450 nonbonded pdb=" OD1 ASP A3701 " pdb=" HE2 HIS A3774 " model vdw 1.561 2.450 nonbonded pdb=" OD2 ASP A3819 " pdb=" HG SER A3863 " model vdw 1.583 2.450 nonbonded pdb=" O ALA A3541 " pdb=" HG SER A3544 " model vdw 1.629 2.450 ... (remaining 158476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 11.910 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: 0.070 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.000 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.003 0.046 5186 Z= 0.157 Angle : 0.604 6.801 7039 Z= 0.332 Chirality : 0.034 0.133 864 Planarity : 0.005 0.061 868 Dihedral : 15.280 76.683 1903 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.52 % Allowed : 18.06 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.34), residues: 630 helix: 1.27 (0.24), residues: 459 sheet: 0.91 (1.40), residues: 17 loop : 0.79 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3810 TYR 0.011 0.001 TYR A4392 PHE 0.014 0.002 PHE A3812 TRP 0.008 0.001 TRP A3456 HIS 0.004 0.001 HIS A4256 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5186) covalent geometry : angle 0.60420 ( 7039) hydrogen bonds : bond 0.13947 ( 343) hydrogen bonds : angle 5.50946 ( 1014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.329 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 83 average time/residue: 0.9373 time to fit residues: 82.4451 Evaluate side-chains 76 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4083 ILE Chi-restraints excluded: chain A residue 4191 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3709 ASN A4482 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.152930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.129265 restraints weight = 15039.499| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.33 r_work: 0.3394 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5186 Z= 0.178 Angle : 0.595 7.043 7039 Z= 0.301 Chirality : 0.036 0.149 864 Planarity : 0.005 0.059 868 Dihedral : 4.382 31.734 691 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.74 % Allowed : 17.01 % Favored : 81.25 % 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: 1.97 (0.33), residues: 630 helix: 1.54 (0.24), residues: 462 sheet: 0.95 (1.38), residues: 17 loop : 0.88 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3449 TYR 0.016 0.002 TYR A4392 PHE 0.020 0.002 PHE A3807 TRP 0.007 0.001 TRP A3456 HIS 0.005 0.001 HIS A3846 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 5186) covalent geometry : angle 0.59506 ( 7039) hydrogen bonds : bond 0.04722 ( 343) hydrogen bonds : angle 4.30373 ( 1014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3810 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.6729 (ttm-80) REVERT: A 4198 SER cc_start: 0.7652 (t) cc_final: 0.7335 (p) outliers start: 10 outliers final: 5 residues processed: 80 average time/residue: 1.0175 time to fit residues: 85.8086 Evaluate side-chains 76 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3679 THR Chi-restraints excluded: chain A residue 3754 GLN Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3981 MET Chi-restraints excluded: chain A residue 4083 ILE Chi-restraints excluded: chain A residue 4191 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.154057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130821 restraints weight = 15167.671| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.31 r_work: 0.3483 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5186 Z= 0.201 Angle : 0.604 6.784 7039 Z= 0.305 Chirality : 0.037 0.149 864 Planarity : 0.005 0.060 868 Dihedral : 4.457 31.237 691 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.12 % Allowed : 15.62 % Favored : 81.25 % 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: 1.99 (0.33), residues: 630 helix: 1.65 (0.24), residues: 456 sheet: 0.92 (1.37), residues: 17 loop : 0.61 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3810 TYR 0.017 0.002 TYR A4392 PHE 0.020 0.002 PHE A3807 TRP 0.008 0.001 TRP A3456 HIS 0.004 0.001 HIS A4256 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 5186) covalent geometry : angle 0.60400 ( 7039) hydrogen bonds : bond 0.04653 ( 343) hydrogen bonds : angle 4.17907 ( 1014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 3709 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7678 (p0) REVERT: A 3810 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.6671 (ttm-80) REVERT: A 4198 SER cc_start: 0.7736 (t) cc_final: 0.7444 (p) outliers start: 18 outliers final: 9 residues processed: 81 average time/residue: 1.0243 time to fit residues: 87.3657 Evaluate side-chains 81 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3679 THR Chi-restraints excluded: chain A residue 3709 ASN Chi-restraints excluded: chain A residue 3804 ILE Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3857 THR Chi-restraints excluded: chain A residue 4068 GLN Chi-restraints excluded: chain A residue 4083 ILE Chi-restraints excluded: chain A residue 4191 VAL Chi-restraints excluded: chain A residue 4244 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.154585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.131346 restraints weight = 15160.164| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.31 r_work: 0.3488 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5186 Z= 0.180 Angle : 0.586 6.680 7039 Z= 0.294 Chirality : 0.036 0.148 864 Planarity : 0.005 0.058 868 Dihedral : 4.409 31.047 691 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.78 % Allowed : 16.32 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.33), residues: 630 helix: 1.72 (0.24), residues: 456 sheet: 0.88 (1.35), residues: 17 loop : 0.64 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3836 TYR 0.016 0.002 TYR A4392 PHE 0.020 0.002 PHE A3807 TRP 0.007 0.001 TRP A3456 HIS 0.004 0.001 HIS A4256 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 5186) covalent geometry : angle 0.58572 ( 7039) hydrogen bonds : bond 0.04315 ( 343) hydrogen bonds : angle 4.08221 ( 1014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 3709 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7638 (p0) REVERT: A 3810 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.6704 (ttm-80) REVERT: A 4198 SER cc_start: 0.7715 (t) cc_final: 0.7381 (p) outliers start: 16 outliers final: 5 residues processed: 81 average time/residue: 1.0840 time to fit residues: 92.3593 Evaluate side-chains 78 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3679 THR Chi-restraints excluded: chain A residue 3709 ASN Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 4068 GLN Chi-restraints excluded: chain A residue 4083 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 48 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.154680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131500 restraints weight = 14994.713| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.31 r_work: 0.3428 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5186 Z= 0.176 Angle : 0.583 6.624 7039 Z= 0.292 Chirality : 0.036 0.148 864 Planarity : 0.005 0.056 868 Dihedral : 4.250 30.667 690 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.30 % Allowed : 15.97 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.33), residues: 630 helix: 1.75 (0.24), residues: 458 sheet: 0.90 (1.36), residues: 17 loop : 0.84 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3449 TYR 0.015 0.002 TYR A4392 PHE 0.019 0.002 PHE A3807 TRP 0.007 0.001 TRP A3456 HIS 0.004 0.001 HIS A4256 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 5186) covalent geometry : angle 0.58282 ( 7039) hydrogen bonds : bond 0.04229 ( 343) hydrogen bonds : angle 4.04140 ( 1014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 3709 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7623 (p0) REVERT: A 3752 THR cc_start: 0.8329 (m) cc_final: 0.8080 (p) REVERT: A 3810 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.6700 (ttm-80) REVERT: A 4198 SER cc_start: 0.7709 (t) cc_final: 0.7383 (p) outliers start: 19 outliers final: 8 residues processed: 84 average time/residue: 0.9903 time to fit residues: 87.9283 Evaluate side-chains 81 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3679 THR Chi-restraints excluded: chain A residue 3709 ASN Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3857 THR Chi-restraints excluded: chain A residue 3980 GLU Chi-restraints excluded: chain A residue 4068 GLN Chi-restraints excluded: chain A residue 4083 ILE Chi-restraints excluded: chain A residue 4191 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 0.0770 chunk 40 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.155798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.132594 restraints weight = 15172.323| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.32 r_work: 0.3502 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5186 Z= 0.139 Angle : 0.555 6.579 7039 Z= 0.275 Chirality : 0.034 0.146 864 Planarity : 0.005 0.056 868 Dihedral : 4.112 29.747 690 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.78 % Allowed : 16.84 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.33), residues: 630 helix: 1.91 (0.24), residues: 458 sheet: 0.93 (1.34), residues: 17 loop : 0.93 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A3836 TYR 0.012 0.001 TYR A4392 PHE 0.017 0.002 PHE A3807 TRP 0.007 0.001 TRP A3456 HIS 0.003 0.001 HIS A3503 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5186) covalent geometry : angle 0.55495 ( 7039) hydrogen bonds : bond 0.03894 ( 343) hydrogen bonds : angle 3.95377 ( 1014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 3520 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: A 3709 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7588 (p0) REVERT: A 3810 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.6638 (ttm-80) REVERT: A 3827 GLN cc_start: 0.8120 (mt0) cc_final: 0.7427 (mp10) REVERT: A 4198 SER cc_start: 0.7698 (t) cc_final: 0.7370 (p) outliers start: 16 outliers final: 5 residues processed: 84 average time/residue: 1.0642 time to fit residues: 94.3048 Evaluate side-chains 80 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3520 GLU Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3709 ASN Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3857 THR Chi-restraints excluded: chain A residue 3980 GLU Chi-restraints excluded: chain A residue 4068 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 9 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3975 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.155881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.132667 restraints weight = 14997.280| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.32 r_work: 0.3503 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5186 Z= 0.143 Angle : 0.551 6.500 7039 Z= 0.273 Chirality : 0.034 0.146 864 Planarity : 0.005 0.054 868 Dihedral : 3.895 19.023 688 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.60 % Allowed : 16.32 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.33), residues: 630 helix: 2.01 (0.24), residues: 458 sheet: 0.93 (1.35), residues: 17 loop : 0.98 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3836 TYR 0.013 0.001 TYR A4392 PHE 0.016 0.002 PHE A3807 TRP 0.007 0.001 TRP A3456 HIS 0.003 0.001 HIS A3503 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5186) covalent geometry : angle 0.55148 ( 7039) hydrogen bonds : bond 0.03849 ( 343) hydrogen bonds : angle 3.89764 ( 1014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.386 Fit side-chains REVERT: A 3520 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: A 3709 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7584 (p0) REVERT: A 3810 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.6643 (ttm-80) REVERT: A 3827 GLN cc_start: 0.8118 (mt0) cc_final: 0.7431 (mp10) REVERT: A 4198 SER cc_start: 0.7690 (t) cc_final: 0.7358 (p) outliers start: 15 outliers final: 6 residues processed: 80 average time/residue: 1.1213 time to fit residues: 94.4596 Evaluate side-chains 80 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3520 GLU Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3709 ASN Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3857 THR Chi-restraints excluded: chain A residue 3980 GLU Chi-restraints excluded: chain A residue 4068 GLN Chi-restraints excluded: chain A residue 4191 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3975 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128964 restraints weight = 15133.197| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.36 r_work: 0.3393 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5186 Z= 0.162 Angle : 0.569 6.490 7039 Z= 0.283 Chirality : 0.035 0.147 864 Planarity : 0.005 0.054 868 Dihedral : 3.946 19.306 688 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.60 % Allowed : 16.49 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.33), residues: 630 helix: 1.98 (0.23), residues: 458 sheet: 1.07 (1.37), residues: 17 loop : 0.97 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3810 TYR 0.016 0.002 TYR A4392 PHE 0.018 0.002 PHE A3807 TRP 0.007 0.001 TRP A3456 HIS 0.004 0.001 HIS A3503 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5186) covalent geometry : angle 0.56856 ( 7039) hydrogen bonds : bond 0.04016 ( 343) hydrogen bonds : angle 3.91686 ( 1014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.229 Fit side-chains REVERT: A 3520 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: A 3709 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7574 (p0) REVERT: A 3810 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.6664 (ttm-80) REVERT: A 3827 GLN cc_start: 0.8146 (mt0) cc_final: 0.7427 (mt0) REVERT: A 4198 SER cc_start: 0.7671 (t) cc_final: 0.7321 (p) REVERT: A 4362 GLU cc_start: 0.7126 (tt0) cc_final: 0.6871 (mm-30) outliers start: 15 outliers final: 9 residues processed: 80 average time/residue: 1.1432 time to fit residues: 96.0838 Evaluate side-chains 84 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3520 GLU Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3679 THR Chi-restraints excluded: chain A residue 3709 ASN Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3857 THR Chi-restraints excluded: chain A residue 3980 GLU Chi-restraints excluded: chain A residue 3981 MET Chi-restraints excluded: chain A residue 4068 GLN Chi-restraints excluded: chain A residue 4191 VAL Chi-restraints excluded: chain A residue 4244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 0.0370 chunk 39 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.152703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128830 restraints weight = 15063.510| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.35 r_work: 0.3392 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5186 Z= 0.168 Angle : 0.570 6.480 7039 Z= 0.284 Chirality : 0.035 0.146 864 Planarity : 0.005 0.054 868 Dihedral : 3.973 19.372 688 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.78 % Allowed : 16.67 % Favored : 80.56 % 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: 2.48 (0.33), residues: 630 helix: 1.95 (0.23), residues: 458 sheet: 1.08 (1.37), residues: 17 loop : 0.98 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3810 TYR 0.015 0.002 TYR A4392 PHE 0.018 0.002 PHE A3807 TRP 0.007 0.001 TRP A3456 HIS 0.004 0.001 HIS A3503 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 5186) covalent geometry : angle 0.56995 ( 7039) hydrogen bonds : bond 0.04064 ( 343) hydrogen bonds : angle 3.93944 ( 1014) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.314 Fit side-chains REVERT: A 3520 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: A 3709 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7574 (p0) REVERT: A 3810 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.6655 (ttm-80) REVERT: A 3827 GLN cc_start: 0.8154 (mt0) cc_final: 0.7433 (mt0) REVERT: A 4198 SER cc_start: 0.7667 (t) cc_final: 0.7329 (p) REVERT: A 4362 GLU cc_start: 0.7120 (tt0) cc_final: 0.6866 (mm-30) outliers start: 16 outliers final: 11 residues processed: 82 average time/residue: 1.1913 time to fit residues: 102.4509 Evaluate side-chains 85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3520 GLU Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3631 LEU Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3679 THR Chi-restraints excluded: chain A residue 3709 ASN Chi-restraints excluded: chain A residue 3804 ILE Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3857 THR Chi-restraints excluded: chain A residue 3980 GLU Chi-restraints excluded: chain A residue 3981 MET Chi-restraints excluded: chain A residue 4068 GLN Chi-restraints excluded: chain A residue 4191 VAL Chi-restraints excluded: chain A residue 4244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 38 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 31 optimal weight: 0.0770 overall best weight: 0.3096 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.154893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131075 restraints weight = 15071.626| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.36 r_work: 0.3421 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5186 Z= 0.114 Angle : 0.534 6.423 7039 Z= 0.263 Chirality : 0.033 0.142 864 Planarity : 0.005 0.054 868 Dihedral : 3.726 18.335 688 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.91 % Allowed : 17.71 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.33), residues: 630 helix: 2.24 (0.24), residues: 458 sheet: 0.99 (1.38), residues: 17 loop : 1.17 (0.53), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4314 TYR 0.010 0.001 TYR A4392 PHE 0.012 0.001 PHE A3807 TRP 0.006 0.001 TRP A3456 HIS 0.003 0.001 HIS A3846 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 5186) covalent geometry : angle 0.53449 ( 7039) hydrogen bonds : bond 0.03505 ( 343) hydrogen bonds : angle 3.80772 ( 1014) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.243 Fit side-chains REVERT: A 3520 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: A 3709 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7500 (p0) REVERT: A 3810 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6624 (ttm-80) REVERT: A 3827 GLN cc_start: 0.8090 (mt0) cc_final: 0.7397 (mp10) REVERT: A 4198 SER cc_start: 0.7617 (t) cc_final: 0.7312 (p) outliers start: 11 outliers final: 5 residues processed: 80 average time/residue: 1.1188 time to fit residues: 94.1016 Evaluate side-chains 80 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3520 GLU Chi-restraints excluded: chain A residue 3619 SER Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3679 THR Chi-restraints excluded: chain A residue 3709 ASN Chi-restraints excluded: chain A residue 3810 ARG Chi-restraints excluded: chain A residue 3980 GLU Chi-restraints excluded: chain A residue 4068 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 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: A4180 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.153541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129349 restraints weight = 15141.611| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.37 r_work: 0.3397 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5186 Z= 0.162 Angle : 0.571 6.563 7039 Z= 0.283 Chirality : 0.035 0.143 864 Planarity : 0.005 0.052 868 Dihedral : 3.875 19.278 688 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.39 % Allowed : 18.23 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.74 (0.33), residues: 630 helix: 2.12 (0.23), residues: 458 sheet: 1.11 (1.40), residues: 17 loop : 1.15 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4314 TYR 0.015 0.002 TYR A4392 PHE 0.017 0.002 PHE A3807 TRP 0.007 0.001 TRP A3456 HIS 0.004 0.001 HIS A3503 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 5186) covalent geometry : angle 0.57057 ( 7039) hydrogen bonds : bond 0.03955 ( 343) hydrogen bonds : angle 3.86312 ( 1014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4849.59 seconds wall clock time: 82 minutes 57.29 seconds (4977.29 seconds total)