Starting phenix.real_space_refine on Fri Feb 14 19:47:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e2h_27836/02_2025/8e2h_27836.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2h_27836/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e2h_27836/02_2025/8e2h_27836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2h_27836/02_2025/8e2h_27836.map" model { file = "/net/cci-nas-00/data/ceres_data/8e2h_27836/02_2025/8e2h_27836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2h_27836/02_2025/8e2h_27836.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.64, per 1000 atoms: 0.64 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: 2.98 Conformation dependent library (CDL) restraints added in 837.2 milliseconds 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: 0.68 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: 3.95 Time building geometry restraints manager: 3.51 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: 11.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.210 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.740 ------------------------------------------------------------------------------- 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= 0.225 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (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 TRP 0.008 0.001 TRP A3456 HIS 0.004 0.001 HIS A4256 PHE 0.014 0.002 PHE A3812 TYR 0.011 0.001 TYR A4392 ARG 0.004 0.000 ARG A3810 *********************** 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 : 0.863 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 83 average time/residue: 1.8587 time to fit residues: 164.1601 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 : 0.795 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3709 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.153699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130108 restraints weight = 14937.076| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.33 r_work: 0.3406 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5186 Z= 0.224 Angle : 0.579 7.062 7039 Z= 0.292 Chirality : 0.035 0.150 864 Planarity : 0.005 0.059 868 Dihedral : 4.289 31.158 691 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.91 % Allowed : 17.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.34), residues: 630 helix: 1.60 (0.24), residues: 468 sheet: 0.96 (1.39), residues: 17 loop : 1.11 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3456 HIS 0.005 0.001 HIS A3846 PHE 0.018 0.002 PHE A3807 TYR 0.014 0.001 TYR A4392 ARG 0.002 0.000 ARG A3449 *********************** 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 84 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.857 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 81 average time/residue: 1.8593 time to fit residues: 160.4322 Evaluate side-chains 74 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3679 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4180 HIS A4482 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.154908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131651 restraints weight = 15173.647| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.31 r_work: 0.3493 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5186 Z= 0.256 Angle : 0.583 6.722 7039 Z= 0.293 Chirality : 0.036 0.148 864 Planarity : 0.005 0.059 868 Dihedral : 4.306 29.731 691 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.33), residues: 630 helix: 1.80 (0.24), residues: 456 sheet: 0.99 (1.37), residues: 17 loop : 0.74 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3456 HIS 0.004 0.001 HIS A3846 PHE 0.018 0.002 PHE A3807 TYR 0.015 0.002 TYR A4392 ARG 0.002 0.000 ARG A4400 *********************** 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: 15 poor density : 72 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 3709 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7638 (p0) REVERT: A 3810 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.6671 (ttm-80) REVERT: A 4198 SER cc_start: 0.7685 (t) cc_final: 0.7377 (p) outliers start: 15 outliers final: 3 residues processed: 82 average time/residue: 1.9645 time to fit residues: 170.7372 Evaluate side-chains 77 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.154816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131638 restraints weight = 14878.210| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.30 r_work: 0.3429 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1071 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= 0.260 Angle : 0.581 6.725 7039 Z= 0.290 Chirality : 0.036 0.147 864 Planarity : 0.005 0.057 868 Dihedral : 4.053 19.733 688 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.40 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.33), residues: 630 helix: 1.81 (0.24), residues: 456 sheet: 0.85 (1.35), residues: 17 loop : 0.71 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3456 HIS 0.004 0.001 HIS A3846 PHE 0.020 0.002 PHE A3807 TYR 0.015 0.002 TYR A4392 ARG 0.002 0.000 ARG A3449 *********************** 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 85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 3709 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7628 (p0) REVERT: A 3810 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.6687 (ttm-80) REVERT: A 4198 SER cc_start: 0.7706 (t) cc_final: 0.7401 (p) outliers start: 16 outliers final: 8 residues processed: 80 average time/residue: 2.0198 time to fit residues: 171.1839 Evaluate side-chains 80 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 3754 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.154930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131731 restraints weight = 14972.933| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.31 r_work: 0.3432 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1155 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= 0.252 Angle : 0.577 6.626 7039 Z= 0.287 Chirality : 0.035 0.147 864 Planarity : 0.005 0.056 868 Dihedral : 4.022 19.581 688 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.12 % Allowed : 16.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.33), residues: 630 helix: 1.85 (0.24), residues: 458 sheet: 0.85 (1.35), residues: 17 loop : 0.89 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3456 HIS 0.004 0.001 HIS A4256 PHE 0.019 0.002 PHE A3807 TYR 0.015 0.002 TYR A4392 ARG 0.002 0.000 ARG A3810 *********************** 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 89 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 3709 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7619 (p0) REVERT: A 3810 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.6687 (ttm-80) REVERT: A 3827 GLN cc_start: 0.8149 (mt0) cc_final: 0.7451 (mp10) REVERT: A 4198 SER cc_start: 0.7690 (t) cc_final: 0.7363 (p) outliers start: 18 outliers final: 7 residues processed: 83 average time/residue: 2.1851 time to fit residues: 191.6522 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 : 0.796 ------------------------------------------------------------------------------- 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 3754 GLN Chi-restraints excluded: chain A residue 3810 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.155448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132097 restraints weight = 15128.235| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.32 r_work: 0.3495 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1292 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= 0.229 Angle : 0.564 6.593 7039 Z= 0.281 Chirality : 0.035 0.146 864 Planarity : 0.005 0.055 868 Dihedral : 3.957 19.285 688 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.60 % Allowed : 16.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.33), residues: 630 helix: 1.94 (0.24), residues: 458 sheet: 0.82 (1.34), residues: 17 loop : 0.94 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3456 HIS 0.003 0.001 HIS A3503 PHE 0.018 0.002 PHE A3807 TYR 0.014 0.001 TYR A4392 ARG 0.002 0.000 ARG A3836 *********************** 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 86 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 3709 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7594 (p0) REVERT: A 3810 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.6692 (ttm-80) REVERT: A 3827 GLN cc_start: 0.8121 (mt0) cc_final: 0.7433 (mp10) REVERT: A 3975 GLN cc_start: 0.8322 (tp40) cc_final: 0.8102 (tm-30) REVERT: A 4198 SER cc_start: 0.7703 (t) cc_final: 0.7373 (p) outliers start: 15 outliers final: 7 residues processed: 81 average time/residue: 2.0772 time to fit residues: 178.0004 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 : 0.805 ------------------------------------------------------------------------------- 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 3709 ASN Chi-restraints excluded: chain A residue 3754 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 24 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 0.0010 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.156405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133179 restraints weight = 15161.863| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.32 r_work: 0.3509 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1371 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= 0.190 Angle : 0.542 6.476 7039 Z= 0.268 Chirality : 0.034 0.143 864 Planarity : 0.005 0.054 868 Dihedral : 3.820 18.689 688 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.33), residues: 630 helix: 2.10 (0.24), residues: 458 sheet: 0.83 (1.35), residues: 17 loop : 1.02 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3456 HIS 0.003 0.001 HIS A3503 PHE 0.015 0.002 PHE A3807 TYR 0.012 0.001 TYR A4392 ARG 0.002 0.000 ARG A4314 *********************** 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 91 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.767 Fit side-chains REVERT: A 3520 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: A 3566 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8092 (mt) REVERT: A 3709 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7557 (p0) REVERT: A 3810 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.6615 (ttm-80) REVERT: A 3827 GLN cc_start: 0.8094 (mt0) cc_final: 0.7418 (mp10) REVERT: A 4198 SER cc_start: 0.7664 (t) cc_final: 0.7348 (p) outliers start: 16 outliers final: 6 residues processed: 87 average time/residue: 1.9648 time to fit residues: 181.4244 Evaluate side-chains 82 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3520 GLU Chi-restraints excluded: chain A residue 3566 ILE 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 3981 MET Chi-restraints excluded: chain A residue 4068 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.155344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132023 restraints weight = 14975.747| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.32 r_work: 0.3435 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5186 Z= 0.248 Angle : 0.572 6.541 7039 Z= 0.284 Chirality : 0.035 0.147 864 Planarity : 0.005 0.053 868 Dihedral : 3.936 19.367 688 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.78 % Allowed : 16.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.33), residues: 630 helix: 2.01 (0.23), residues: 458 sheet: 0.91 (1.36), residues: 17 loop : 0.96 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3456 HIS 0.004 0.001 HIS A3503 PHE 0.018 0.002 PHE A3807 TYR 0.016 0.002 TYR A4392 ARG 0.002 0.000 ARG A3810 *********************** 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 88 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.777 Fit side-chains REVERT: A 3520 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: A 3566 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8091 (mt) REVERT: A 3709 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7583 (p0) REVERT: A 3810 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.6649 (ttm-80) REVERT: A 3827 GLN cc_start: 0.8128 (mt0) cc_final: 0.7442 (mt0) REVERT: A 4198 SER cc_start: 0.7692 (t) cc_final: 0.7361 (p) outliers start: 16 outliers final: 9 residues processed: 84 average time/residue: 2.1292 time to fit residues: 188.9547 Evaluate side-chains 85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3520 GLU Chi-restraints excluded: chain A residue 3566 ILE 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 4451 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.156245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133089 restraints weight = 15077.601| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.32 r_work: 0.3448 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5186 Z= 0.202 Angle : 0.550 6.517 7039 Z= 0.272 Chirality : 0.034 0.144 864 Planarity : 0.005 0.054 868 Dihedral : 3.837 18.865 688 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 2.26 % Allowed : 17.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.33), residues: 630 helix: 2.12 (0.24), residues: 458 sheet: 0.95 (1.38), residues: 17 loop : 1.11 (0.53), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3456 HIS 0.003 0.001 HIS A4257 PHE 0.015 0.002 PHE A3807 TYR 0.012 0.001 TYR A4392 ARG 0.002 0.000 ARG A4314 *********************** 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 85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.791 Fit side-chains REVERT: A 3520 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: A 3566 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8091 (mt) REVERT: A 3709 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7567 (p0) REVERT: A 3810 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.6623 (ttm-80) REVERT: A 3827 GLN cc_start: 0.8102 (mt0) cc_final: 0.7425 (mp10) REVERT: A 4198 SER cc_start: 0.7680 (t) cc_final: 0.7369 (p) outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 2.1897 time to fit residues: 187.0088 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 : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3520 GLU Chi-restraints excluded: chain A residue 3566 ILE 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 4451 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 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 = 0.3810 r_free = 0.3810 target = 0.152986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128890 restraints weight = 15122.269| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.36 r_work: 0.3391 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5186 Z= 0.254 Angle : 0.575 6.536 7039 Z= 0.286 Chirality : 0.035 0.144 864 Planarity : 0.005 0.053 868 Dihedral : 3.946 19.391 688 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.43 % Allowed : 17.36 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.33), residues: 630 helix: 2.01 (0.23), residues: 458 sheet: 1.08 (1.40), residues: 17 loop : 1.05 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3456 HIS 0.004 0.001 HIS A4257 PHE 0.018 0.002 PHE A3807 TYR 0.015 0.002 TYR A4392 ARG 0.002 0.000 ARG A4314 ********************** 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 89 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.909 Fit side-chains REVERT: A 3520 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7503 (tt0) REVERT: A 3566 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8074 (mt) REVERT: A 3709 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7571 (p0) REVERT: A 3810 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.6641 (ttm-80) REVERT: A 3827 GLN cc_start: 0.8179 (mt0) cc_final: 0.7441 (mt0) REVERT: A 4198 SER cc_start: 0.7675 (t) cc_final: 0.7343 (p) REVERT: A 4308 GLN cc_start: 0.6441 (tm130) cc_final: 0.6127 (pp30) outliers start: 14 outliers final: 8 residues processed: 84 average time/residue: 2.1379 time to fit residues: 189.3931 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 : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3520 GLU Chi-restraints excluded: chain A residue 3566 ILE 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 4451 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.153269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129206 restraints weight = 15046.478| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.36 r_work: 0.3395 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5186 Z= 0.237 Angle : 0.568 6.803 7039 Z= 0.282 Chirality : 0.035 0.144 864 Planarity : 0.005 0.054 868 Dihedral : 3.927 19.292 688 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.26 % Allowed : 17.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.33), residues: 630 helix: 2.03 (0.23), residues: 458 sheet: 1.06 (1.40), residues: 17 loop : 1.09 (0.53), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3456 HIS 0.004 0.001 HIS A4257 PHE 0.017 0.002 PHE A3807 TYR 0.015 0.001 TYR A4392 ARG 0.002 0.000 ARG A4314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9134.35 seconds wall clock time: 161 minutes 17.38 seconds (9677.38 seconds total)