Starting phenix.real_space_refine on Sat Dec 9 07:01:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2h_27836/12_2023/8e2h_27836.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2h_27836/12_2023/8e2h_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2h_27836/12_2023/8e2h_27836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2h_27836/12_2023/8e2h_27836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2h_27836/12_2023/8e2h_27836.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2h_27836/12_2023/8e2h_27836.pdb" } 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 Residue "A ASP 3448": "OD1" <-> "OD2" Residue "A GLU 3520": "OE1" <-> "OE2" Residue "A GLU 3621": "OE1" <-> "OE2" Residue "A ASP 3819": "OD1" <-> "OD2" Residue "A GLU 3980": "OE1" <-> "OE2" Residue "A GLU 4172": "OE1" <-> "OE2" Residue "A ASP 4194": "OD1" <-> "OD2" Residue "A ASP 4230": "OD1" <-> "OD2" Residue "A GLU 4240": "OE1" <-> "OE2" Residue "A ASP 4305": "OD1" <-> "OD2" Residue "A GLU 4317": "OE1" <-> "OE2" Residue "A GLU 4318": "OE1" <-> "OE2" Residue "A ASP 4445": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10412 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 10412 Classifications: {'peptide': 656, 'water': 40} Link IDs: {'PTRANS': 36, 'TRANS': 619, None: 40} Not linked: pdbres="ASN A4499 " pdbres="HOH A4901 " Not linked: pdbres="HOH A4901 " pdbres="HOH A4902 " Not linked: pdbres="HOH A4902 " pdbres="HOH A4903 " Not linked: pdbres="HOH A4903 " pdbres="HOH A4904 " Not linked: pdbres="HOH A4904 " pdbres="HOH A4905 " ... (remaining 35 not shown) Chain breaks: 12 Time building chain proxies: 5.16, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 9.34 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.82 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: 3.58 Time building geometry restraints manager: 9.58 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: 100.00 - 106.79: 223 106.79 - 113.58: 12927 113.58 - 120.37: 3157 120.37 - 127.17: 2652 127.17 - 133.96: 72 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: 4261 15.34 - 30.67: 388 30.67 - 46.01: 126 46.01 - 61.35: 36 61.35 - 76.68: 8 Dihedral angle restraints: 4819 sinusoidal: 2634 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 4816 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 1.850 nonbonded pdb="HH11 ARG A3809 " pdb=" O LEU A4189 " model vdw 1.561 1.850 nonbonded pdb=" OD1 ASP A3701 " pdb=" HE2 HIS A3774 " model vdw 1.561 1.850 nonbonded pdb=" OD2 ASP A3819 " pdb=" HG SER A3863 " model vdw 1.583 1.850 nonbonded pdb=" O ALA A3541 " pdb=" HG SER A3544 " model vdw 1.629 1.850 ... (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: 8.680 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: 0.150 Extract box with map and model: 23.930 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 37.850 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.240 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.894 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 83 average time/residue: 1.7559 time to fit residues: 155.1336 Evaluate side-chains 76 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.0576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.0370 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 overall best weight: 0.6256 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5186 Z= 0.231 Angle : 0.573 7.005 7039 Z= 0.286 Chirality : 0.035 0.150 864 Planarity : 0.005 0.060 868 Dihedral : 4.027 18.850 688 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.60 % Allowed : 16.67 % 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: 2.13 (0.34), residues: 630 helix: 1.66 (0.24), residues: 462 sheet: 0.84 (1.38), residues: 17 loop : 0.98 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3456 HIS 0.004 0.001 HIS A4256 PHE 0.020 0.002 PHE A3807 TYR 0.016 0.002 TYR A4392 ARG 0.003 0.000 ARG A4235 *********************** 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 91 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.908 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 86 average time/residue: 1.9063 time to fit residues: 173.9260 Evaluate side-chains 80 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1302 time to fit residues: 1.3012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 42 optimal weight: 0.0040 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 50.0000 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 47 optimal weight: 0.8980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5186 Z= 0.186 Angle : 0.535 6.657 7039 Z= 0.264 Chirality : 0.033 0.146 864 Planarity : 0.005 0.058 868 Dihedral : 3.878 18.315 688 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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 (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: 2.59 (0.34), residues: 630 helix: 1.95 (0.24), residues: 468 sheet: 0.95 (1.40), residues: 17 loop : 1.28 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A3456 HIS 0.004 0.001 HIS A4256 PHE 0.015 0.002 PHE A3807 TYR 0.012 0.001 TYR A4392 ARG 0.002 0.000 ARG A4235 *********************** 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 90 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.839 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 84 average time/residue: 1.9189 time to fit residues: 171.0934 Evaluate side-chains 79 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1306 time to fit residues: 1.3305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 50.0000 chunk 59 optimal weight: 0.2980 chunk 17 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0965 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= 0.254 Angle : 0.568 6.744 7039 Z= 0.283 Chirality : 0.035 0.149 864 Planarity : 0.005 0.056 868 Dihedral : 4.041 19.129 688 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: 2.51 (0.33), residues: 630 helix: 1.99 (0.24), residues: 456 sheet: 0.97 (1.41), residues: 17 loop : 0.95 (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 A4256 PHE 0.020 0.002 PHE A3807 TYR 0.017 0.002 TYR A4392 ARG 0.004 0.000 ARG A4235 *********************** 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 79 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.773 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 77 average time/residue: 1.9878 time to fit residues: 162.1868 Evaluate side-chains 79 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 3 average time/residue: 0.7176 time to fit residues: 3.4453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5186 Z= 0.200 Angle : 0.533 6.615 7039 Z= 0.262 Chirality : 0.034 0.144 864 Planarity : 0.005 0.055 868 Dihedral : 3.898 18.569 688 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.56 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: 2.81 (0.34), residues: 630 helix: 2.19 (0.24), residues: 456 sheet: 0.93 (1.40), residues: 17 loop : 1.15 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A3456 HIS 0.004 0.001 HIS A4256 PHE 0.017 0.002 PHE A3807 TYR 0.012 0.001 TYR A4392 ARG 0.002 0.000 ARG A4235 *********************** 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 88 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.917 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 83 average time/residue: 1.9787 time to fit residues: 173.9950 Evaluate side-chains 78 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.0433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 50.0000 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1175 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= 0.247 Angle : 0.560 6.565 7039 Z= 0.278 Chirality : 0.035 0.146 864 Planarity : 0.005 0.054 868 Dihedral : 3.998 19.018 688 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.91 % Allowed : 17.53 % 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: 2.05 (0.24), residues: 458 sheet: 0.92 (1.39), residues: 17 loop : 1.19 (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 0.016 0.002 TYR A4392 ARG 0.003 0.000 ARG A3810 *********************** 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 83 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.895 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 80 average time/residue: 1.8249 time to fit residues: 155.3183 Evaluate side-chains 76 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.2123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 66 optimal weight: 50.0000 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3827 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5186 Z= 0.243 Angle : 0.554 6.595 7039 Z= 0.275 Chirality : 0.035 0.146 864 Planarity : 0.005 0.055 868 Dihedral : 4.001 19.070 688 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.95 % Allowed : 16.49 % 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: 2.67 (0.33), residues: 630 helix: 2.06 (0.24), residues: 458 sheet: 0.77 (1.38), residues: 17 loop : 1.20 (0.51), 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 0.018 0.002 PHE A3807 TYR 0.014 0.002 TYR A4392 ARG 0.002 0.000 ARG A4235 *********************** 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 88 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.774 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 80 average time/residue: 2.0065 time to fit residues: 169.8603 Evaluate side-chains 80 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.5996 time to fit residues: 3.2374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 37 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1339 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= 0.234 Angle : 0.556 6.555 7039 Z= 0.275 Chirality : 0.035 0.146 864 Planarity : 0.005 0.054 868 Dihedral : 3.995 18.903 688 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.12 % Allowed : 16.67 % 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: 2.71 (0.33), residues: 630 helix: 2.08 (0.24), residues: 458 sheet: 0.83 (1.39), residues: 17 loop : 1.25 (0.51), 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 0.017 0.002 PHE A3807 TYR 0.014 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 fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.836 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 80 average time/residue: 2.0649 time to fit residues: 174.6510 Evaluate side-chains 77 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1526 time to fit residues: 1.5696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5186 Z= 0.244 Angle : 0.557 6.569 7039 Z= 0.277 Chirality : 0.035 0.147 864 Planarity : 0.005 0.053 868 Dihedral : 4.002 19.013 688 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.43 % Allowed : 17.53 % Favored : 80.03 % 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: 2.69 (0.33), residues: 630 helix: 2.07 (0.24), residues: 458 sheet: 0.85 (1.41), residues: 17 loop : 1.25 (0.51), 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 0.018 0.002 PHE A3807 TYR 0.015 0.002 TYR A4392 ARG 0.008 0.000 ARG A3810 *********************** 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 86 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.816 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 82 average time/residue: 1.9603 time to fit residues: 170.4884 Evaluate side-chains 80 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.9323 time to fit residues: 3.3516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 50.0000 chunk 63 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5186 Z= 0.197 Angle : 0.535 6.515 7039 Z= 0.263 Chirality : 0.034 0.144 864 Planarity : 0.005 0.054 868 Dihedral : 3.888 18.433 688 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.56 % Allowed : 18.58 % Favored : 79.86 % 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: 2.91 (0.33), residues: 630 helix: 2.21 (0.24), residues: 458 sheet: 0.83 (1.40), residues: 17 loop : 1.40 (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 0.015 0.002 PHE A3807 TYR 0.015 0.001 TYR A4392 ARG 0.003 0.000 ARG A3810 ********************** 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 80 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.891 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 1.9794 time to fit residues: 163.8239 Evaluate side-chains 77 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1287 time to fit residues: 1.3087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 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 = 0.3886 r_free = 0.3886 target = 0.158294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135813 restraints weight = 14857.155| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.26 r_work: 0.3436 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5186 Z= 0.278 Angle : 0.574 6.558 7039 Z= 0.286 Chirality : 0.036 0.146 864 Planarity : 0.005 0.053 868 Dihedral : 4.063 19.196 688 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.91 % Allowed : 18.40 % Favored : 79.69 % 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: 2.62 (0.33), residues: 630 helix: 2.00 (0.24), residues: 458 sheet: 0.84 (1.41), residues: 17 loop : 1.24 (0.51), 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 0.019 0.002 PHE A3807 TYR 0.016 0.002 TYR A4392 ARG 0.005 0.000 ARG A3810 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4742.38 seconds wall clock time: 84 minutes 36.75 seconds (5076.75 seconds total)