Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:53:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/04_2023/7zyz_15029_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/04_2023/7zyz_15029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/04_2023/7zyz_15029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/04_2023/7zyz_15029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/04_2023/7zyz_15029_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/04_2023/7zyz_15029_updated.pdb" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.010 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 Mn 1 7.51 5 S 19 5.16 5 C 2740 2.51 5 N 731 2.21 5 O 858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 460": "NH1" <-> "NH2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A GLU 896": "OE1" <-> "OE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A GLU 947": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 4349 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4349 Unusual residues: {' MN': 1, 'OAA': 1} Classifications: {'peptide': 541, 'undetermined': 2, 'water': 38} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 515, None: 40} Not linked: pdbres="GLY A1000 " pdbres=" MN A1201 " Not linked: pdbres=" MN A1201 " pdbres="OAA A1202 " Not linked: pdbres="OAA A1202 " pdbres="HOH A1301 " Not linked: pdbres="HOH A1301 " pdbres="HOH A1302 " Not linked: pdbres="HOH A1302 " pdbres="HOH A1303 " ... (remaining 35 not shown) Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.92, per 1000 atoms: 0.67 Number of scatterers: 4349 At special positions: 0 Unit cell: (73.14, 77.38, 80.56, 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) Mn 1 24.99 S 19 16.00 O 858 8.00 N 731 7.00 C 2740 6.00 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: 2.09 Conformation dependent library (CDL) restraints added in 660.3 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 2 sheets defined 50.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 503 through 521 removed outlier: 8.050A pdb=" N ALA A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N ASP A 513 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.801A pdb=" N TYR A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 618 through 631 Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 682 through 695 removed outlier: 3.502A pdb=" N THR A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 722 Processing helix chain 'A' and resid 740 through 750 Processing helix chain 'A' and resid 760 through 762 No H-bonds generated for 'chain 'A' and resid 760 through 762' Processing helix chain 'A' and resid 771 through 778 removed outlier: 3.567A pdb=" N TYR A 775 " --> pdb=" O MET A 771 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 809 removed outlier: 3.518A pdb=" N HIS A 797 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 804 " --> pdb=" O GLU A 800 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR A 805 " --> pdb=" O ASP A 801 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 806 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) Proline residue: A 808 - end of helix Processing helix chain 'A' and resid 818 through 821 Processing helix chain 'A' and resid 827 through 835 Processing helix chain 'A' and resid 844 through 859 removed outlier: 4.194A pdb=" N ASP A 847 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 849 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS A 850 " --> pdb=" O ASP A 847 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 856 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 857 " --> pdb=" O ARG A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 883 Processing helix chain 'A' and resid 887 through 890 No H-bonds generated for 'chain 'A' and resid 887 through 890' Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 920 through 926 Processing helix chain 'A' and resid 937 through 940 Processing helix chain 'A' and resid 946 through 957 removed outlier: 3.908A pdb=" N LYS A 956 " --> pdb=" O ASP A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 973 through 985 Processing helix chain 'A' and resid 989 through 991 No H-bonds generated for 'chain 'A' and resid 989 through 991' Processing helix chain 'A' and resid 994 through 999 Processing sheet with id= A, first strand: chain 'A' and resid 526 through 529 Processing sheet with id= B, first strand: chain 'A' and resid 728 through 731 removed outlier: 6.338A pdb=" N ALA A 566 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU A 604 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N MET A 568 " --> pdb=" O LEU A 604 " (cutoff:3.500A) 161 hydrogen bonds defined for protein. 447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1426 1.34 - 1.46: 731 1.46 - 1.57: 2210 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 4404 Sorted by residual: bond pdb=" C VAL A 702 " pdb=" N KCX A 703 " ideal model delta sigma weight residual 1.329 1.427 -0.098 1.40e-02 5.10e+03 4.94e+01 bond pdb=" C3 OAA A1202 " pdb=" O3 OAA A1202 " ideal model delta sigma weight residual 1.214 1.307 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" NZ KCX A 703 " pdb=" CX KCX A 703 " ideal model delta sigma weight residual 1.411 1.324 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C1 OAA A1202 " pdb=" O2 OAA A1202 " ideal model delta sigma weight residual 1.242 1.311 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C4 OAA A1202 " pdb=" O4 OAA A1202 " ideal model delta sigma weight residual 1.241 1.308 -0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 4399 not shown) Histogram of bond angle deviations from ideal: 84.70 - 94.57: 1 94.57 - 104.43: 78 104.43 - 114.30: 2596 114.30 - 124.16: 3206 124.16 - 134.02: 80 Bond angle restraints: 5961 Sorted by residual: angle pdb=" O VAL A 702 " pdb=" C VAL A 702 " pdb=" N KCX A 703 " ideal model delta sigma weight residual 123.00 84.70 38.30 1.60e+00 3.91e-01 5.73e+02 angle pdb=" CA GLU A 480 " pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " pdb=" CD GLU A 480 " ideal model delta sigma weight residual 112.60 118.50 -5.90 1.70e+00 3.46e-01 1.21e+01 angle pdb=" CA LYS A 501 " pdb=" CB LYS A 501 " pdb=" CG LYS A 501 " ideal model delta sigma weight residual 114.10 119.85 -5.75 2.00e+00 2.50e-01 8.28e+00 angle pdb=" N ALA A 837 " pdb=" CA ALA A 837 " pdb=" C ALA A 837 " ideal model delta sigma weight residual 112.72 109.10 3.62 1.28e+00 6.10e-01 7.99e+00 ... (remaining 5956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.62: 2517 32.62 - 65.24: 118 65.24 - 97.86: 13 97.86 - 130.48: 0 130.48 - 163.10: 1 Dihedral angle restraints: 2649 sinusoidal: 1080 harmonic: 1569 Sorted by residual: dihedral pdb=" C1 OAA A1202 " pdb=" C2 OAA A1202 " pdb=" C3 OAA A1202 " pdb=" O3 OAA A1202 " ideal model delta sinusoidal sigma weight residual -102.23 60.87 -163.10 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CA ASN A 609 " pdb=" C ASN A 609 " pdb=" N ALA A 610 " pdb=" CA ALA A 610 " ideal model delta harmonic sigma weight residual -180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA MET A 648 " pdb=" C MET A 648 " pdb=" N GLU A 649 " pdb=" CA GLU A 649 " ideal model delta harmonic sigma weight residual -180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 2646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 322 0.031 - 0.062: 203 0.062 - 0.093: 90 0.093 - 0.124: 28 0.124 - 0.155: 7 Chirality restraints: 650 Sorted by residual: chirality pdb=" CG LEU A 645 " pdb=" CB LEU A 645 " pdb=" CD1 LEU A 645 " pdb=" CD2 LEU A 645 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA LYS A 500 " pdb=" N LYS A 500 " pdb=" C LYS A 500 " pdb=" CB LYS A 500 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA THR A 994 " pdb=" N THR A 994 " pdb=" C THR A 994 " pdb=" CB THR A 994 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 647 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 702 " 0.143 2.00e-02 2.50e+03 2.27e-01 5.14e+02 pdb=" C VAL A 702 " -0.390 2.00e-02 2.50e+03 pdb=" O VAL A 702 " 0.156 2.00e-02 2.50e+03 pdb=" N KCX A 703 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 501 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C LYS A 501 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS A 501 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 502 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 867 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO A 868 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 868 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 868 " -0.019 5.00e-02 4.00e+02 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 61 2.56 - 3.14: 3641 3.14 - 3.73: 7568 3.73 - 4.31: 10735 4.31 - 4.90: 16729 Nonbonded interactions: 38734 Sorted by model distance: nonbonded pdb=" OQ2 KCX A 703 " pdb="MN MN A1201 " model vdw 1.973 2.320 nonbonded pdb="MN MN A1201 " pdb=" O HOH A1320 " model vdw 2.002 2.320 nonbonded pdb=" NE2 HIS A 734 " pdb="MN MN A1201 " model vdw 2.030 2.400 nonbonded pdb=" OD2 ASP A 534 " pdb="MN MN A1201 " model vdw 2.143 2.320 nonbonded pdb=" O HIS A 823 " pdb=" ND1 HIS A 823 " model vdw 2.151 2.520 ... (remaining 38729 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: 1.130 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: 5.670 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 16.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 : 0.007 0.098 4404 Z= 0.479 Angle : 0.871 38.295 5961 Z= 0.491 Chirality : 0.047 0.155 650 Planarity : 0.009 0.227 780 Dihedral : 18.664 163.102 1645 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 5.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.36), residues: 536 helix: -0.09 (0.30), residues: 294 sheet: -0.53 (0.73), residues: 43 loop : 0.14 (0.44), residues: 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 36 time to evaluate : 0.533 Fit side-chains outliers start: 25 outliers final: 24 residues processed: 60 average time/residue: 1.0697 time to fit residues: 67.3374 Evaluate side-chains 57 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 33 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 23 residues processed: 1 average time/residue: 1.1828 time to fit residues: 1.9412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.0040 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 4404 Z= 0.209 Angle : 0.499 6.497 5961 Z= 0.266 Chirality : 0.041 0.129 650 Planarity : 0.003 0.037 780 Dihedral : 8.744 159.884 597 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 7.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.36), residues: 536 helix: 0.45 (0.31), residues: 285 sheet: -0.60 (0.69), residues: 43 loop : 0.51 (0.45), residues: 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 33 time to evaluate : 0.537 Fit side-chains outliers start: 33 outliers final: 21 residues processed: 62 average time/residue: 0.9113 time to fit residues: 59.6531 Evaluate side-chains 54 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 33 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 1.0464 time to fit residues: 1.7808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 50.0000 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4404 Z= 0.213 Angle : 0.483 5.176 5961 Z= 0.256 Chirality : 0.041 0.129 650 Planarity : 0.003 0.036 780 Dihedral : 8.662 158.945 597 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 6.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.37), residues: 536 helix: 0.68 (0.31), residues: 285 sheet: -0.65 (0.69), residues: 43 loop : 0.54 (0.46), residues: 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 33 time to evaluate : 0.550 Fit side-chains outliers start: 28 outliers final: 21 residues processed: 60 average time/residue: 0.8490 time to fit residues: 54.0199 Evaluate side-chains 52 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 31 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 0.9350 time to fit residues: 1.6595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 50.0000 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4404 Z= 0.190 Angle : 0.467 5.131 5961 Z= 0.249 Chirality : 0.040 0.128 650 Planarity : 0.003 0.034 780 Dihedral : 8.553 157.653 597 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 6.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.37), residues: 536 helix: 0.77 (0.32), residues: 286 sheet: -0.60 (0.70), residues: 43 loop : 0.60 (0.46), residues: 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 33 time to evaluate : 0.508 Fit side-chains outliers start: 28 outliers final: 19 residues processed: 59 average time/residue: 0.9258 time to fit residues: 57.7327 Evaluate side-chains 51 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 32 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 1.0354 time to fit residues: 1.7525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8444 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 4404 Z= 0.332 Angle : 0.566 9.348 5961 Z= 0.298 Chirality : 0.044 0.132 650 Planarity : 0.003 0.036 780 Dihedral : 8.904 160.261 597 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 6.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.37), residues: 536 helix: 0.72 (0.32), residues: 286 sheet: -0.65 (0.69), residues: 43 loop : 0.40 (0.46), residues: 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 32 time to evaluate : 0.517 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 58 average time/residue: 0.8600 time to fit residues: 52.7601 Evaluate side-chains 49 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 31 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 1.0016 time to fit residues: 1.6939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 50.0000 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 54 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 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: 0.8418 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 4404 Z= 0.229 Angle : 0.540 11.992 5961 Z= 0.276 Chirality : 0.041 0.133 650 Planarity : 0.003 0.035 780 Dihedral : 8.685 158.095 597 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 5.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.37), residues: 536 helix: 0.75 (0.32), residues: 286 sheet: -0.64 (0.69), residues: 43 loop : 0.50 (0.46), residues: 207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 32 time to evaluate : 0.502 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 55 average time/residue: 0.9612 time to fit residues: 55.6800 Evaluate side-chains 49 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 31 time to evaluate : 0.531 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 1.1204 time to fit residues: 1.8869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.0370 chunk 55 optimal weight: 50.0000 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.0270 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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: 0.8391 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4404 Z= 0.172 Angle : 0.507 10.951 5961 Z= 0.258 Chirality : 0.040 0.127 650 Planarity : 0.003 0.034 780 Dihedral : 8.449 155.945 597 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 4.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.38), residues: 536 helix: 0.79 (0.32), residues: 288 sheet: -0.56 (0.70), residues: 43 loop : 0.63 (0.47), residues: 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 35 time to evaluate : 0.616 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 17 residues processed: 56 average time/residue: 0.9652 time to fit residues: 56.9975 Evaluate side-chains 49 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 32 time to evaluate : 0.526 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 0.7187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.0570 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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: 0.8399 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 4404 Z= 0.194 Angle : 0.505 7.214 5961 Z= 0.263 Chirality : 0.040 0.146 650 Planarity : 0.003 0.034 780 Dihedral : 8.345 152.563 597 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 4.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.37), residues: 536 helix: 0.85 (0.32), residues: 286 sheet: -0.54 (0.71), residues: 43 loop : 0.57 (0.46), residues: 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 31 time to evaluate : 0.556 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 50 average time/residue: 0.8792 time to fit residues: 46.6471 Evaluate side-chains 48 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 30 time to evaluate : 0.512 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 1.1386 time to fit residues: 1.9060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.0370 chunk 49 optimal weight: 0.0170 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 50.0000 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 57 optimal weight: 50.0000 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4404 Z= 0.170 Angle : 0.489 7.086 5961 Z= 0.254 Chirality : 0.040 0.127 650 Planarity : 0.003 0.034 780 Dihedral : 8.205 150.845 597 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 4.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.37), residues: 536 helix: 0.87 (0.32), residues: 287 sheet: -0.51 (0.71), residues: 43 loop : 0.48 (0.45), residues: 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 32 time to evaluate : 0.562 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 19 residues processed: 51 average time/residue: 0.9799 time to fit residues: 52.8199 Evaluate side-chains 50 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 31 time to evaluate : 0.481 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 1.0383 time to fit residues: 1.7350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 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: 0.8398 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 4404 Z= 0.201 Angle : 0.511 7.488 5961 Z= 0.265 Chirality : 0.040 0.128 650 Planarity : 0.003 0.034 780 Dihedral : 8.250 150.566 597 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 4.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.37), residues: 536 helix: 0.83 (0.32), residues: 287 sheet: -0.50 (0.72), residues: 43 loop : 0.45 (0.45), residues: 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 31 time to evaluate : 0.539 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 18 residues processed: 49 average time/residue: 0.9437 time to fit residues: 48.8761 Evaluate side-chains 48 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 30 time to evaluate : 0.527 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 0.7313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.069536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.061140 restraints weight = 12125.877| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.59 r_work: 0.3069 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 4404 Z= 0.194 Angle : 0.507 6.846 5961 Z= 0.262 Chirality : 0.040 0.128 650 Planarity : 0.003 0.034 780 Dihedral : 8.225 150.074 597 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 4.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.37), residues: 536 helix: 0.81 (0.32), residues: 287 sheet: -0.49 (0.72), residues: 43 loop : 0.44 (0.45), residues: 206 =============================================================================== Job complete usr+sys time: 1759.20 seconds wall clock time: 32 minutes 23.14 seconds (1943.14 seconds total)