Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:57:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz2_15032/04_2023/7zz2_15032_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz2_15032/04_2023/7zz2_15032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz2_15032/04_2023/7zz2_15032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz2_15032/04_2023/7zz2_15032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz2_15032/04_2023/7zz2_15032_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz2_15032/04_2023/7zz2_15032_updated.pdb" } resolution = 2.48 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= 0.009 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 Mg 1 5.21 5 S 19 5.16 5 C 2739 2.51 5 N 731 2.21 5 O 875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 583": "OE1" <-> "OE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 847": "OD1" <-> "OD2" Residue "A PHE 879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 884": "OD1" <-> "OD2" Residue "A GLU 947": "OE1" <-> "OE2" Residue "A ASP 993": "OD1" <-> "OD2" 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: 4366 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4366 Unusual residues: {' MG': 1, ' MN': 1, 'PYR': 1} Classifications: {'peptide': 541, 'undetermined': 3, 'water': 57} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 515, None: 60} Not linked: pdbres="GLY A1000 " pdbres=" MG A1201 " Not linked: pdbres=" MG A1201 " pdbres=" MN A1202 " Not linked: pdbres=" MN A1202 " pdbres="PYR A1203 " Not linked: pdbres="PYR A1203 " pdbres="HOH A1301 " Not linked: pdbres="HOH A1301 " pdbres="HOH A1302 " ... (remaining 55 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: 2.88, per 1000 atoms: 0.66 Number of scatterers: 4366 At special positions: 0 Unit cell: (67.84, 76.32, 78.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 19 16.00 Mg 1 11.99 O 875 8.00 N 731 7.00 C 2739 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: 1.88 Conformation dependent library (CDL) restraints added in 663.5 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 1 sheets defined 52.9% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 512 through 521 Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 546 through 549 No H-bonds generated for 'chain 'A' and resid 546 through 549' Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.818A 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 658 removed outlier: 3.597A pdb=" N GLU A 649 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS A 650 " --> pdb=" O GLN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 695 Processing helix chain 'A' and resid 711 through 724 Processing helix chain 'A' and resid 735 through 737 No H-bonds generated for 'chain 'A' and resid 735 through 737' 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 777 Processing helix chain 'A' and resid 789 through 809 removed outlier: 3.790A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR A 805 " --> pdb=" O ASP A 801 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR A 806 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 4.334A 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 823 removed outlier: 3.901A pdb=" N HIS A 823 " --> pdb=" O VAL A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 840 Processing helix chain 'A' and resid 843 through 860 removed outlier: 3.865A pdb=" N PHE A 846 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASP A 847 " --> pdb=" O HIS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 883 Processing helix chain 'A' and resid 887 through 893 Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 920 through 926 Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 973 through 986 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 754 through 757 removed outlier: 6.522A pdb=" N LEU A 526 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL A 757 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR A 528 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASP A 529 " --> pdb=" O PHE A 564 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA A 566 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU A 604 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY A 570 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 635 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE A 605 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ARG A 637 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 661 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 638 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU A 663 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 699 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL A 702 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N HIS A 730 " --> pdb=" O VAL A 702 " (cutoff:3.500A) 167 hydrogen bonds defined for protein. 429 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: 1.14 Time building geometry restraints manager: 2.02 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: 1418 1.34 - 1.46: 878 1.46 - 1.58: 2068 1.58 - 1.70: 0 1.70 - 1.82: 37 Bond restraints: 4401 Sorted by residual: bond pdb=" C1 PYR A1203 " pdb=" C2 PYR A1203 " ideal model delta sigma weight residual 1.558 1.388 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" C2 PYR A1203 " pdb=" O3 PYR A1203 " ideal model delta sigma weight residual 1.210 1.309 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" NZ KCX A 703 " pdb=" CX KCX A 703 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C1 PYR A1203 " pdb=" O1 PYR A1203 " ideal model delta sigma weight residual 1.239 1.307 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 PYR A1203 " pdb=" O2 PYR A1203 " ideal model delta sigma weight residual 1.243 1.308 -0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 4396 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.42: 134 106.42 - 113.34: 2327 113.34 - 120.26: 1599 120.26 - 127.17: 1850 127.17 - 134.09: 47 Bond angle restraints: 5957 Sorted by residual: angle pdb=" CB MET A 982 " pdb=" CG MET A 982 " pdb=" SD MET A 982 " ideal model delta sigma weight residual 112.70 124.08 -11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" CA GLN A 817 " pdb=" CB GLN A 817 " pdb=" CG GLN A 817 " ideal model delta sigma weight residual 114.10 121.49 -7.39 2.00e+00 2.50e-01 1.36e+01 angle pdb=" CB MET A 858 " pdb=" CG MET A 858 " pdb=" SD MET A 858 " ideal model delta sigma weight residual 112.70 123.53 -10.83 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CA LYS A 921 " pdb=" CB LYS A 921 " pdb=" CG LYS A 921 " ideal model delta sigma weight residual 114.10 121.14 -7.04 2.00e+00 2.50e-01 1.24e+01 angle pdb=" CB GLU A 960 " pdb=" CG GLU A 960 " pdb=" CD GLU A 960 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.70e+00 3.46e-01 1.06e+01 ... (remaining 5952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2293 17.82 - 35.65: 263 35.65 - 53.47: 62 53.47 - 71.30: 23 71.30 - 89.12: 6 Dihedral angle restraints: 2647 sinusoidal: 1078 harmonic: 1569 Sorted by residual: dihedral pdb=" CA ARG A 533 " pdb=" C ARG A 533 " pdb=" N ASP A 534 " pdb=" CA ASP A 534 " ideal model delta harmonic sigma weight residual -180.00 -161.35 -18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE A 918 " pdb=" C PHE A 918 " pdb=" N PRO A 919 " pdb=" CA PRO A 919 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB GLU A 583 " pdb=" CG GLU A 583 " pdb=" CD GLU A 583 " pdb=" OE1 GLU A 583 " ideal model delta sinusoidal sigma weight residual 0.00 89.12 -89.12 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 2644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 480 0.047 - 0.094: 137 0.094 - 0.141: 28 0.141 - 0.188: 4 0.188 - 0.235: 1 Chirality restraints: 650 Sorted by residual: chirality pdb=" CB ILE A 742 " pdb=" CA ILE A 742 " pdb=" CG1 ILE A 742 " pdb=" CG2 ILE A 742 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE A 552 " pdb=" CA ILE A 552 " pdb=" CG1 ILE A 552 " pdb=" CG2 ILE A 552 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CB VAL A 840 " pdb=" CA VAL A 840 " pdb=" CG1 VAL A 840 " pdb=" CG2 VAL A 840 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 647 not shown) Planarity restraints: 779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 899 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO A 900 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 900 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 900 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 749 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" CD GLN A 749 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLN A 749 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN A 749 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 768 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 769 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 769 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 769 " -0.020 5.00e-02 4.00e+02 ... (remaining 776 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 143 2.69 - 3.24: 4306 3.24 - 3.79: 7972 3.79 - 4.35: 10326 4.35 - 4.90: 16244 Nonbonded interactions: 38991 Sorted by model distance: nonbonded pdb=" OQ1 KCX A 703 " pdb="MN MN A1202 " model vdw 2.132 2.320 nonbonded pdb="MN MN A1202 " pdb=" O HOH A1308 " model vdw 2.176 2.320 nonbonded pdb=" NE2 HIS A 734 " pdb="MN MN A1202 " model vdw 2.202 2.400 nonbonded pdb=" OD2 ASP A 534 " pdb="MN MN A1202 " model vdw 2.213 2.320 nonbonded pdb=" OQ2 KCX A 703 " pdb="MN MN A1202 " model vdw 2.216 2.320 ... (remaining 38986 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: 5.620 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.820 Find NCS groups from input model: 0.120 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 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 : 0.005 0.170 4401 Z= 0.339 Angle : 0.764 11.381 5957 Z= 0.407 Chirality : 0.046 0.235 650 Planarity : 0.005 0.040 779 Dihedral : 17.253 89.122 1643 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 3.27 % 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: -0.30 (0.33), residues: 536 helix: -0.15 (0.27), residues: 299 sheet: -0.07 (0.79), residues: 43 loop : 0.01 (0.43), residues: 194 *********************** 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 46 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 31 time to evaluate : 0.552 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 45 average time/residue: 0.8596 time to fit residues: 41.1619 Evaluate side-chains 44 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 30 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 0.7324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0570 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4401 Z= 0.202 Angle : 0.474 5.243 5957 Z= 0.252 Chirality : 0.039 0.129 650 Planarity : 0.004 0.032 779 Dihedral : 4.424 27.806 595 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer Outliers : 5.01 % 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: 0.64 (0.34), residues: 536 helix: 0.73 (0.29), residues: 298 sheet: -0.00 (0.79), residues: 43 loop : 0.27 (0.43), residues: 195 *********************** 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 53 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 30 time to evaluate : 0.528 Fit side-chains outliers start: 23 outliers final: 17 residues processed: 48 average time/residue: 0.9003 time to fit residues: 45.9572 Evaluate side-chains 46 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 29 time to evaluate : 0.505 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.4524 time to fit residues: 2.1955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 50.0000 chunk 48 optimal weight: 0.0000 chunk 18 optimal weight: 0.0570 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 overall best weight: 0.3702 ------------------------------------------------------------------------------- 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: 0.8827 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 4401 Z= 0.133 Angle : 0.441 7.029 5957 Z= 0.228 Chirality : 0.038 0.123 650 Planarity : 0.004 0.029 779 Dihedral : 4.074 21.931 595 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 0.88 (0.36), residues: 536 helix: 0.95 (0.30), residues: 300 sheet: 0.04 (0.80), residues: 43 loop : 0.35 (0.43), residues: 193 *********************** 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 50 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 29 time to evaluate : 0.565 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 44 average time/residue: 0.8208 time to fit residues: 38.5633 Evaluate side-chains 44 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 28 time to evaluate : 0.485 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.4228 time to fit residues: 2.0340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 50.0000 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4401 Z= 0.197 Angle : 0.459 6.368 5957 Z= 0.238 Chirality : 0.039 0.125 650 Planarity : 0.003 0.028 779 Dihedral : 4.164 24.176 595 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer Outliers : 5.23 % 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: 1.04 (0.36), residues: 536 helix: 1.08 (0.30), residues: 298 sheet: 0.03 (0.79), residues: 43 loop : 0.46 (0.43), residues: 195 *********************** 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 53 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 29 time to evaluate : 0.536 Fit side-chains outliers start: 24 outliers final: 17 residues processed: 47 average time/residue: 0.9810 time to fit residues: 48.6376 Evaluate side-chains 45 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 28 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.6041 time to fit residues: 1.9855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 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: 0.8857 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4401 Z= 0.197 Angle : 0.463 6.756 5957 Z= 0.239 Chirality : 0.040 0.124 650 Planarity : 0.003 0.029 779 Dihedral : 4.185 22.794 595 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: 1.07 (0.36), residues: 536 helix: 1.10 (0.31), residues: 298 sheet: 0.05 (0.77), residues: 43 loop : 0.48 (0.44), residues: 195 *********************** 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 54 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 29 time to evaluate : 0.518 Fit side-chains outliers start: 25 outliers final: 18 residues processed: 49 average time/residue: 0.9585 time to fit residues: 49.5331 Evaluate side-chains 48 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 30 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.5338 time to fit residues: 1.8412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 50.0000 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 50.0000 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8851 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4401 Z= 0.176 Angle : 0.463 7.186 5957 Z= 0.240 Chirality : 0.039 0.129 650 Planarity : 0.003 0.028 779 Dihedral : 4.142 21.804 595 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.08 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: 1.11 (0.36), residues: 536 helix: 1.13 (0.31), residues: 300 sheet: 0.07 (0.77), residues: 43 loop : 0.49 (0.44), residues: 193 *********************** 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 48 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 28 time to evaluate : 0.567 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 46 average time/residue: 0.9994 time to fit residues: 48.4102 Evaluate side-chains 43 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 27 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 1.0833 time to fit residues: 1.8704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 50.0000 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.194 Angle : 0.487 9.628 5957 Z= 0.248 Chirality : 0.040 0.133 650 Planarity : 0.003 0.028 779 Dihedral : 4.150 22.075 595 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.49 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: 1.16 (0.36), residues: 536 helix: 1.18 (0.31), residues: 298 sheet: 0.05 (0.77), residues: 43 loop : 0.51 (0.44), residues: 195 *********************** 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 47 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 27 time to evaluate : 0.572 Fit side-chains outliers start: 20 outliers final: 15 residues processed: 45 average time/residue: 0.9755 time to fit residues: 46.3330 Evaluate side-chains 42 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 27 time to evaluate : 0.562 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 0.9092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 50.0000 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.0060 chunk 32 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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: 0.8858 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4401 Z= 0.201 Angle : 0.483 8.018 5957 Z= 0.248 Chirality : 0.040 0.137 650 Planarity : 0.003 0.028 779 Dihedral : 4.168 21.986 595 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: 1.19 (0.36), residues: 536 helix: 1.22 (0.31), residues: 295 sheet: 0.06 (0.77), residues: 43 loop : 0.49 (0.44), residues: 198 *********************** 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 49 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 27 time to evaluate : 0.493 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 45 average time/residue: 0.9886 time to fit residues: 46.9007 Evaluate side-chains 43 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 27 time to evaluate : 0.481 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.0978 time to fit residues: 0.8583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 35 optimal weight: 0.0570 chunk 56 optimal weight: 50.0000 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 50.0000 chunk 55 optimal weight: 50.0000 chunk 47 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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: 0.8847 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.169 Angle : 0.467 7.746 5957 Z= 0.240 Chirality : 0.039 0.137 650 Planarity : 0.003 0.028 779 Dihedral : 4.098 20.501 595 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 3.49 % 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: 1.14 (0.36), residues: 536 helix: 1.20 (0.31), residues: 298 sheet: 0.13 (0.78), residues: 43 loop : 0.42 (0.44), residues: 195 *********************** 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 43 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 27 time to evaluate : 0.468 Fit side-chains outliers start: 16 outliers final: 15 residues processed: 42 average time/residue: 0.9929 time to fit residues: 44.0483 Evaluate side-chains 42 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 27 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 0.7328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8867 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 4401 Z= 0.234 Angle : 0.498 7.591 5957 Z= 0.256 Chirality : 0.040 0.147 650 Planarity : 0.003 0.029 779 Dihedral : 4.238 22.442 595 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 3.49 % 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: 1.15 (0.36), residues: 536 helix: 1.19 (0.31), residues: 295 sheet: 0.04 (0.76), residues: 43 loop : 0.48 (0.44), residues: 198 ********************** 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 43 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 27 time to evaluate : 0.493 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 43 average time/residue: 0.9880 time to fit residues: 44.9398 Evaluate side-chains 40 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 27 time to evaluate : 0.553 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 0.7866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.053549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047766 restraints weight = 15598.376| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.92 r_work: 0.2909 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 4401 Z= 0.246 Angle : 0.502 7.922 5957 Z= 0.259 Chirality : 0.041 0.145 650 Planarity : 0.003 0.029 779 Dihedral : 4.278 22.068 595 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 3.27 % 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: 1.11 (0.36), residues: 536 helix: 1.17 (0.31), residues: 295 sheet: 0.04 (0.76), residues: 43 loop : 0.44 (0.44), residues: 198 =============================================================================== Job complete usr+sys time: 1610.16 seconds wall clock time: 29 minutes 32.54 seconds (1772.54 seconds total)