Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 10:11:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/04_2023/7psn_13615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/04_2023/7psn_13615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/04_2023/7psn_13615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/04_2023/7psn_13615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/04_2023/7psn_13615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/04_2023/7psn_13615_updated.pdb" } resolution = 2.9 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= -0.001 sd= 0.089 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 P 10 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 6088 2.51 5 N 1604 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B GLU 652": "OE1" <-> "OE2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B GLU 669": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9464 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'LOP:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'LOP:plan-2': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.46, per 1000 atoms: 0.58 Number of scatterers: 9464 At special positions: 0 Unit cell: (83.628, 75.348, 141.588, 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) S 34 16.00 P 10 15.00 Mg 2 11.99 O 1726 8.00 N 1604 7.00 C 6088 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: 4.09 Conformation dependent library (CDL) restraints added in 1.4 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 6 sheets defined 61.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 105 through 139 Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 152 through 200 removed outlier: 3.796A pdb=" N ASN A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 211 through 232 Processing helix chain 'A' and resid 237 through 252 Processing helix chain 'A' and resid 257 through 303 removed outlier: 3.964A pdb=" N TRP A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N HIS A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE A 283 " --> pdb=" O TRP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 314 through 366 Processing helix chain 'A' and resid 372 through 395 Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 400 through 414 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 575 through 589 Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 105 through 139 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 152 through 200 removed outlier: 3.796A pdb=" N ASN B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 211 through 232 Processing helix chain 'B' and resid 237 through 252 Processing helix chain 'B' and resid 257 through 303 removed outlier: 3.964A pdb=" N TRP B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N HIS B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE B 283 " --> pdb=" O TRP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 314 through 366 Processing helix chain 'B' and resid 372 through 395 Proline residue: B 388 - end of helix Processing helix chain 'B' and resid 400 through 414 Processing helix chain 'B' and resid 476 through 482 Processing helix chain 'B' and resid 500 through 502 No H-bonds generated for 'chain 'B' and resid 500 through 502' Processing helix chain 'B' and resid 505 through 508 No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 539 through 548 Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 575 through 589 Processing helix chain 'B' and resid 605 through 616 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 656 through 660 Processing helix chain 'B' and resid 666 through 675 Processing sheet with id= A, first strand: chain 'A' and resid 457 through 459 Processing sheet with id= B, first strand: chain 'A' and resid 649 through 654 removed outlier: 6.924A pdb=" N VAL A 644 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU A 653 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 642 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 641 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER A 626 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE A 467 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR A 628 " --> pdb=" O ILE A 467 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 441 through 443 removed outlier: 7.792A pdb=" N PHE A 443 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS A 453 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 457 through 459 Processing sheet with id= E, first strand: chain 'B' and resid 649 through 654 removed outlier: 6.924A pdb=" N VAL B 644 " --> pdb=" O ARG B 651 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU B 653 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 642 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 641 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER B 626 " --> pdb=" O THR B 465 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE B 467 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR B 628 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 441 through 443 removed outlier: 7.792A pdb=" N PHE B 443 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS B 453 " --> pdb=" O PHE B 443 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1508 1.31 - 1.43: 2478 1.43 - 1.56: 5568 1.56 - 1.68: 14 1.68 - 1.80: 68 Bond restraints: 9636 Sorted by residual: bond pdb=" C3' ANP A 701 " pdb=" C4' ANP A 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' ANP B 701 " pdb=" C4' ANP B 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C4' ANP B 701 " pdb=" O4' ANP B 701 " ideal model delta sigma weight residual 1.431 1.626 -0.195 2.00e-02 2.50e+03 9.47e+01 bond pdb=" C4' ANP A 701 " pdb=" O4' ANP A 701 " ideal model delta sigma weight residual 1.431 1.625 -0.194 2.00e-02 2.50e+03 9.45e+01 bond pdb=" C6 ANP A 701 " pdb=" N6 ANP A 701 " ideal model delta sigma weight residual 1.340 1.471 -0.131 2.00e-02 2.50e+03 4.32e+01 ... (remaining 9631 not shown) Histogram of bond angle deviations from ideal: 99.62 - 107.47: 276 107.47 - 115.33: 5970 115.33 - 123.19: 6411 123.19 - 131.05: 323 131.05 - 138.91: 40 Bond angle restraints: 13020 Sorted by residual: angle pdb=" C1' ANP B 701 " pdb=" N9 ANP B 701 " pdb=" C4 ANP B 701 " ideal model delta sigma weight residual 125.38 111.54 13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C1' ANP A 701 " pdb=" N9 ANP A 701 " pdb=" C4 ANP A 701 " ideal model delta sigma weight residual 125.38 111.59 13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O3 LOP A 704 " pdb=" P1 LOP A 704 " pdb=" O4 LOP A 704 " ideal model delta sigma weight residual 120.67 109.29 11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" O3 LOP B 704 " pdb=" P1 LOP B 704 " pdb=" O4 LOP B 704 " ideal model delta sigma weight residual 120.67 109.32 11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" O5' ANP A 701 " ideal model delta sigma weight residual 98.09 109.28 -11.19 3.00e+00 1.11e-01 1.39e+01 ... (remaining 13015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.69: 5469 25.69 - 51.38: 267 51.38 - 77.07: 18 77.07 - 102.76: 0 102.76 - 128.44: 2 Dihedral angle restraints: 5756 sinusoidal: 2372 harmonic: 3384 Sorted by residual: dihedral pdb=" O1A ANP B 701 " pdb=" O3A ANP B 701 " pdb=" PA ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sinusoidal sigma weight residual 83.11 -45.33 128.44 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" O1A ANP A 701 " pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sinusoidal sigma weight residual 83.11 -45.31 128.42 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" CB MET B 199 " pdb=" CG MET B 199 " pdb=" SD MET B 199 " pdb=" CE MET B 199 " ideal model delta sinusoidal sigma weight residual 60.00 117.46 -57.46 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 5753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 954 0.036 - 0.072: 408 0.072 - 0.108: 114 0.108 - 0.144: 14 0.144 - 0.180: 6 Chirality restraints: 1496 Sorted by residual: chirality pdb=" C2' ANP A 701 " pdb=" C1' ANP A 701 " pdb=" C3' ANP A 701 " pdb=" O2' ANP A 701 " both_signs ideal model delta sigma weight residual False -2.72 -2.54 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" C2' ANP B 701 " pdb=" C1' ANP B 701 " pdb=" C3' ANP B 701 " pdb=" O2' ANP B 701 " both_signs ideal model delta sigma weight residual False -2.72 -2.55 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" C4 LOP A 704 " pdb=" C3 LOP A 704 " pdb=" C5 LOP A 704 " pdb=" O5 LOP A 704 " both_signs ideal model delta sigma weight residual False -2.34 -2.50 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 1493 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 LOP B 703 " 0.204 2.00e-02 2.50e+03 2.05e-01 4.21e+02 pdb=" C14 LOP B 703 " -0.200 2.00e-02 2.50e+03 pdb=" C15 LOP B 703 " -0.210 2.00e-02 2.50e+03 pdb=" C16 LOP B 703 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 LOP A 703 " -0.204 2.00e-02 2.50e+03 2.05e-01 4.20e+02 pdb=" C14 LOP A 703 " 0.200 2.00e-02 2.50e+03 pdb=" C15 LOP A 703 " 0.210 2.00e-02 2.50e+03 pdb=" C16 LOP A 703 " -0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 387 " -0.005 2.00e-02 2.50e+03 8.91e-03 7.93e-01 pdb=" C VAL A 387 " 0.015 2.00e-02 2.50e+03 pdb=" O VAL A 387 " -0.006 2.00e-02 2.50e+03 pdb=" N PRO A 388 " -0.005 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 70 2.52 - 3.11: 7664 3.11 - 3.71: 14400 3.71 - 4.30: 21027 4.30 - 4.90: 35808 Nonbonded interactions: 78969 Sorted by model distance: nonbonded pdb=" OE1 GLN B 517 " pdb="MG MG B 702 " model vdw 1.923 2.170 nonbonded pdb=" OE1 GLN A 517 " pdb="MG MG A 702 " model vdw 1.923 2.170 nonbonded pdb=" O2G ANP A 701 " pdb="MG MG A 702 " model vdw 1.963 2.170 nonbonded pdb=" O2G ANP B 701 " pdb="MG MG B 702 " model vdw 1.963 2.170 nonbonded pdb=" O2B ANP B 701 " pdb="MG MG B 702 " model vdw 2.047 2.170 ... (remaining 78964 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.00 max=1.00 mean=0.98 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: 3.210 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: 7.740 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.600 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 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 : 0.009 0.224 9636 Z= 0.588 Angle : 0.823 13.840 13020 Z= 0.365 Chirality : 0.042 0.180 1496 Planarity : 0.008 0.205 1620 Dihedral : 14.292 128.445 3572 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.21), residues: 1166 helix: -1.13 (0.16), residues: 772 sheet: -3.80 (0.43), residues: 52 loop : -3.49 (0.26), residues: 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.062 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 1.2839 time to fit residues: 168.0920 Evaluate side-chains 73 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 59 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN B 127 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9636 Z= 0.181 Angle : 0.509 7.516 13020 Z= 0.258 Chirality : 0.039 0.148 1496 Planarity : 0.003 0.027 1620 Dihedral : 9.839 130.348 1374 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 1166 helix: 0.58 (0.18), residues: 774 sheet: -3.43 (0.45), residues: 52 loop : -2.58 (0.29), residues: 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.118 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 122 average time/residue: 1.1926 time to fit residues: 156.7637 Evaluate side-chains 93 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.5624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 346 GLN A 618 ASN B 304 ASN B 346 GLN B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 9636 Z= 0.248 Angle : 0.530 7.386 13020 Z= 0.269 Chirality : 0.041 0.154 1496 Planarity : 0.003 0.034 1620 Dihedral : 9.152 125.502 1374 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1166 helix: 1.03 (0.18), residues: 774 sheet: -2.44 (0.52), residues: 62 loop : -2.15 (0.32), residues: 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.102 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 117 average time/residue: 1.1449 time to fit residues: 144.6803 Evaluate side-chains 105 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.0904 time to fit residues: 2.1397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 9636 Z= 0.247 Angle : 0.510 6.978 13020 Z= 0.260 Chirality : 0.041 0.149 1496 Planarity : 0.003 0.023 1620 Dihedral : 8.795 120.802 1374 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.24), residues: 1166 helix: 1.20 (0.18), residues: 776 sheet: -2.16 (0.55), residues: 62 loop : -1.89 (0.33), residues: 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 0.984 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 134 average time/residue: 1.1889 time to fit residues: 171.8483 Evaluate side-chains 110 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.5241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 0.0970 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 346 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9636 Z= 0.213 Angle : 0.492 6.381 13020 Z= 0.249 Chirality : 0.040 0.144 1496 Planarity : 0.003 0.023 1620 Dihedral : 8.556 119.879 1374 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1166 helix: 1.47 (0.18), residues: 776 sheet: -2.04 (0.56), residues: 62 loop : -1.75 (0.33), residues: 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.106 Fit side-chains outliers start: 27 outliers final: 6 residues processed: 124 average time/residue: 1.0635 time to fit residues: 143.3395 Evaluate side-chains 109 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.5982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 112 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN B 134 GLN B 346 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9636 Z= 0.187 Angle : 0.479 6.775 13020 Z= 0.245 Chirality : 0.039 0.141 1496 Planarity : 0.003 0.023 1620 Dihedral : 8.322 118.522 1374 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1166 helix: 1.67 (0.18), residues: 776 sheet: -1.89 (0.58), residues: 62 loop : -1.65 (0.33), residues: 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.123 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 122 average time/residue: 1.1350 time to fit residues: 149.7390 Evaluate side-chains 116 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0898 time to fit residues: 1.9135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 0.0170 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 346 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9636 Z= 0.163 Angle : 0.466 6.894 13020 Z= 0.239 Chirality : 0.038 0.138 1496 Planarity : 0.003 0.023 1620 Dihedral : 8.084 116.977 1374 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1166 helix: 1.85 (0.18), residues: 776 sheet: -1.89 (0.57), residues: 62 loop : -1.60 (0.34), residues: 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.157 Fit side-chains outliers start: 22 outliers final: 10 residues processed: 123 average time/residue: 1.1796 time to fit residues: 157.3882 Evaluate side-chains 112 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1023 time to fit residues: 1.8320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 346 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9636 Z= 0.181 Angle : 0.469 6.376 13020 Z= 0.240 Chirality : 0.039 0.140 1496 Planarity : 0.003 0.024 1620 Dihedral : 8.010 116.541 1374 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1166 helix: 1.87 (0.18), residues: 776 sheet: -1.85 (0.57), residues: 62 loop : -1.57 (0.34), residues: 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 1.179 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 114 average time/residue: 1.1184 time to fit residues: 138.4688 Evaluate side-chains 111 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0935 time to fit residues: 1.8710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 98 optimal weight: 0.0980 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 346 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9636 Z= 0.187 Angle : 0.482 6.313 13020 Z= 0.249 Chirality : 0.039 0.140 1496 Planarity : 0.003 0.027 1620 Dihedral : 7.949 116.281 1374 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1166 helix: 1.80 (0.18), residues: 778 sheet: -1.84 (0.57), residues: 62 loop : -1.53 (0.34), residues: 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.087 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 120 average time/residue: 1.0746 time to fit residues: 140.2795 Evaluate side-chains 112 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.8094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 346 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9636 Z= 0.207 Angle : 0.493 6.296 13020 Z= 0.253 Chirality : 0.039 0.140 1496 Planarity : 0.003 0.030 1620 Dihedral : 7.905 116.340 1374 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1166 helix: 1.79 (0.18), residues: 778 sheet: -1.85 (0.56), residues: 62 loop : -1.51 (0.34), residues: 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.143 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 116 average time/residue: 1.0873 time to fit residues: 137.0502 Evaluate side-chains 111 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.5291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 11 optimal weight: 0.0030 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 346 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112352 restraints weight = 10854.178| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.06 r_work: 0.3232 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9636 Z= 0.184 Angle : 0.481 6.268 13020 Z= 0.248 Chirality : 0.039 0.139 1496 Planarity : 0.003 0.030 1620 Dihedral : 7.724 115.986 1374 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1166 helix: 1.88 (0.18), residues: 778 sheet: -1.89 (0.56), residues: 62 loop : -1.44 (0.34), residues: 326 =============================================================================== Job complete usr+sys time: 3176.41 seconds wall clock time: 57 minutes 24.95 seconds (3444.95 seconds total)