Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 08:40:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxi_32880/04_2023/7wxi_32880_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxi_32880/04_2023/7wxi_32880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxi_32880/04_2023/7wxi_32880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxi_32880/04_2023/7wxi_32880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxi_32880/04_2023/7wxi_32880_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxi_32880/04_2023/7wxi_32880_updated.pdb" } resolution = 4.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 30 5.16 5 C 4064 2.51 5 N 1174 2.21 5 O 1252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A ASP 579": "OD1" <-> "OD2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "B ASP 579": "OD1" <-> "OD2" Residue "B TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6522 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3247 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 414} Chain: "B" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3247 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 414} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Time building chain proxies: 4.12, per 1000 atoms: 0.63 Number of scatterers: 6522 At special positions: 0 Unit cell: (98.58, 92.22, 62.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 2 15.00 O 1252 8.00 N 1174 7.00 C 4064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB RGP A 801 " pdb=" CB RGP B 801 " Number of C-beta restraints generated: 1596 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 8 sheets defined 42.2% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 349 through 364 removed outlier: 4.096A pdb=" N ALA A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 496 through 512 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 580 through 591 Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 667 through 676 Processing helix chain 'A' and resid 690 through 699 Processing helix chain 'A' and resid 711 through 713 No H-bonds generated for 'chain 'A' and resid 711 through 713' Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 740 through 743 Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing helix chain 'B' and resid 349 through 364 removed outlier: 4.096A pdb=" N ALA B 364 " --> pdb=" O ARG B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 416 through 432 Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 496 through 512 Processing helix chain 'B' and resid 528 through 533 Processing helix chain 'B' and resid 547 through 556 Processing helix chain 'B' and resid 580 through 591 Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 615 through 625 Processing helix chain 'B' and resid 634 through 639 Processing helix chain 'B' and resid 667 through 676 Processing helix chain 'B' and resid 690 through 699 Processing helix chain 'B' and resid 711 through 713 No H-bonds generated for 'chain 'B' and resid 711 through 713' Processing helix chain 'B' and resid 717 through 719 No H-bonds generated for 'chain 'B' and resid 717 through 719' Processing helix chain 'B' and resid 740 through 743 Processing helix chain 'B' and resid 758 through 760 No H-bonds generated for 'chain 'B' and resid 758 through 760' Processing sheet with id= A, first strand: chain 'A' and resid 455 through 458 Processing sheet with id= B, first strand: chain 'A' and resid 487 through 490 removed outlier: 6.555A pdb=" N LEU A 462 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LYS A 490 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 464 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 605 through 607 removed outlier: 7.626A pdb=" N GLU A 662 " --> pdb=" O ILE A 606 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 443 through 447 removed outlier: 6.945A pdb=" N LEU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 455 through 458 Processing sheet with id= F, first strand: chain 'B' and resid 487 through 490 removed outlier: 6.555A pdb=" N LEU B 462 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LYS B 490 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 464 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 605 through 607 removed outlier: 7.626A pdb=" N GLU B 662 " --> pdb=" O ILE B 606 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.945A pdb=" N LEU B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 684 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: 1.62 Time building geometry restraints manager: 2.86 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: 1140 1.31 - 1.43: 1536 1.43 - 1.56: 3896 1.56 - 1.68: 2 1.68 - 1.81: 46 Bond restraints: 6620 Sorted by residual: bond pdb=" OE2 RGP A 801 " pdb=" PA RGP A 801 " ideal model delta sigma weight residual 1.798 1.646 0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" OE2 RGP B 801 " pdb=" PA RGP B 801 " ideal model delta sigma weight residual 1.798 1.646 0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" CD RGP A 801 " pdb=" OE2 RGP A 801 " ideal model delta sigma weight residual 1.302 1.395 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" CD RGP B 801 " pdb=" OE2 RGP B 801 " ideal model delta sigma weight residual 1.302 1.395 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" N VAL A 455 " pdb=" CA VAL A 455 " ideal model delta sigma weight residual 1.459 1.437 0.022 1.25e-02 6.40e+03 3.13e+00 ... (remaining 6615 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.52: 184 106.52 - 113.39: 3874 113.39 - 120.26: 2292 120.26 - 127.12: 2554 127.12 - 133.99: 60 Bond angle restraints: 8964 Sorted by residual: angle pdb=" OE2 RGP B 801 " pdb=" PA RGP B 801 " pdb=" OA3 RGP B 801 " ideal model delta sigma weight residual 97.78 109.37 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" OE2 RGP A 801 " pdb=" PA RGP A 801 " pdb=" OA3 RGP A 801 " ideal model delta sigma weight residual 97.78 109.37 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CG RGP B 801 " pdb=" CD RGP B 801 " pdb=" OE2 RGP B 801 " ideal model delta sigma weight residual 112.09 119.96 -7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" CG RGP A 801 " pdb=" CD RGP A 801 " pdb=" OE2 RGP A 801 " ideal model delta sigma weight residual 112.09 119.96 -7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" N ARG A 544 " pdb=" CA ARG A 544 " pdb=" C ARG A 544 " ideal model delta sigma weight residual 114.75 111.53 3.22 1.26e+00 6.30e-01 6.53e+00 ... (remaining 8959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 3506 16.01 - 32.02: 416 32.02 - 48.02: 98 48.02 - 64.03: 18 64.03 - 80.04: 14 Dihedral angle restraints: 4052 sinusoidal: 1588 harmonic: 2464 Sorted by residual: dihedral pdb=" CA ILE A 732 " pdb=" C ILE A 732 " pdb=" N HIS A 733 " pdb=" CA HIS A 733 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ILE B 732 " pdb=" C ILE B 732 " pdb=" N HIS B 733 " pdb=" CA HIS B 733 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA THR A 366 " pdb=" C THR A 366 " pdb=" N PRO A 367 " pdb=" CA PRO A 367 " ideal model delta harmonic sigma weight residual 180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 562 0.030 - 0.059: 276 0.059 - 0.089: 136 0.089 - 0.118: 52 0.118 - 0.148: 22 Chirality restraints: 1048 Sorted by residual: chirality pdb=" CA ILE A 574 " pdb=" N ILE A 574 " pdb=" C ILE A 574 " pdb=" CB ILE A 574 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ILE B 574 " pdb=" N ILE B 574 " pdb=" C ILE B 574 " pdb=" CB ILE B 574 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA VAL B 519 " pdb=" N VAL B 519 " pdb=" C VAL B 519 " pdb=" CB VAL B 519 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1045 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 643 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO B 644 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 643 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 644 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 664 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B 665 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " 0.018 5.00e-02 4.00e+02 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 372 2.70 - 3.25: 7752 3.25 - 3.80: 10467 3.80 - 4.35: 12480 4.35 - 4.90: 20263 Nonbonded interactions: 51334 Sorted by model distance: nonbonded pdb=" O ILE A 429 " pdb=" OG SER A 433 " model vdw 2.148 2.440 nonbonded pdb=" O ILE B 429 " pdb=" OG SER B 433 " model vdw 2.148 2.440 nonbonded pdb=" O ALA A 509 " pdb=" OG1 THR A 512 " model vdw 2.181 2.440 nonbonded pdb=" O ALA B 509 " pdb=" OG1 THR B 512 " model vdw 2.181 2.440 nonbonded pdb=" O CYS B 570 " pdb=" ND1 HIS B 571 " model vdw 2.224 2.520 ... (remaining 51329 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.190 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: 0.010 Extract box with map and model: 5.850 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.940 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.008 0.152 6620 Z= 0.520 Angle : 0.875 11.589 8964 Z= 0.460 Chirality : 0.046 0.148 1048 Planarity : 0.005 0.043 1174 Dihedral : 15.473 80.038 2456 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.22 % Favored : 81.78 % Rotamer Outliers : 0.58 % 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: -4.77 (0.24), residues: 856 helix: -2.25 (0.22), residues: 354 sheet: -4.26 (0.37), residues: 112 loop : -3.68 (0.28), residues: 390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 135 average time/residue: 0.2100 time to fit residues: 36.7301 Evaluate side-chains 90 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0622 time to fit residues: 1.1609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 369 GLN A 400 GLN A 454 GLN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS A 770 HIS B 354 ASN B 369 GLN B 400 GLN B 454 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS B 770 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6620 Z= 0.205 Angle : 0.641 7.313 8964 Z= 0.328 Chirality : 0.044 0.169 1048 Planarity : 0.005 0.037 1174 Dihedral : 5.478 37.606 934 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer Outliers : 0.29 % 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: -3.02 (0.27), residues: 856 helix: -0.33 (0.26), residues: 364 sheet: -3.44 (0.40), residues: 114 loop : -3.26 (0.28), residues: 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.1545 time to fit residues: 31.1176 Evaluate side-chains 112 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6620 Z= 0.214 Angle : 0.645 8.356 8964 Z= 0.321 Chirality : 0.042 0.154 1048 Planarity : 0.005 0.039 1174 Dihedral : 5.231 36.464 934 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % 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: -2.24 (0.28), residues: 856 helix: 0.44 (0.27), residues: 364 sheet: -3.06 (0.40), residues: 126 loop : -2.95 (0.29), residues: 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1557 time to fit residues: 32.1943 Evaluate side-chains 108 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 0.0770 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN B 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 6620 Z= 0.194 Angle : 0.653 9.189 8964 Z= 0.321 Chirality : 0.045 0.334 1048 Planarity : 0.005 0.037 1174 Dihedral : 5.208 35.822 934 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % 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: -1.82 (0.28), residues: 856 helix: 0.82 (0.27), residues: 364 sheet: -2.95 (0.35), residues: 142 loop : -2.66 (0.31), residues: 350 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1543 time to fit residues: 32.6249 Evaluate side-chains 113 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 6620 Z= 0.246 Angle : 0.668 8.681 8964 Z= 0.332 Chirality : 0.044 0.172 1048 Planarity : 0.005 0.039 1174 Dihedral : 5.293 35.260 934 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % 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: -1.75 (0.28), residues: 856 helix: 0.84 (0.27), residues: 368 sheet: -3.02 (0.36), residues: 132 loop : -2.59 (0.31), residues: 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1450 time to fit residues: 29.5301 Evaluate side-chains 118 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 6620 Z= 0.276 Angle : 0.665 8.249 8964 Z= 0.333 Chirality : 0.044 0.181 1048 Planarity : 0.005 0.037 1174 Dihedral : 5.403 34.614 934 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % 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: -1.67 (0.29), residues: 856 helix: 0.86 (0.27), residues: 366 sheet: -2.76 (0.37), residues: 142 loop : -2.55 (0.32), residues: 348 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1500 time to fit residues: 28.2220 Evaluate side-chains 111 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.787 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 0.0270 chunk 49 optimal weight: 2.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 6620 Z= 0.259 Angle : 0.681 9.040 8964 Z= 0.337 Chirality : 0.044 0.189 1048 Planarity : 0.005 0.040 1174 Dihedral : 5.388 34.173 934 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % 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: -1.52 (0.29), residues: 856 helix: 1.01 (0.27), residues: 366 sheet: -2.69 (0.37), residues: 142 loop : -2.50 (0.32), residues: 348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1620 time to fit residues: 31.5212 Evaluate side-chains 109 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN A 565 HIS ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 6620 Z= 0.191 Angle : 0.667 8.496 8964 Z= 0.326 Chirality : 0.043 0.187 1048 Planarity : 0.005 0.036 1174 Dihedral : 5.210 33.758 934 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % 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: -1.30 (0.29), residues: 856 helix: 1.14 (0.28), residues: 366 sheet: -2.53 (0.38), residues: 142 loop : -2.35 (0.32), residues: 348 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1480 time to fit residues: 29.8108 Evaluate side-chains 110 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 81 optimal weight: 0.0010 chunk 49 optimal weight: 5.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN ** B 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6620 Z= 0.172 Angle : 0.657 8.750 8964 Z= 0.323 Chirality : 0.043 0.184 1048 Planarity : 0.004 0.036 1174 Dihedral : 5.078 33.404 934 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % 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: -1.25 (0.29), residues: 856 helix: 1.07 (0.28), residues: 364 sheet: -2.42 (0.39), residues: 142 loop : -2.20 (0.32), residues: 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1721 time to fit residues: 34.8858 Evaluate side-chains 114 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN ** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 6620 Z= 0.186 Angle : 0.676 9.070 8964 Z= 0.336 Chirality : 0.044 0.201 1048 Planarity : 0.005 0.039 1174 Dihedral : 4.969 32.924 934 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % 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: -1.20 (0.29), residues: 856 helix: 1.08 (0.28), residues: 362 sheet: -2.32 (0.39), residues: 142 loop : -2.14 (0.32), residues: 352 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1628 time to fit residues: 31.4750 Evaluate side-chains 112 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 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 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 HIS ** 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 = 0.3727 r_free = 0.3727 target = 0.130611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101914 restraints weight = 11874.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105507 restraints weight = 7657.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108219 restraints weight = 5637.357| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 6620 Z= 0.193 Angle : 0.680 8.527 8964 Z= 0.340 Chirality : 0.043 0.196 1048 Planarity : 0.005 0.040 1174 Dihedral : 4.959 32.624 934 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % 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: -1.11 (0.29), residues: 856 helix: 1.13 (0.28), residues: 358 sheet: -2.18 (0.40), residues: 142 loop : -2.08 (0.32), residues: 356 =============================================================================== Job complete usr+sys time: 1535.44 seconds wall clock time: 28 minutes 40.68 seconds (1720.68 seconds total)