Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:28:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr0_24649/11_2022/7rr0_24649.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr0_24649/11_2022/7rr0_24649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr0_24649/11_2022/7rr0_24649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr0_24649/11_2022/7rr0_24649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr0_24649/11_2022/7rr0_24649.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr0_24649/11_2022/7rr0_24649.pdb" } resolution = 3.12 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= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3297 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1528 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "C" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.48, per 1000 atoms: 0.75 Number of scatterers: 3297 At special positions: 0 Unit cell: (58.3, 68.9, 104.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 630 8.00 N 561 7.00 C 2088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 509.3 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 10.9% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.773A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.329A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.640A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.060A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.868A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.519A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.528A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 11 removed outlier: 7.033A pdb=" N GLU B 10 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TRP B 50 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 7.033A pdb=" N GLU B 10 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.750A pdb=" N SER C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 22 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 19 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 76 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.528A pdb=" N THR C 103 " --> pdb=" O TYR C 87 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 252 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: 0.86 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1053 1.34 - 1.46: 887 1.46 - 1.59: 1418 1.59 - 1.71: 0 1.71 - 1.83: 22 Bond restraints: 3380 Sorted by residual: bond pdb=" CB PRO A 479 " pdb=" CG PRO A 479 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.53e+00 bond pdb=" CG LEU C 48 " pdb=" CD1 LEU C 48 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.10e+00 bond pdb=" CB GLN B 6 " pdb=" CG GLN B 6 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CA THR A 470 " pdb=" C THR A 470 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.35e-02 5.49e+03 1.63e+00 bond pdb=" C ARG A 403 " pdb=" N GLY A 404 " ideal model delta sigma weight residual 1.334 1.350 -0.016 1.27e-02 6.20e+03 1.55e+00 ... (remaining 3375 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.61: 108 106.61 - 113.45: 1689 113.45 - 120.29: 1221 120.29 - 127.13: 1539 127.13 - 133.97: 38 Bond angle restraints: 4595 Sorted by residual: angle pdb=" C GLY C 51 " pdb=" N ALA C 52 " pdb=" CA ALA C 52 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" OG1 THR A 470 " pdb=" CB THR A 470 " pdb=" CG2 THR A 470 " ideal model delta sigma weight residual 109.30 101.40 7.90 2.00e+00 2.50e-01 1.56e+01 angle pdb=" CA PRO A 479 " pdb=" N PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 112.00 107.13 4.87 1.40e+00 5.10e-01 1.21e+01 angle pdb=" C ARG A 403 " pdb=" N GLY A 404 " pdb=" CA GLY A 404 " ideal model delta sigma weight residual 119.99 123.77 -3.78 1.13e+00 7.83e-01 1.12e+01 angle pdb=" CA ARG A 403 " pdb=" CB ARG A 403 " pdb=" CG ARG A 403 " ideal model delta sigma weight residual 114.10 120.54 -6.44 2.00e+00 2.50e-01 1.04e+01 ... (remaining 4590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.43: 1794 14.43 - 28.86: 157 28.86 - 43.28: 37 43.28 - 57.71: 10 57.71 - 72.14: 3 Dihedral angle restraints: 2001 sinusoidal: 782 harmonic: 1219 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual -86.00 -112.35 26.35 1 1.00e+01 1.00e-02 9.97e+00 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 118.76 -25.76 1 1.00e+01 1.00e-02 9.54e+00 dihedral pdb=" CA LEU A 461 " pdb=" C LEU A 461 " pdb=" N LYS A 462 " pdb=" CA LYS A 462 " ideal model delta harmonic sigma weight residual 180.00 164.57 15.43 0 5.00e+00 4.00e-02 9.52e+00 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 292 0.040 - 0.080: 124 0.080 - 0.119: 56 0.119 - 0.159: 16 0.159 - 0.199: 6 Chirality restraints: 494 Sorted by residual: chirality pdb=" CB THR A 470 " pdb=" CA THR A 470 " pdb=" OG1 THR A 470 " pdb=" CG2 THR A 470 " both_signs ideal model delta sigma weight residual False 2.55 2.75 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CB THR B 91 " pdb=" CA THR B 91 " pdb=" OG1 THR B 91 " pdb=" CG2 THR B 91 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA VAL B 52 " pdb=" N VAL B 52 " pdb=" C VAL B 52 " pdb=" CB VAL B 52 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 491 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 68 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C VAL B 68 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL B 68 " 0.014 2.00e-02 2.50e+03 pdb=" N THR B 69 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO A 521 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 91 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C GLN C 91 " -0.035 2.00e-02 2.50e+03 pdb=" O GLN C 91 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR C 92 " 0.012 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1035 2.84 - 3.36: 2598 3.36 - 3.87: 5389 3.87 - 4.39: 5842 4.39 - 4.90: 10738 Nonbonded interactions: 25602 Sorted by model distance: nonbonded pdb=" OD2 ASP B 73 " pdb=" OG1 THR B 76 " model vdw 2.327 2.440 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.332 2.440 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.340 2.440 nonbonded pdb=" O VAL A 367 " pdb=" OG SER A 371 " model vdw 2.343 2.440 nonbonded pdb=" OE2 GLU B 46 " pdb=" NH1 ARG B 63 " model vdw 2.352 2.520 ... (remaining 25597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2088 2.51 5 N 561 2.21 5 O 630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 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: 1.490 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 14.070 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.004 0.080 3380 Z= 0.263 Angle : 0.966 11.211 4595 Z= 0.523 Chirality : 0.056 0.199 494 Planarity : 0.008 0.065 596 Dihedral : 12.179 72.140 1206 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.12 (0.38), residues: 416 helix: -1.69 (0.96), residues: 25 sheet: 0.90 (0.44), residues: 131 loop : -0.12 (0.35), residues: 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1912 time to fit residues: 25.8283 Evaluate side-chains 87 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 360 ASN B 6 GLN B 57 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.088 3380 Z= 0.405 Angle : 0.711 15.470 4595 Z= 0.374 Chirality : 0.048 0.277 494 Planarity : 0.005 0.032 596 Dihedral : 4.769 16.833 475 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 4.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.01 (0.39), residues: 416 helix: -2.26 (0.88), residues: 26 sheet: 0.79 (0.40), residues: 155 loop : -0.22 (0.37), residues: 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 96 average time/residue: 0.1794 time to fit residues: 20.3994 Evaluate side-chains 88 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0385 time to fit residues: 1.1300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 GLN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 3380 Z= 0.249 Angle : 0.642 15.856 4595 Z= 0.322 Chirality : 0.044 0.225 494 Planarity : 0.004 0.031 596 Dihedral : 4.353 15.737 475 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.11 (0.39), residues: 416 helix: -2.47 (0.80), residues: 32 sheet: 0.94 (0.43), residues: 140 loop : -0.30 (0.36), residues: 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 92 average time/residue: 0.1978 time to fit residues: 21.3570 Evaluate side-chains 78 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0325 time to fit residues: 0.5805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN C 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 3380 Z= 0.222 Angle : 0.620 14.881 4595 Z= 0.312 Chirality : 0.043 0.182 494 Planarity : 0.004 0.030 596 Dihedral : 4.185 16.297 475 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.19 (0.38), residues: 416 helix: -2.38 (0.86), residues: 32 sheet: 0.78 (0.41), residues: 149 loop : -0.34 (0.36), residues: 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 88 average time/residue: 0.2207 time to fit residues: 22.5781 Evaluate side-chains 85 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0303 time to fit residues: 0.8159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.074 3380 Z= 0.500 Angle : 0.729 15.942 4595 Z= 0.377 Chirality : 0.047 0.246 494 Planarity : 0.005 0.035 596 Dihedral : 4.912 22.243 475 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.38 (0.39), residues: 416 helix: -2.32 (0.83), residues: 32 sheet: 0.50 (0.41), residues: 158 loop : -0.42 (0.38), residues: 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.395 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 83 average time/residue: 0.2231 time to fit residues: 21.3690 Evaluate side-chains 76 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0387 time to fit residues: 0.7952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0170 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 3380 Z= 0.210 Angle : 0.646 15.455 4595 Z= 0.325 Chirality : 0.044 0.211 494 Planarity : 0.004 0.029 596 Dihedral : 4.356 17.039 475 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.25 (0.39), residues: 416 helix: -2.16 (0.89), residues: 32 sheet: 0.51 (0.42), residues: 154 loop : -0.27 (0.37), residues: 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.412 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 83 average time/residue: 0.2140 time to fit residues: 20.5010 Evaluate side-chains 80 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0326 time to fit residues: 0.5936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 25 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 3380 Z= 0.298 Angle : 0.664 15.221 4595 Z= 0.338 Chirality : 0.045 0.212 494 Planarity : 0.004 0.028 596 Dihedral : 4.436 19.293 475 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.32 (0.40), residues: 416 helix: -1.97 (0.93), residues: 32 sheet: 0.40 (0.42), residues: 155 loop : -0.30 (0.38), residues: 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.433 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 81 average time/residue: 0.2091 time to fit residues: 19.6872 Evaluate side-chains 80 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0342 time to fit residues: 0.7560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 3380 Z= 0.218 Angle : 0.639 15.055 4595 Z= 0.322 Chirality : 0.044 0.199 494 Planarity : 0.004 0.028 596 Dihedral : 4.198 16.883 475 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.15 (0.40), residues: 416 helix: -1.94 (0.94), residues: 32 sheet: 0.51 (0.43), residues: 154 loop : -0.17 (0.37), residues: 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.2078 time to fit residues: 18.9984 Evaluate side-chains 79 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.0060 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 3380 Z= 0.259 Angle : 0.672 15.050 4595 Z= 0.339 Chirality : 0.045 0.202 494 Planarity : 0.004 0.027 596 Dihedral : 4.282 18.291 475 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.14 (0.41), residues: 416 helix: -1.91 (0.95), residues: 32 sheet: 0.43 (0.42), residues: 160 loop : -0.10 (0.39), residues: 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.391 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 0.2034 time to fit residues: 18.8637 Evaluate side-chains 75 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0346 time to fit residues: 0.5886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.0170 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 3380 Z= 0.216 Angle : 0.657 14.826 4595 Z= 0.326 Chirality : 0.044 0.193 494 Planarity : 0.004 0.037 596 Dihedral : 4.129 16.506 475 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.07 (0.41), residues: 416 helix: -1.99 (0.85), residues: 38 sheet: 0.55 (0.44), residues: 154 loop : -0.01 (0.39), residues: 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.401 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.2130 time to fit residues: 19.8056 Evaluate side-chains 76 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 0.0070 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.134980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108894 restraints weight = 5143.853| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.01 r_work: 0.3492 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work: 0.3468 rms_B_bonded: 2.80 restraints_weight: 0.1250 r_work: 0.3456 rms_B_bonded: 2.88 restraints_weight: 0.0625 r_work: 0.3443 rms_B_bonded: 2.99 restraints_weight: 0.0312 r_work: 0.3429 rms_B_bonded: 3.13 restraints_weight: 0.0156 r_work: 0.3415 rms_B_bonded: 3.31 restraints_weight: 0.0078 r_work: 0.3400 rms_B_bonded: 3.52 restraints_weight: 0.0039 r_work: 0.3384 rms_B_bonded: 3.76 restraints_weight: 0.0020 r_work: 0.3368 rms_B_bonded: 4.03 restraints_weight: 0.0010 r_work: 0.3350 rms_B_bonded: 4.34 restraints_weight: 0.0005 r_work: 0.3332 rms_B_bonded: 4.69 restraints_weight: 0.0002 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 3380 Z= 0.220 Angle : 0.673 14.928 4595 Z= 0.335 Chirality : 0.044 0.194 494 Planarity : 0.004 0.037 596 Dihedral : 4.100 16.750 475 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.41), residues: 416 helix: -1.89 (0.96), residues: 32 sheet: 0.52 (0.43), residues: 154 loop : -0.09 (0.38), residues: 230 =============================================================================== Job complete usr+sys time: 1209.35 seconds wall clock time: 22 minutes 39.88 seconds (1359.88 seconds total)