Starting phenix.real_space_refine on Sun Mar 10 16:24:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr0_24649/03_2024/7rr0_24649.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr0_24649/03_2024/7rr0_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_24649/03_2024/7rr0_24649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr0_24649/03_2024/7rr0_24649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr0_24649/03_2024/7rr0_24649.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr0_24649/03_2024/7rr0_24649.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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-5265/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.31, per 1000 atoms: 0.70 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: 1.22 Conformation dependent library (CDL) restraints added in 650.6 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: 0.41 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: 0.88 Time building geometry restraints manager: 1.33 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=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 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 ... (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: 1807 14.43 - 28.86: 157 28.86 - 43.28: 37 43.28 - 57.71: 12 57.71 - 72.14: 3 Dihedral angle restraints: 2016 sinusoidal: 797 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 2013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 290 0.040 - 0.080: 125 0.080 - 0.119: 57 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 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.360 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.080 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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= 0.272 Angle : 0.968 11.211 4595 Z= 0.520 Chirality : 0.056 0.199 494 Planarity : 0.008 0.065 596 Dihedral : 12.282 72.140 1221 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 % Allowed : 0.56 % Favored : 99.44 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 50 PHE 0.011 0.001 PHE A 374 TYR 0.011 0.001 TYR B 95 ARG 0.014 0.001 ARG C 78 *********************** 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 : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 PHE cc_start: 0.4991 (m-10) cc_final: 0.4646 (m-10) REVERT: B 73 ASP cc_start: 0.7696 (t70) cc_final: 0.7373 (t70) REVERT: C 37 TYR cc_start: 0.8370 (m-80) cc_final: 0.8165 (m-80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2014 time to fit residues: 27.0479 Evaluate side-chains 88 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 12 optimal weight: 0.0370 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 3380 Z= 0.341 Angle : 0.686 16.110 4595 Z= 0.358 Chirality : 0.047 0.265 494 Planarity : 0.005 0.032 596 Dihedral : 5.732 57.254 490 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.49 % Allowed : 11.52 % Favored : 83.99 % 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: 0.10 (0.39), residues: 416 helix: -2.23 (0.89), residues: 26 sheet: 0.83 (0.41), residues: 151 loop : -0.10 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 50 PHE 0.020 0.002 PHE A 377 TYR 0.016 0.002 TYR B 95 ARG 0.005 0.001 ARG A 509 *********************** 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 101 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.7811 (tt0) cc_final: 0.7380 (tt0) REVERT: B 73 ASP cc_start: 0.7703 (t70) cc_final: 0.7240 (t70) REVERT: B 107 TYR cc_start: 0.7875 (t80) cc_final: 0.7438 (t80) REVERT: C 24 ARG cc_start: 0.6956 (mmm-85) cc_final: 0.6564 (mmm-85) outliers start: 16 outliers final: 9 residues processed: 95 average time/residue: 0.1875 time to fit residues: 20.8084 Evaluate side-chains 90 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 83 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 1 GLN B 6 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 3380 Z= 0.211 Angle : 0.626 15.568 4595 Z= 0.313 Chirality : 0.044 0.233 494 Planarity : 0.004 0.029 596 Dihedral : 5.292 54.024 490 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.81 % Allowed : 16.57 % Favored : 80.62 % 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 (0.38), residues: 416 helix: -2.56 (0.77), residues: 32 sheet: 0.94 (0.42), residues: 145 loop : -0.08 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 PHE 0.013 0.001 PHE A 377 TYR 0.014 0.001 TYR B 95 ARG 0.005 0.000 ARG C 55 *********************** 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 98 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.5916 (mp0) REVERT: A 517 LEU cc_start: 0.8353 (mt) cc_final: 0.8137 (mt) REVERT: B 73 ASP cc_start: 0.7616 (t70) cc_final: 0.7109 (t70) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.1971 time to fit residues: 22.1343 Evaluate side-chains 88 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN C 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3605 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= 0.221 Angle : 0.619 15.186 4595 Z= 0.311 Chirality : 0.043 0.214 494 Planarity : 0.004 0.032 596 Dihedral : 5.251 54.993 490 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.53 % Allowed : 18.82 % Favored : 78.65 % 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: -2.40 (0.84), residues: 32 sheet: 1.03 (0.42), residues: 145 loop : -0.11 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 PHE 0.012 0.001 PHE A 377 TYR 0.013 0.001 TYR B 95 ARG 0.005 0.000 ARG B 87 *********************** 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 94 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 GLU cc_start: 0.7742 (pm20) cc_final: 0.7423 (tm-30) REVERT: B 73 ASP cc_start: 0.7612 (t70) cc_final: 0.7093 (t70) outliers start: 9 outliers final: 7 residues processed: 91 average time/residue: 0.2095 time to fit residues: 22.0776 Evaluate side-chains 85 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 29 VAL 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: 0.9980 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 0.0670 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3960 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= 0.289 Angle : 0.645 15.156 4595 Z= 0.326 Chirality : 0.044 0.209 494 Planarity : 0.004 0.033 596 Dihedral : 5.492 56.824 490 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.65 % Allowed : 18.26 % Favored : 78.09 % 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 (0.39), residues: 416 helix: -2.20 (0.88), residues: 32 sheet: 0.81 (0.41), residues: 151 loop : -0.25 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 PHE 0.011 0.001 PHE A 377 TYR 0.015 0.001 TYR B 95 ARG 0.006 0.001 ARG C 55 *********************** 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 98 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8280 (p0) cc_final: 0.7993 (p0) REVERT: B 66 GLU cc_start: 0.7756 (pm20) cc_final: 0.7426 (tm-30) REVERT: B 73 ASP cc_start: 0.7424 (t70) cc_final: 0.6892 (t70) REVERT: C 5 THR cc_start: 0.7366 (m) cc_final: 0.7004 (p) REVERT: C 46 ARG cc_start: 0.8377 (ttp-170) cc_final: 0.7766 (ttp-170) outliers start: 13 outliers final: 12 residues processed: 90 average time/residue: 0.2319 time to fit residues: 23.9293 Evaluate side-chains 92 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 3380 Z= 0.232 Angle : 0.619 14.878 4595 Z= 0.311 Chirality : 0.044 0.193 494 Planarity : 0.004 0.031 596 Dihedral : 5.302 54.973 490 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.37 % Allowed : 20.22 % Favored : 76.40 % 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: -0.00 (0.39), residues: 416 helix: -2.12 (0.90), residues: 32 sheet: 0.76 (0.41), residues: 155 loop : -0.15 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 PHE 0.011 0.001 PHE A 377 TYR 0.014 0.001 TYR B 95 ARG 0.004 0.000 ARG B 87 *********************** 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 96 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8300 (p0) cc_final: 0.8025 (p0) REVERT: A 471 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6070 (mp0) REVERT: B 47 TRP cc_start: 0.8570 (t60) cc_final: 0.8320 (t60) REVERT: B 66 GLU cc_start: 0.7741 (pm20) cc_final: 0.7435 (tm-30) REVERT: B 73 ASP cc_start: 0.7431 (t70) cc_final: 0.6929 (t70) REVERT: C 46 ARG cc_start: 0.8347 (ttp-170) cc_final: 0.7721 (ttp-170) outliers start: 12 outliers final: 9 residues processed: 90 average time/residue: 0.2204 time to fit residues: 22.9257 Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3380 Z= 0.240 Angle : 0.621 14.885 4595 Z= 0.314 Chirality : 0.043 0.181 494 Planarity : 0.004 0.029 596 Dihedral : 5.314 55.646 490 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.93 % Allowed : 19.38 % Favored : 76.69 % 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: 0.13 (0.40), residues: 416 helix: -1.95 (0.93), residues: 32 sheet: 0.79 (0.42), residues: 156 loop : -0.02 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 PHE 0.010 0.001 PHE A 377 TYR 0.012 0.001 TYR B 95 ARG 0.007 0.001 ARG C 55 *********************** 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 93 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8276 (p0) cc_final: 0.8006 (p0) REVERT: B 47 TRP cc_start: 0.8607 (t60) cc_final: 0.8356 (t60) REVERT: B 65 GLN cc_start: 0.8108 (tt0) cc_final: 0.7676 (mt0) REVERT: B 66 GLU cc_start: 0.7802 (pm20) cc_final: 0.7401 (tm-30) REVERT: B 73 ASP cc_start: 0.7423 (t70) cc_final: 0.6928 (t70) REVERT: B 84 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8863 (p) REVERT: C 46 ARG cc_start: 0.8348 (ttp-170) cc_final: 0.7922 (tmm160) outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 0.2177 time to fit residues: 22.5819 Evaluate side-chains 88 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 29 VAL 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: 0.7980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.0170 chunk 37 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 3380 Z= 0.246 Angle : 0.623 15.195 4595 Z= 0.315 Chirality : 0.044 0.218 494 Planarity : 0.004 0.028 596 Dihedral : 5.316 55.712 490 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.21 % Allowed : 19.38 % Favored : 76.40 % 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 (0.40), residues: 416 helix: -1.94 (0.93), residues: 32 sheet: 0.78 (0.42), residues: 155 loop : -0.04 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 PHE 0.011 0.001 PHE A 377 TYR 0.011 0.001 TYR B 95 ARG 0.006 0.001 ARG B 87 *********************** 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 96 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8287 (p0) cc_final: 0.8021 (p0) REVERT: A 444 LYS cc_start: 0.8148 (tppt) cc_final: 0.7924 (tppt) REVERT: B 47 TRP cc_start: 0.8615 (t60) cc_final: 0.8379 (t60) REVERT: B 73 ASP cc_start: 0.7413 (t70) cc_final: 0.6920 (t70) REVERT: B 84 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8870 (p) REVERT: C 46 ARG cc_start: 0.8351 (ttp-170) cc_final: 0.7922 (tmm160) REVERT: C 55 ARG cc_start: 0.7046 (ttm110) cc_final: 0.6838 (ttm110) REVERT: C 80 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8193 (mm-30) outliers start: 15 outliers final: 11 residues processed: 90 average time/residue: 0.2122 time to fit residues: 22.0425 Evaluate side-chains 92 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 3380 Z= 0.270 Angle : 0.648 15.189 4595 Z= 0.328 Chirality : 0.045 0.219 494 Planarity : 0.004 0.028 596 Dihedral : 5.450 56.478 490 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.37 % Allowed : 20.51 % Favored : 76.12 % 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: 0.08 (0.40), residues: 416 helix: -1.94 (0.93), residues: 32 sheet: 0.72 (0.42), residues: 156 loop : -0.02 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 PHE 0.011 0.001 PHE A 377 TYR 0.013 0.001 TYR B 95 ARG 0.006 0.001 ARG B 87 *********************** 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 94 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8280 (p0) cc_final: 0.7985 (p0) REVERT: B 47 TRP cc_start: 0.8619 (t60) cc_final: 0.8391 (t60) REVERT: B 66 GLU cc_start: 0.8025 (pm20) cc_final: 0.7496 (tm-30) REVERT: B 73 ASP cc_start: 0.7598 (t70) cc_final: 0.7078 (t70) REVERT: B 84 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8879 (p) REVERT: C 46 ARG cc_start: 0.8367 (ttp-170) cc_final: 0.7934 (tmm160) outliers start: 12 outliers final: 10 residues processed: 89 average time/residue: 0.2295 time to fit residues: 23.4810 Evaluate side-chains 90 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.0470 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 3380 Z= 0.209 Angle : 0.645 14.885 4595 Z= 0.322 Chirality : 0.044 0.209 494 Planarity : 0.004 0.030 596 Dihedral : 5.208 54.123 490 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.81 % Allowed : 21.07 % Favored : 76.12 % 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: 0.12 (0.40), residues: 416 helix: -1.95 (0.93), residues: 32 sheet: 0.78 (0.42), residues: 156 loop : -0.03 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 PHE 0.011 0.001 PHE A 377 TYR 0.009 0.001 TYR B 95 ARG 0.007 0.001 ARG B 87 ********************** 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 91 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8274 (p0) cc_final: 0.8009 (p0) REVERT: A 498 GLN cc_start: 0.8306 (mm110) cc_final: 0.7808 (mm-40) REVERT: B 47 TRP cc_start: 0.8580 (t60) cc_final: 0.8363 (t60) REVERT: B 66 GLU cc_start: 0.8012 (pm20) cc_final: 0.7461 (tm-30) REVERT: B 73 ASP cc_start: 0.7605 (t70) cc_final: 0.7103 (t70) REVERT: C 46 ARG cc_start: 0.8337 (ttp-170) cc_final: 0.7916 (tmm160) outliers start: 10 outliers final: 8 residues processed: 87 average time/residue: 0.2209 time to fit residues: 22.1997 Evaluate side-chains 88 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.133499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.107157 restraints weight = 5125.010| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.96 r_work: 0.3359 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 3380 Z= 0.241 Angle : 0.657 15.021 4595 Z= 0.329 Chirality : 0.044 0.215 494 Planarity : 0.004 0.029 596 Dihedral : 5.350 55.929 490 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.53 % Allowed : 21.35 % Favored : 76.12 % 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: 0.10 (0.40), residues: 416 helix: -1.88 (0.95), residues: 32 sheet: 0.72 (0.42), residues: 158 loop : -0.01 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 PHE 0.010 0.001 PHE A 377 TYR 0.012 0.001 TYR B 95 ARG 0.007 0.001 ARG B 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1327.31 seconds wall clock time: 24 minutes 25.95 seconds (1465.95 seconds total)